surgery of transcription insight

8/14/2019 Surgery of Transcription Insight

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Surgery of transcription insight

1. Cc khi nim c bn

GTFs(general transcription factors orbasal transcription factors ):

- General transcription factors (GTF's) or basal transcription factors are proteintranscription factors that have been shown to be important in the transcription ofclass IIgenes to mRNA templates [1]. Many of them are involved in the formation of a preinitiation complex, which, together with RNA polymerase II, bind to and read thesingle-stranded DNA gene template. < A class II gene is a type ofgene that codes for aprotein. Class II genes are transcribed by RNAP II.Class II genes have a promoter thatoften contains a TATA box.Basal transcription of class II genes requires the formation ofapreinitiation complex.They are transcribed by RNA polymerase II, include both intron

and exon, and code for polypeptide>

- GTFs are intimately involved in the process of gene regulation, and most are requiredfor life. TATA binding protein, (TBP) is a GTF that binds to the TATAA box(T=Thymine, A=Adenine) the motif of nucleic acids that is directly upstream from thecoding region in all genes. TBP is responsible for the recruitment of the RNA Pol IIholoenzyme, the final event in transcription initiation. These proteins are ubiquitous andinteract with the core promoter region of DNA, which contains the transcription startsite(s) of all class II genes.

Not all GTFs play a role in transcriptional initiation; some are required for the second

general step in transcription, elongation. For example, members of the FACT complex(Spt16/Pob3 in S. cerevisiae, SUPT16H/SSRP1 in humans) facilitate the rapid movementof RNA Pol II over the encoding region of genes. This is accomplished by moving thehistone octamer out of the way of an active polymerase and thereby decondensing thechromatin.

The definition of downstream and upstream:

- In molecular biology, upstream and downstream both refer to a relative position inDNA orRNA. Each strand of DNA or RNA has a 5' end and a 3' end, so named for thecarbons on the deoxyribose (or ribose) ring. Relative to the position on the strand,

downstream is the region towards the 3' end of the strand. Since DNA strands run inopposite directions, downstream on one strand is upstream on the other strand.

Examples
http://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Transcription_factorhttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Class_II_genehttp://en.wikipedia.org/wiki/Class_II_genehttp://en.wikipedia.org/wiki/Class_II_genehttp://en.wikipedia.org/wiki/MRNAhttp://en.wikipedia.org/wiki/General_transcription_factor#cite_note-pmid11092823-0%23cite_note-pmid11092823-0http://en.wikipedia.org/wiki/General_transcription_factor#cite_note-pmid11092823-0%23cite_note-pmid11092823-0http://en.wikipedia.org/wiki/Preinitiation_complexhttp://en.wikipedia.org/wiki/RNA_polymerase_IIhttp://en.wikipedia.org/wiki/RNA_polymerase_IIhttp://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/RNAPhttp://en.wikipedia.org/wiki/RNAPhttp://en.wikipedia.org/wiki/Promoterhttp://en.wikipedia.org/wiki/TATA_boxhttp://en.wikipedia.org/wiki/Preinitiation_complexhttp://en.wikipedia.org/wiki/TATA_binding_proteinhttp://en.wikipedia.org/wiki/Thyminehttp://en.wikipedia.org/wiki/Adeninehttp://en.wikipedia.org/wiki/RNA_Pol_IIhttp://en.wikipedia.org/wiki/Elongationhttp://en.wikipedia.org/wiki/FACT_(biology)http://en.wikipedia.org/wiki/FACT_(biology)http://en.wikipedia.org/wiki/Histonehttp://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/RNAhttp://en.wikipedia.org/wiki/5'_endhttp://en.wikipedia.org/wiki/3'_endhttp://en.wikipedia.org/wiki/Deoxyribosehttp://en.wikipedia.org/wiki/Ribosehttp://en.wikipedia.org/wiki/File:Upstream-downstream.JPGhttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Transcription_factorhttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Class_II_genehttp://en.wikipedia.org/wiki/Class_II_genehttp://en.wikipedia.org/wiki/MRNAhttp://en.wikipedia.org/wiki/General_transcription_factor#cite_note-pmid11092823-0%23cite_note-pmid11092823-0http://en.wikipedia.org/wiki/Preinitiation_complexhttp://en.wikipedia.org/wiki/RNA_polymerase_IIhttp://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/RNAPhttp://en.wikipedia.org/wiki/Promoterhttp://en.wikipedia.org/wiki/TATA_boxhttp://en.wikipedia.org/wiki/Preinitiation_complexhttp://en.wikipedia.org/wiki/TATA_binding_proteinhttp://en.wikipedia.org/wiki/Thyminehttp://en.wikipedia.org/wiki/Adeninehttp://en.wikipedia.org/wiki/RNA_Pol_IIhttp://en.wikipedia.org/wiki/Elongationhttp://en.wikipedia.org/wiki/FACT_(biology)http://en.wikipedia.org/wiki/Histonehttp://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/RNAhttp://en.wikipedia.org/wiki/5'_endhttp://en.wikipedia.org/wiki/3'_endhttp://en.wikipedia.org/wiki/Deoxyribosehttp://en.wikipedia.org/wiki/Ribose


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Transcription and translation of DNA and mRNA, respectively, have their directiondefined by the newly synthesized strand, that is, in downstream direction (5' --> 3').However, this is in upstream direction (3' --> 5') for the copied template strand.

Nh vy down stream ngh l hng v pha u 3, m on DNA c c theo

chiu 3-5 trong sut qu trnh phin m, nh vy c ngha l t phn downstream sangupstream, quy c ny ht sc quan trng bi v n c lin quan n v tr ca ccpromoter cc enhancer v cc v tr bm sau ny ca DNA na ca cc protein lin ktvi cc promoter.

Ex: Promoter lies downstream of the startpoint.

Chiu ca qu trnh phin m: As in DNA replication, DNA is read from 3' 5' duringtranscription. Meanwhile, the complementary RNA is created from the 5' 3' direction.Although DNA is arranged as two antiparallel strands in a double helix, only one of thetwo DNA strands, called the template strand, is used for transcription. This is because

RNA is only single-stranded, as opposed to double-stranded DNA. The other DNA strandis called the coding strand, because its sequence is the same as the newly created RNAtranscript (except for the substitution of uracil for thymine). The use of only the 3' 5'strand eliminates the need for theOkazaki fragments seen in DNA replication.

Rpb1: It isthe largest subunit of Pol II .It has a domain at its C-terminus that is calledthe CTD (C-terminal domain). This is the target of kinases and phosphatases. The phosphorylation of the CTD is an important regulation mechanism, as this allowsattraction and rejection of factors that have a function in the transcription process. TheCTD can be considered as a platform for transcription factors. Nh vy ta c th nhnthy rng CTD, mt domain nm trong tiu n v ln nht Rpb1 ca Pol II l ch cho

qu trnh kinases v phosphatase, bn thn s photphoryl ho ca CTD l mt c chiu khin rt quan trng, n c th cho php s hp dn v loi b cc yu t m cchc nng trong qu trnh phin m. V vy, CTD c xem nh l mt sn ga cho ccyu t phin m.

RNA polymerase II (also called RNAP II and Pol II):

- RNAP II: is an enzyme found in eukaryotic cells. It catalyzes thetranscription ofDNAto synthesize precursors ofmRNA and mostsnRNA and microRNA.[1][2]

- A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNApolymerase. A wide range of transcription factors are required for it to bind to its

promoters and begin transcriptionC mt h thng cc yu t sao m TF v cc phc h c yu cu i km vi hotng ca enzyme ny.

The stages of Transcription:

In the process oftranscription(by any polymerase) there are three main stages:
http://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Translation_(biology)http://en.wikipedia.org/wiki/Double_helixhttp://en.wikipedia.org/wiki/Okazaki_fragmenthttp://en.wikipedia.org/wiki/Okazaki_fragmenthttp://en.wikipedia.org/wiki/Protein_kinasehttp://en.wikipedia.org/wiki/Phosphataseshttp://en.wikipedia.org/wiki/Transcription_factorshttp://en.wikipedia.org/wiki/Eukaryotehttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/MRNAhttp://en.wikipedia.org/wiki/SnRNAhttp://en.wikipedia.org/wiki/SnRNAhttp://en.wikipedia.org/wiki/MicroRNAhttp://en.wikipedia.org/wiki/MicroRNAhttp://en.wikipedia.org/wiki/RNA_polymerase_II#cite_note-0%23cite_note-0http://en.wikipedia.org/wiki/RNA_polymerase_II#cite_note-1%23cite_note-1http://en.wikipedia.org/wiki/KDahttp://en.wikipedia.org/wiki/RNA_polymerasehttp://en.wikipedia.org/wiki/RNA_polymerasehttp://en.wikipedia.org/wiki/RNA_polymerasehttp://en.wikipedia.org/wiki/Transcription_factorshttp://en.wikipedia.org/wiki/Promoterhttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Translation_(biology)http://en.wikipedia.org/wiki/Double_helixhttp://en.wikipedia.org/wiki/Okazaki_fragmenthttp://en.wikipedia.org/wiki/Protein_kinasehttp://en.wikipedia.org/wiki/Phosphataseshttp://en.wikipedia.org/wiki/Transcription_factorshttp://en.wikipedia.org/wiki/Eukaryotehttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/MRNAhttp://en.wikipedia.org/wiki/SnRNAhttp://en.wikipedia.org/wiki/MicroRNAhttp://en.wikipedia.org/wiki/RNA_polymerase_II#cite_note-0%23cite_note-0http://en.wikipedia.org/wiki/RNA_polymerase_II#cite_note-1%23cite_note-1http://en.wikipedia.org/wiki/KDahttp://en.wikipedia.org/wiki/RNA_polymerasehttp://en.wikipedia.org/wiki/RNA_polymerasehttp://en.wikipedia.org/wiki/Transcription_factorshttp://en.wikipedia.org/wiki/Promoterhttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Transcription_(genetics)


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1. Initiation; the construction of the RNA polymerase complex on the gene'spromoterwith the help oftranscription factors.

2. Elongation; the actual transcription of the majority of the gene into acorresponding RNA sequence, highly moderated by several methods.

3. Termination; the cessation of RNA transcription and the disassembly of the RNA

polymerase complex.Due to the range of genes Pol II transcribes this is the polymerase that experiencesgreatest regulation, by a range of factors, at each stage of transcription. It is also one ofthe most complex in terms of polymerase cofactors involved.

Initiation of Transcription

- Preinitiation complex (PIC): the construction of the polymerase complex on the promoter. The TATA box is one well-studied example of a promoter element. It isconserved-bo v, gi gn, bo tn in many (though not all) model eukaryotes and is

found in a fraction of the promoters in these organisms. The sequence TATA is located atapproximately 25 nucleotides upstream of the Transcription Start Point (TSP)-im khiu phin m, im ny thng nm cch hp TA mt khong trnh t khong 25nucleotide v pha sau (upstream). In addition, there are also some weakly conservedfeatures including the TFIIB-Recognition Element (BRE), approximately 5 nucleotidesupstream (BREu) and 5 nucleotides downstream (BREd) of the TATA box[1].

- Order in which the GTFs(general transcription factors) attach

The following is the order in which the GTFs (general transcription factors) attach:

1. TBP (TATA Binding Protein) and an attached complex of TAFs (TBPAssociated Factors), collectively known as TFIID (Transcription Factor forpolymerase II D), bind at the TATA box.

2. TFIIA (three subunits) binds TFIID and DNA, stabilizing the first interactions.3. TFIIBbinds between TFIID and the location of Pol II binding in the near future.

TFIIB binds partially sequence specifically, with some preference for BRE.4. TFIIF (two subunits, RAP30 and RAP74, showing some similarity to bacterial

sigma factors) and Pol II enter the complex together. TFIIF helps to speed up thepolymerization process.

5. TFIIE enters the complex, and helps to open and close the Pol IIs Jaw likestructure, which enables movement down the DNA strand. TFIIE and TFIIH enter

concomitantly.6. Finally TFIIH and TFIIJ to the complex together. TFIIH is a large proteincomplex that contains among others the CDK7/cyclin H kinase complex and aDNA helicase. TFIIH has three functions: it binds specifically to the templatestrand to ensure that the correct strand of DNA is transcribed and melts orunwinds the DNA (ATP dependently) to separate the two strands using itsHelicase activity. It has a kinase activity that phosphorylates the C-terminaldomain (CTD) of Pol II at the amino acid serine. This switches the RNA
http://en.wikipedia.org/wiki/Promoterhttp://en.wikipedia.org/wiki/Transcription_factorshttp://en.wikipedia.org/wiki/Preinitiation_complexhttp://en.wikipedia.org/wiki/TATA_boxhttp://en.wikipedia.org/wiki/Conservation_(genetics)http://en.wikipedia.org/wiki/Conservation_(genetics)http://www.als.lbl.gov/als/science/sci_archive/polymerase2.htmlhttp://en.wikipedia.org/wiki/General_transcription_factorhttp://en.wikipedia.org/wiki/TATA_Binding_Proteinhttp://en.wikipedia.org/wiki/TATA_Binding_Proteinhttp://en.wikipedia.org/wiki/TATA_Binding_Proteinhttp://en.wikipedia.org/wiki/TATA_Binding_Proteinhttp://en.wikipedia.org/wiki/TATA_Binding_Proteinhttp://en.wikipedia.org/wiki/TATA_Binding_Proteinhttp://en.wikipedia.org/wiki/Transcription_Factor_II_Dhttp://en.wikipedia.org/wiki/Transcription_Factor_II_Dhttp://en.wikipedia.org/wiki/Transcription_Factor_II_Dhttp://en.wikipedia.org/wiki/TATA_boxhttp://en.wikipedia.org/wiki/TFIIAhttp://en.wikipedia.org/wiki/Transcription_Factor_II_Bhttp://en.wikipedia.org/wiki/Transcription_Factor_II_Fhttp://en.wikipedia.org/wiki/Transcription_Factor_II_Ehttp://en.wikipedia.org/wiki/Transcription_Factor_II_Hhttp://en.wikipedia.org/wiki/Transcription_Factor_II_Hhttp://en.wikipedia.org/wiki/Transcription_Factor_II_Hhttp://en.wikipedia.org/wiki/Helicasehttp://en.wikipedia.org/wiki/Helicasehttp://en.wikipedia.org/wiki/C-terminal_domainhttp://en.wikipedia.org/wiki/C-terminal_domainhttp://en.wikipedia.org/wiki/Promoterhttp://en.wikipedia.org/wiki/Transcription_factorshttp://en.wikipedia.org/wiki/Preinitiation_complexhttp://en.wikipedia.org/wiki/TATA_boxhttp://en.wikipedia.org/wiki/Conservation_(genetics)http://en.wikipedia.org/wiki/Conservation_(genetics)http://www.als.lbl.gov/als/science/sci_archive/polymerase2.htmlhttp://en.wikipedia.org/wiki/General_transcription_factorhttp://en.wikipedia.org/wiki/TATA_Binding_Proteinhttp://en.wikipedia.org/wiki/Transcription_Factor_II_Dhttp://en.wikipedia.org/wiki/TATA_boxhttp://en.wikipedia.org/wiki/TFIIAhttp://en.wikipedia.org/wiki/Transcription_Factor_II_Bhttp://en.wikipedia.org/wiki/Transcription_Factor_II_Fhttp://en.wikipedia.org/wiki/Transcription_Factor_II_Ehttp://en.wikipedia.org/wiki/Transcription_Factor_II_Hhttp://en.wikipedia.org/wiki/Helicasehttp://en.wikipedia.org/wiki/C-terminal_domainhttp://en.wikipedia.org/wiki/C-terminal_domain


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polymerase to start producing RNA, which marks the end of initiation and thestart of elongation. Finally it is essential forNucleotide Excision Repair(NER) ofdamaged DNA. TFIIH and TFIIE strongly interact with one another. TFIIEaffects TFIIHs catalytic activity. Without TFIIE, TFIIH will not unwind thepromoter.

7. Mediator-cht mi gii then encases- bao bc all the transcription factors and thePol II. Mediator interacts with enhancers, areas very far away (upstream ordownstream) that help regulate transcription [3]. Trong bc cui cng, cc chtmi gii hay gi chung l MEDIATOR s bao bc tt c cc yu t phin m nitrn v RNA pol II, sau bn thn mediator ny s tng tc vi cc enhancerv cc khu vc rt xa c th l upstream or downstream v sau s gip iukhin qu trnh phin m trong t bo.

Occasionally there is no TATA box at the promoter. In this case a TAF will bindsequence specifically, and force the TBP to bind non sequence specifically. TAFs arehighly variable, and add a level of control to the initiation. Nu nh ko c hp TA

promoter, TAF s lin kt vi cc trnh t nht nh v sau p TBP lin kt vi trnh tko c hiu . Bn thn yu t TAFs cng rt a dng v c th c thm cc mc khc nhau trong vic iu khin s khi u qu trnh phin m.

Initiation Regulation

Initiation is regulated by many mechanisms. These can be separated into two maincategories:

1. Protein interference-cc protein can thip hay l gy nhiu.2. Regulation by phosphorylation-s iu ho bi c ch phosphoryl ho.

Regulation by Protein interference:

- Protein interference is the process where some signaling protein interacts, either withthe promoter or some stage of the partially constructed complex, to prevent furtherconstruction of the polymerase complex, so preventing initiation. This is generally a veryrapid response and is used for fine level, individual gene control and for 'cascade'processes for a group of genes useful under a specific conditions (for example DNArepair genes or heat shock genes) da trn c s l s tng tc vi cc protein, cpromotor v mt vi bc ca cc phc h cu trc ny sau s ngn cn s hnh thnhca cc phc h ca polymerase v sau ngn cn s khi u phin m. Bn thn qu

trnh p ng da trn cc tn hiu l cc protein ny cng thc hin rt nhanh v thngc chia thnh nhiu mc khc nhau, c qu trnh iu khin ring cho mt genering bit v ng thi cng cho c nhm gen di s p ng vi cc tn hiu c bit vd nh l s sa cha ca gen hoc l sc nhit.

Chromatin structure inhibition is the process where the promoter is hidden by chromatinstructure. Chromatin structure is controlled by post-translational modification of thehistones involved and leads to gross levels of high or low transcription levels. See:
http://en.wikipedia.org/wiki/Nucleotide_excision_repairhttp://en.wikipedia.org/wiki/Mediator_complexhttp://en.wikipedia.org/wiki/Enhancerhttp://en.wikipedia.org/wiki/Enhancerhttp://en.wikipedia.org/wiki/RNA_polymerase_II#cite_note-2%23cite_note-2http://en.wikipedia.org/wiki/Chromatinhttp://en.wikipedia.org/wiki/Chromatinhttp://en.wikipedia.org/wiki/Histonehttp://en.wikipedia.org/wiki/Nucleotide_excision_repairhttp://en.wikipedia.org/wiki/Mediator_complexhttp://en.wikipedia.org/wiki/Enhancerhttp://en.wikipedia.org/wiki/RNA_polymerase_II#cite_note-2%23cite_note-2http://en.wikipedia.org/wiki/Chromatinhttp://en.wikipedia.org/wiki/Chromatinhttp://en.wikipedia.org/wiki/Histone


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chromatin, histone and nucleosome. i lc chnh bn thn nhim sc th cng c chqu trnh gn ca cc nhim sc th, cu trc ca NST li c iu khin bi cc c chbin i sau qu trnh dch m ca cc protein histone v gn n s iu ho cc mc sao chp cao hay thp ca cc gen.

These methods of control can be combined in a modular method, allowing very highspecificity in transcription initiation control.

Regulation by Phosphorylation

1. iu ho bng c ch photphoryl ho ca CTD trong tiu phn ca Pol II.

- The largest subunit of Pol II (Rpb1) has a domain at its C-terminus that is called theCTD (C-terminal domain). This is the target of kinases and phosphatases. The phosphorylation of the CTD is an important regulation mechanism, as this allowsattraction and rejection of factors that have a function in the transcription process. The

CTD can be considered as a platform fortranscription factors.The CTD consists of repetitions of anamino acid motif, YSPTSPS, of which SerinesandThreonines can bephosphorylated. The number of these repeats varies; the mammalianprotein contains 52, while the yeast protein contains 26. Site-directed-mutagenesis of theyeast protein has found at least 10 repeats are needed for viability. There are manydifferent combinations of phosphorylations possible on these repeats and these canchange rapidly during transcription. The regulation of these phosphorylations and theconsequences for the association of transcription factors plays a major role in theregulation of transcription. S iu khin ca cc c ch phosphoryl ho v kt qu can c mi lin quan rt mt thit ca n vi cc yu t phin m bt m mt chc

nng quan trng trong s iu khin ca qu trnh phin m.C ch ch yu ca qu trnh iu khin cc chu trnh sao m theo c ch ny c trnhby nh sau: Trong sut qu trnh phin m, tiu n v CTD ca RNAPII thngxuyn c photphoryl ho lun phin, s phin m thng thng sy ra v tr ca vngprotein c cc axit amin lp li v bn thn vng ny th s photphoryl ho thng sy ra v tr ca acid amin serin. During the transcription cycle, the CTD of the large subunitof RNAP II is reversibly phosphorylated. RNAP II containing unphosphorylated CTD isrecruited to the promoter, whereas the hyperphosphorylated CTD form is involved inactive transcription. Phosphorylation occurs at two sites within the heptapeptide repeat, atSerine 5 and Serine 2. Serine 5 phosphorylation is confined to promoter regions and is

necessary for the initiation of transcription, whereas Serine 2 phosphorylation isimportant for mRNA elongation and 3'-end processing.

- VY PAF COMPLEX THAM GIA VO QU TRNH NO TRONG HTHNG NY V CU TRC CNG NH L VAI TR CA N L G?

Elongation
http://en.wikipedia.org/wiki/Chromatinhttp://en.wikipedia.org/wiki/Histonehttp://en.wikipedia.org/wiki/Nucleosomehttp://en.wikipedia.org/wiki/Protein_kinasehttp://en.wikipedia.org/wiki/Protein_kinasehttp://en.wikipedia.org/wiki/Phosphataseshttp://en.wikipedia.org/wiki/Phosphataseshttp://en.wikipedia.org/wiki/Transcription_factorshttp://en.wikipedia.org/wiki/Transcription_factorshttp://en.wikipedia.org/wiki/Amino_acidhttp://en.wikipedia.org/wiki/Amino_acidhttp://en.wikipedia.org/wiki/Serinehttp://en.wikipedia.org/wiki/Serinehttp://en.wikipedia.org/wiki/Threoninehttp://en.wikipedia.org/wiki/Phosphorylatedhttp://en.wikipedia.org/wiki/Phosphorylatedhttp://en.wikipedia.org/wiki/Chromatinhttp://en.wikipedia.org/wiki/Histonehttp://en.wikipedia.org/wiki/Nucleosomehttp://en.wikipedia.org/wiki/Protein_kinasehttp://en.wikipedia.org/wiki/Phosphataseshttp://en.wikipedia.org/wiki/Transcription_factorshttp://en.wikipedia.org/wiki/Amino_acidhttp://en.wikipedia.org/wiki/Serinehttp://en.wikipedia.org/wiki/Threoninehttp://en.wikipedia.org/wiki/Phosphorylated


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The process of elongation is the synthesis of a copy of the DNA into messenger RNA.RNA Pol II matches complementary RNA nucleotides to the template DNA byWatson-Crickbase pairing. These RNA nucleotides are ligated and this results ina strand ofmessenger RNA.

Elongation RegulationRNA Pol II elongation promoters can be summarised in 3 classes:

1. Drug/sequence-dependent arrest-bt gi affected factors.

Eg. SII (TFIIS) and P-TEFb protein families.

2. Chromatin structure oriented factors. Based on histone post translationalmodifications - phosphorylation, acetylation, methylation and ubiquination. bnthn s bin i cu trc di 4 dng ni trn phosphorylation, acetylation,

methylation and ubiquination, c s tham gia v lin quan ca epigenetic tronglnh vc ny.

See: chromatin, histone, andnucleosome

3. RNA Pol II catalysis improving factors. Improve the Vmax or Km of RNA Pol II,so improving the catalytic quality of the polymerase enzyme. Eg. TFIIF, Elonginand ELL families.

See: Enzyme kinetics, Henri-Michaelis-Menten kinetics, Michaelis constant, and

LineweaverBurk plot

As for initiation, protein interference, seen as the "drug/sequence-dependent arrestaffected factors" and "RNA Pol II catalysis improving factors" provide a very rapidresponse and is used for fine level individual gene control. Elongation down regulation isalso possible, in this case usually by blocking polymerase progress or by deactivating thepolymerase.

Chromatin structure oriented factors are more complex than for initiation control. Oftenthe chromating altering factor becomes bound to the polymerase complex, altering thehistones as they are encountered and providing a semi-permanent 'memory' of previouspromotion and transcription.

Termination

- Termination is the process of breaking up of the polymerase complex and ending of theRNA strand. In eukaryotes using RNA Pol II this termination is very variable (up to 2000 bases), relying on post transcriptional modification. See: Messenger RNA andPolyadenylation.
http://en.wikipedia.org/wiki/Complementarity_(molecular_biology)http://en.wikipedia.org/wiki/Base_pairhttp://en.wikipedia.org/wiki/Base_pairhttp://en.wikipedia.org/wiki/Messenger_RNAhttp://en.wikipedia.org/wiki/P-TEFbhttp://en.wikipedia.org/wiki/Chromatinhttp://en.wikipedia.org/wiki/Histonehttp://en.wikipedia.org/wiki/Nucleosomehttp://en.wikipedia.org/wiki/Nucleosomehttp://en.wikipedia.org/wiki/Enzyme_kineticshttp://en.wikipedia.org/wiki/Henri-Michaelis-Menten_kineticshttp://en.wikipedia.org/wiki/Henri-Michaelis-Menten_kineticshttp://en.wikipedia.org/wiki/Michaelis_constanthttp://en.wikipedia.org/wiki/Lineweaver%E2%80%93Burk_plothttp://en.wikipedia.org/wiki/Eukaryoteshttp://en.wikipedia.org/wiki/Messenger_RNAhttp://en.wikipedia.org/wiki/Polyadenylationhttp://en.wikipedia.org/wiki/Complementarity_(molecular_biology)http://en.wikipedia.org/wiki/Base_pairhttp://en.wikipedia.org/wiki/Messenger_RNAhttp://en.wikipedia.org/wiki/P-TEFbhttp://en.wikipedia.org/wiki/Chromatinhttp://en.wikipedia.org/wiki/Histonehttp://en.wikipedia.org/wiki/Nucleosomehttp://en.wikipedia.org/wiki/Enzyme_kineticshttp://en.wikipedia.org/wiki/Henri-Michaelis-Menten_kineticshttp://en.wikipedia.org/wiki/Michaelis_constanthttp://en.wikipedia.org/wiki/Lineweaver%E2%80%93Burk_plothttp://en.wikipedia.org/wiki/Eukaryoteshttp://en.wikipedia.org/wiki/Messenger_RNAhttp://en.wikipedia.org/wiki/Polyadenylation


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Little regulation occurs at termination, although it has been proposed newly transcribedRNA is held in place if proper termination is inhibited, allowing very fast expression ofgenes given a stimulus. This has not been demonstrated in eukaryotesas of yet.

Transcription factor TFIIA:

- TFIIA: is a nuclearprotein involved in theRNA polymerase II-dependent transcriptionofDNA.[1]TFIIA is one of several general (basal) transcription factors (GTFs) that arerequired for all transcription events that use RNA polymerase II. Other GTFs includeTFIID, a complex composed of the TATA binding protein TBP and TBP-associatedfactors (TAFs), as well as the factors TFIIB, TFIIE, TFIIF, and TFIIH. Together, thesefactors are responsible forpromoter recognition and the formation of a transcriptionpreinitiation complex (PIC) capable of initiatingRNA synthesis from a DNA template.

- The function: TFIIA interacts with the TBP subunit of TFIID and aids in the binding ofTBP to TATA-box containing promoter DNA. Although TFIIA does not recognize DNAitself, its interactions with TBP allow it to stabilize and facilitate formation of the PIC.Binding of TFIIA to TBP also results in the exclusion of negative (repressive) factors thatmight otherwise bind to TBP and interfere with PIC formation. TFIIA also acts as acoactivatorfor some transcriptional activators, assisting with their ability to increase, oractivate, transcription. The requirement for TFIIA in vitro transcription systems has beenvariable, and it can be considered either as a GTF and/or a loosely associated TAF-likecoactivator. Genetic analysis inyeasthas shown that TFIIA is essential for viability.

- Gene encode for TFIIA: It is encoded by two separate genes, one of which encodes alarge subunit (TFIIAalpha/beta, TFIIAL, TOA1; gene name GTF2A1)[2] and anotherwhich encodes a small subunit (TFIIAgamma, TFIIAS, TOA2; gene name GTF2A2).[3] In

humans, the sizes of the encoded proteins are approximately 55 kD and 12 kD. Bothgenes are present in species ranging from humans to yeast, and their protein productsinteract to form a complex composed of abeta barreldomainand an alpha helical bundledomain. It is theN-terminal and C-terminal regions of the large subunit that participate ininteractions with the small subunit. These regions are separated by another domain whosesequence is always present in large subunits from various species but whose size variesand whose sequence is poorly conserved. The large subunit is often observed to beproteolytically processed into two smaller subunits (alpha and beta) of approximately 35kD and 19 kD. A second gene encoding a large TFIIA subunit has been found in somehighereukaryotes. This gene, ALF/TFIIAtau (gene name GTF2A1LF) is expressed onlyin oocytes and spermatocytes, suggesting it has a TFIIA-like regulatory role for gene

expression only in germ cells.

Transcription factor II B (TFIIB):

- (TFIIB): is one of several general transcription factors that make up the RNApolymerase IIpreinitiation complex.It is encoded by the TFIIB gene
http://en.wikipedia.org/wiki/Eukaryoteshttp://en.wikipedia.org/wiki/Eukaryoteshttp://en.wikipedia.org/wiki/Cell_nucleushttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/RNA_polymerase_IIhttp://en.wikipedia.org/wiki/RNA_polymerase_IIhttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/TFIIA#cite_note-pmid17560669-0%23cite_note-pmid17560669-0http://en.wikipedia.org/wiki/TFIIA#cite_note-pmid17560669-0%23cite_note-pmid17560669-0http://en.wikipedia.org/wiki/Transcription_factorhttp://en.wikipedia.org/wiki/General_transcription_factorhttp://en.wikipedia.org/wiki/TFIIDhttp://en.wikipedia.org/wiki/TATA_binding_proteinhttp://en.wikipedia.org/wiki/TFIIBhttp://en.wikipedia.org/wiki/TFIIEhttp://en.wikipedia.org/wiki/TFIIFhttp://en.wikipedia.org/wiki/TFIIHhttp://en.wikipedia.org/wiki/Promoterhttp://en.wikipedia.org/wiki/Promoterhttp://en.wikipedia.org/wiki/Preinitiation_complexhttp://en.wikipedia.org/wiki/RNAhttp://en.wikipedia.org/wiki/RNAhttp://en.wikipedia.org/wiki/TATA_boxhttp://en.wikipedia.org/wiki/Transcription_coregulatorhttp://en.wikipedia.org/wiki/Transcription_coregulatorhttp://en.wikipedia.org/wiki/Activator_(genetics)http://en.wikipedia.org/wiki/Yeasthttp://en.wikipedia.org/wiki/Yeasthttp://en.wikipedia.org/wiki/Yeasthttp://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Protein_subunithttp://www.genenames.org/data/hgnc_data.php?match=GTF2A1http://en.wikipedia.org/wiki/TFIIA#cite_note-pmid8224848-1%23cite_note-pmid8224848-1http://www.genenames.org/data/hgnc_data.php?match=GTF2A2http://en.wikipedia.org/wiki/TFIIA#cite_note-pmid7958899-2%23cite_note-pmid7958899-2http://en.wikipedia.org/wiki/Protein_complexhttp://en.wikipedia.org/wiki/Beta_barrelhttp://en.wikipedia.org/wiki/Protein_domainshttp://en.wikipedia.org/wiki/Protein_domainshttp://en.wikipedia.org/wiki/Helix_bundlehttp://en.wikipedia.org/wiki/N-terminushttp://en.wikipedia.org/wiki/C-terminushttp://en.wikipedia.org/wiki/Conserved_sequencehttp://en.wikipedia.org/wiki/Proteolysishttp://en.wikipedia.org/wiki/Eukaryotehttp://en.wikipedia.org/wiki/Eukaryotehttp://en.wikipedia.org/wiki/Oocytehttp://en.wikipedia.org/wiki/Spermatocytehttp://en.wikipedia.org/wiki/Spermatocytehttp://en.wikipedia.org/wiki/Germ_cellhttp://en.wikipedia.org/wiki/General_transcription_factorhttp://en.wikipedia.org/wiki/General_transcription_factorhttp://en.wikipedia.org/wiki/RNA_polymerase_IIhttp://en.wikipedia.org/wiki/RNA_polymerase_IIhttp://en.wikipedia.org/wiki/RNA_polymerase_IIhttp://en.wikipedia.org/wiki/Preinitiation_complexhttp://en.wikipedia.org/wiki/Preinitiation_complexhttp://www.genenames.org/data/hgnc_data.php?match=TFIIBhttp://en.wikipedia.org/wiki/Eukaryoteshttp://en.wikipedia.org/wiki/Cell_nucleushttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/RNA_polymerase_IIhttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/TFIIA#cite_note-pmid17560669-0%23cite_note-pmid17560669-0http://en.wikipedia.org/wiki/Transcription_factorhttp://en.wikipedia.org/wiki/General_transcription_factorhttp://en.wikipedia.org/wiki/TFIIDhttp://en.wikipedia.org/wiki/TATA_binding_proteinhttp://en.wikipedia.org/wiki/TFIIBhttp://en.wikipedia.org/wiki/TFIIEhttp://en.wikipedia.org/wiki/TFIIFhttp://en.wikipedia.org/wiki/TFIIHhttp://en.wikipedia.org/wiki/Promoterhttp://en.wikipedia.org/wiki/Preinitiation_complexhttp://en.wikipedia.org/wiki/RNAhttp://en.wikipedia.org/wiki/TATA_boxhttp://en.wikipedia.org/wiki/Transcription_coregulatorhttp://en.wikipedia.org/wiki/Activator_(genetics)http://en.wikipedia.org/wiki/Yeasthttp://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Protein_subunithttp://www.genenames.org/data/hgnc_data.php?match=GTF2A1http://en.wikipedia.org/wiki/TFIIA#cite_note-pmid8224848-1%23cite_note-pmid8224848-1http://www.genenames.org/data/hgnc_data.php?match=GTF2A2http://en.wikipedia.org/wiki/TFIIA#cite_note-pmid7958899-2%23cite_note-pmid7958899-2http://en.wikipedia.org/wiki/Protein_complexhttp://en.wikipedia.org/wiki/Beta_barrelhttp://en.wikipedia.org/wiki/Protein_domainshttp://en.wikipedia.org/wiki/Helix_bundlehttp://en.wikipedia.org/wiki/N-terminushttp://en.wikipedia.org/wiki/C-terminushttp://en.wikipedia.org/wiki/Conserved_sequencehttp://en.wikipedia.org/wiki/Proteolysishttp://en.wikipedia.org/wiki/Eukaryotehttp://en.wikipedia.org/wiki/Oocytehttp://en.wikipedia.org/wiki/Spermatocytehttp://en.wikipedia.org/wiki/Germ_cellhttp://en.wikipedia.org/wiki/General_transcription_factorhttp://en.wikipedia.org/wiki/RNA_polymerase_IIhttp://en.wikipedia.org/wiki/RNA_polymerase_IIhttp://en.wikipedia.org/wiki/Preinitiation_complexhttp://www.genenames.org/data/hgnc_data.php?match=TFIIB


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Transcription factor IIB localizes to the nucleus where it forms a complex (the DABcomplex) with transcription factors IID and IIA. The protein serves as a bridge betweenIID, the factor which initially recognizes thepromotersequence, and RNA polymerase II.[4] It is involved in the selection of the transcription start site: mutations in TFIIB causea shift - chuyn di, i ch in the transcription start site.

- FACT (facilitates chromatin transcription) is a heterodimeric protein complex thataffects eukaryotic RNA polymerase II (Pol II) transcription elongation both in vitro andin vivo. It was discovered in 1998 as a factor purified from human cells, consisting of 140and 80 kilodalton (kDa) subunits, that was essential for productive in vitro Pol IItranscription on a chromatinized DNA template. The 140 kDa subunit is encoded by ahuman gene (SUPT16H) which is 36% identical to the S. cerevisiae gene Spt16 and the80 kDa subunit is human SSRP1 (POB3 in S. cerevisiae). Both of these subunits in yeastaffect Pol II transcription elongation, and purified human FACT binds specifically tomononulceosomes and the histone H2A/H2B dimer, but not to the H3/H4 tetramer (see: Nucleosome core particle) or Pol II.[2] Co-immunoprecipitation assays with tagged

recombinant proteins showed that the Spt16 subunit interacts with H2A/H2B dimers andmononucleosomes, but not H3/H4 tetramers, whereas the SSRP1 subunit interacts onlywith H3/H4 tetramers and not mononucleosomes. Deletion of the highly acidic carboxy-terminus of Spt16 (a common feature of known histone chaperones) does not preventSpt16 from forming a stable complex with SSRP1, but it does eliminate interaction withmononucleosomes and ability to stimulate in vitro transcription on chromatinizedtemplates. The two subunits together, but neither alone, can stimulate formation ofnucleosomes from free histones and DNA (histone chaperone activity). These twosubunits are highly conserved across all eukaryotes and in addition to transcription, havebeen shown to affect DNA repair and replication as well.

In cells, FACT is enriched on parts of the genome involved in actively elongating Pol II,as seen in fluorescent-antibody staining ofDrosophila polytene chromosomes andchromatin immunoprecipitation (ChIP) assays onDrosophila Kc cell extracts.

Transcription factor II D (TFIID):

TFIID: is one of several general transcription factors that make up the RNA polymerase II preinitiation complex.[1] TFIID is itself composed of several subunits called TBP-associated factors (TAFs, of which there are 14) and the TATA Binding Protein (TBP).

In a test tube, only TBP is necessary for transcription atpromoters that contain a TATA

box.[2] TAFs, however, add promoter selectivity, especially if there is no TATA boxsequence for TBP to bind to.

2. Cc yu t phin m (Transcription factor TF)

- Transcription factor Dp-1 is aprotein that in humans is encoded by the TFDP1gene.The E2F transcription factor family (see MIM 189971) regulates the expression ofvarious cellular promoters, particularly those involved in the cell cycle. E2F factors bind
http://en.wikipedia.org/wiki/Transcription_Factor_II_Dhttp://en.wikipedia.org/wiki/TFIIAhttp://en.wikipedia.org/wiki/Promoterhttp://en.wikipedia.org/wiki/Promoterhttp://en.wikipedia.org/wiki/Transcription_factor_II_B#cite_note-3%23cite_note-3http://en.wikipedia.org/wiki/RNA_polymerase_IIhttp://en.wikipedia.org/wiki/SUPT16Hhttp://en.wikipedia.org/wiki/Structure_specific_recognition_protein_1http://en.wikipedia.org/wiki/Nucleosome#Structure_of_the_core_particlehttp://en.wikipedia.org/wiki/FACT_(biology)#cite_note-Orphanides_1999-1%23cite_note-Orphanides_1999-1http://en.wikipedia.org/wiki/Chaperone_(protein)http://en.wikipedia.org/wiki/Drosophilahttp://en.wikipedia.org/wiki/Polytene_chromosomehttp://en.wikipedia.org/wiki/Chromatin_immunoprecipitationhttp://en.wikipedia.org/wiki/General_transcription_factorhttp://en.wikipedia.org/wiki/RNA_polymerase_IIhttp://en.wikipedia.org/wiki/Preinitiation_complexhttp://en.wikipedia.org/wiki/Transcription_Factor_II_D#cite_note-isbn0-13-144946-X-0%23cite_note-isbn0-13-144946-X-0http://en.wikipedia.org/wiki/Transcription_Factor_II_D#cite_note-isbn0-13-144946-X-0%23cite_note-isbn0-13-144946-X-0http://en.wikipedia.org/wiki/Protein_subunithttp://en.wikipedia.org/wiki/TATA_Binding_Proteinhttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Promoterhttp://en.wikipedia.org/wiki/TATA_boxhttp://en.wikipedia.org/wiki/TATA_boxhttp://en.wikipedia.org/wiki/Transcription_Factor_II_D#cite_note-pmid11092823-1%23cite_note-pmid11092823-1http://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Transcription_Factor_II_Dhttp://en.wikipedia.org/wiki/TFIIAhttp://en.wikipedia.org/wiki/Promoterhttp://en.wikipedia.org/wiki/Transcription_factor_II_B#cite_note-3%23cite_note-3http://en.wikipedia.org/wiki/RNA_polymerase_IIhttp://en.wikipedia.org/wiki/SUPT16Hhttp://en.wikipedia.org/wiki/Structure_specific_recognition_protein_1http://en.wikipedia.org/wiki/Nucleosome#Structure_of_the_core_particlehttp://en.wikipedia.org/wiki/FACT_(biology)#cite_note-Orphanides_1999-1%23cite_note-Orphanides_1999-1http://en.wikipedia.org/wiki/Chaperone_(protein)http://en.wikipedia.org/wiki/Drosophilahttp://en.wikipedia.org/wiki/Polytene_chromosomehttp://en.wikipedia.org/wiki/Chromatin_immunoprecipitationhttp://en.wikipedia.org/wiki/General_transcription_factorhttp://en.wikipedia.org/wiki/RNA_polymerase_IIhttp://en.wikipedia.org/wiki/Preinitiation_complexhttp://en.wikipedia.org/wiki/Transcription_Factor_II_D#cite_note-isbn0-13-144946-X-0%23cite_note-isbn0-13-144946-X-0http://en.wikipedia.org/wiki/Protein_subunithttp://en.wikipedia.org/wiki/TATA_Binding_Proteinhttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Promoterhttp://en.wikipedia.org/wiki/TATA_boxhttp://en.wikipedia.org/wiki/TATA_boxhttp://en.wikipedia.org/wiki/Transcription_Factor_II_D#cite_note-pmid11092823-1%23cite_note-pmid11092823-1http://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Gene


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to DNA as homodimers or heterodimers in association with dimerization partner DP1.TFDP1 may be the first example of a family of related transcription factors

- E2F is a group of genes that codifies a family of transcription factors (TF) in highereukaryotes. Three of them are activators: E2F1,2 and E2F3a. Six others act as

suppressors: E2F3b, E2F4-8. All of them are involved in the cell cycle regulation andsynthesis of DNA in mammalian cells. E2Fs as TFs bind to the TTTCGCGC consensusbinding site in the targetpromotersequence.

3. Cc phc h phin m (Transcription complex).

The PAF complex in yeast:

- It was first identified in yeast (yPAF) as an RNA polymerase II-associated factor thatinteracts with TATA Binding Protein (TBP) chng c xem nh l mt nhn t cngtc cng vi RNA pol II, chng tng tc vi protein bm vo hp TA, nhn t ko diSpt4-Spt5 v cc yu t thun li cho s sao chp ca nhim sc thtrong sut qu

trnh ko di chui, the elongation factors Spt4Spt5, and FACT during transcription elongation{reviewed by (Shilatifard 2006)} RNAP II-mediated transcription involves successiverecruitment-s tuyn m, s ly thm of various stage-specific factors and mediators thatare required for the formation of a mature elongation complex. This process is furthercoordinated by phosphorylation of the carboxy-terminal domain (CTD) of RNAP II - ssao m ca RNAP II c lin quan n s photphoryl ho ti domain u carboxy caRNAP II . The yPAF complex acts as a mediator-cht mi gii during transcriptionelongation by stimulating the following steps: Rad6-mediated mono-ubiquitination of thecore histone H2B (Ng et al. 2003; Wood et al. 2003; Wood et al. 2005), Set1-mediated

histone H3-K4methylation (Dover et al. 2002; Krogan et al. 2003b; Ng et al. 2003), andDot1-mediatedhistone H3-K79 methylation (Krogan et al. 2003b; Krogan et al. 2003a).FACT, a dimeric protein containing HMG1 (high mobility lu ng, chuyn ng, haybin i group) domain plays a major role in this process by binding and displacing theH2A/H2B dimer from the core nucleosome and allowing elongation to proceed overchromatin (Belotserkovskaya et al. 2003) (Figure 2). The interaction of FACT with thePAF complex is an important step during the process of elongation, and any defects in thePAF complex lead to elongation defects (Mueller et al. 2004). S tng tc ca yu tFACT vi phc h PAF l mt bc rt quan trng trong sut qu trnh ko di chui vbt c s sai st no ca phc h PAF u dn n sai st v khim khuyt ti qu trnhko di chui.

Sau nghin cu tht c th vn ny, ngi ta to ra s thiu ht ca PAF sau nghin cu vai tr c th ca tng tiu n v ca phc h ny i vi qu trnhphin m. Kt qu l ngi ta nhn thy hai tiu n v Paf1 and Ctr9 c chc nng quantrng v cng l thnh phn quan trng nht ca phc h ny.

- To investigate whether all the subunits of the yPAF complex are involved in andinteract during the course of transcription, the effects of loss of each subunit was studied-nh vy l th nghim ny c xu hng l nghin cu s nh hng ca vic thiu ht
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cc thnh phn ca phc h yPAF i vi t bo v h s dng cc chng t bin cmang cc t bin v do chng gn nh l c nhng khim khuyt trong qu trnhpht trin ca chng. Isogenicpaf1 and ctr9 strains showed severe and nearly identicalgrowth defects, while the Cdc73 orRtf1 mutants exhibited less severe phenotypes thatwere a subset of those seen in paf1 and ctr9. The Leo1 strains had few detectable

deficiencies (Betz et al. 2002). These results suggest that Paf1 and Ctr9 have similar rolesand are the most important components of the complex- v kt qu thu c l hai tiuphn subunit l Paf1 v Ctr9 c chc nng tng t nhau v l hai thnh phn quan trngnht ca phc h PAF ny.

The yPAF complex also plays essential roles in other cellular functions. The CTD(carboxy-terminal domain) of the RNA polymerase II large subunit contains twoimportant serine residues, Ser2 and Ser5, which are phosphorylated during transcription nh vy chng ta c th nhn thy rng domain c cha u C ca RNA pol c cc tiuphn ln b photphoryl ho trong sut qu trnh sao m. Phosphorylation of Ser5 isrequired during transcription initiation and the early phase of elongation, whilephosphorylation of Ser2 is linked to elongation (Komarnitsky et al. 2000). C mt iu

quan trng cn ch l hai gc quan trng ser2 v ser5 ca CTD, trong sphotphoryl ho ca ser5 l iu kin cn cho qu trnh khi u phin m v trong giaion sm ca s ko di phin m, trong khi s photphoryl ho ca ser2 c lin quanmt thit ti qu trnh ko di chui. Loss of the PAF complex members results inreduced phosphorylation of RNAP II on Ser2, a prerequisite for transcription elongation,and a shortening of poly(A) tails on mRNA - s loss ca phc h PAF dn n s suygim kh nng photphoryl ho RNAP II ti ser2 cho qu trnh ko di phin m v qutrnh ngn dn ca ui poly A trong mRNA. This indicates that the PAF complex acts asa link between transcriptional and posttranscriptional events - Phc h PAF hot ngnh l mt lin kt gia cc s kin sy ra trong v sau qu trnh phin m. Further, theyPAF-RNA polymerase II complex is involved in regulating the expression of a subset ofcell-cycle genes. This is evidenced by a 2- to 13-fold reduction in the transcriptabundance of many periodically expressed genes, including CLN1, HO, RNR1, andFAR1 in paf1 strain (Porter et al. 2002).

Rtf1 performs histone methylation independent of PAF complex and regulatesNotch signaling- The human PAF complex differs from the yeast complex in having hSki8 subunit andlacking the yeast Rtf1 homolog. In humans and in Drosophila, the Rtf1 subunit does notappear to be a stable part of the PAF complex-ring sinh vt nhn chun Rtf1 xuthin duy tr tnh n nh ca phc h PAF. However, Paf1 and Rtf1 seem to associatein the context of actively transcribing RNAP II in Drosophila (Adelman et al. 2006) and

dRtf1 plays an important role in histone methylation (Tenney et al. 2006). Thus, thefunction of this protein is conserved in yeast and Drosophila suggesting that the humanRtf1 protein may act in tandem-ni tip nhau, ngi n ngi sau ngi kia with hPAF inhistone modification, although not as an integral part of the complex.- Further, Tenney et al. (2006) showed that dRtf1 also plays a role in Notch signaling.The Notch cascade is a crucial signaling pathway that regulates normal development byits effects on cellular differentiation, proliferation and apoptosis. Alterations in thissignaling pathway are associated with various human cancers including T-cell leukemia,


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which involves translocations of the MLL gene (Weng et al. 2004). The MLL gene isthe human homologue of yeast SET1 in the COMPASS (ComplexProteins Associated with Set1) complex involved in histonemethylation. The methylation of histone H3K4 by yeast COMPASS requiresubiquitination of histone H2B by the Rad6 and Bre1 proteins (Figure 2 in the

manuscript). As discussed previously, the PAF complex is required to activateRad6 and Bre1 histone ubiquitination activity in yeast. Tenney et al.(2006) determined that the Drosophila Rtf1 subunit of the PAF complexfacilitates Notch signaling, linking histone ubiquitination andmethylation to gene activation by the Notch pathway. Interestingly,Bre1 is also required for Notch target gene expression in Drosophila(Bray et al. 2005). Therefore, the important functional links betweenthe PAF complex, Rad6/Bre1 and histone methylation seen in yeast isconserved in Drosophilla. Considering the molecular mechanismsunderlying MLL action, it has been predicted by Tenney et al. (2006)that the human PAF complex, along with Rtf1, might participate

in Notch signaling and might be linked to the pathogenesis ofleukemia via the MLL translocations.

3. Cc giai on v iu ho trong qu trnh phin m

CC KHI NIM C BN V QU TRNH SAO M

The transcription undergoes 5 main stages

Pre-initiation Initiation promoter clearance elongation termination.

Transcription, orRNA synthesis, is the process of creating an equivalent RNA copy ofa sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs ofnucleotides as a complementary language that can be converted back and forth fromDNA to RNA in the presence of the correct enzymes. During transcription, a DNAsequence is read by RNA polymerase, which produces a complementary, antiparallelRNA strand. As opposed to DNA replication, transcription results in an RNA complimentthat includes uracil (U) in all instances where thymine (T) would have occurred in a DNAcompliment.

Transcription is the first step leading togene expression. The stretch of DNA transcribedinto an RNA molecule is called a transcription unitand encodes at least onegene. If thegene transcribed encodes for a protein, the result of transcription is messenger RNA(mRNA), which will then be used to create that protein via the process of translation.Alternatively, the transcribed gene may encode for either ribosomal RNA (rRNA) or
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transfer RNA (tRNA), other components of the protein-assembly process, or otherribozymes.

A DNA transcription unit encoding for a protein contains not only the sequence that willeventually be directly translated into the protein (the coding sequence) but also

regulatory sequences that direct and regulate the synthesis of that protein. The regulatorysequence before (upstream 5 from) the coding sequence is called the five primeuntranslated region(5'UTR), and the sequence following (downstream from) the codingsequence is called the three prime untranslated region (3'UTR).

Chng c hai trnh t iu khin trc v sau gi l hai trnh t khi u khng dch m(5'UTR), (3'UTR).

Transcription has some proofreading mechanisms, but they are fewer and less effectivethan the controls for copying DNA; therefore, transcription has a lower copying fidelity-s ng n v chnh xc than DNA replication.

As in DNA replication, DNA is read from 3' 5' during transcription. Meanwhile, thecomplementary RNA is created from the 5' 3' direction. Although DNA is arranged astwo antiparallel strands in a double helix, only one of the two DNA strands, called thetemplate strand, is used for transcription. This is because RNA is only single-stranded, asopposed to double-stranded DNA. The other DNA strand is called the coding strand,because its sequence is the same as the newly created RNA transcript (except for thesubstitution of uracil for thymine). The use of only the 3' 5' strand eliminates the needfor the Okazaki fragments seen in DNA replication.

Prokaryotic vs. eukaryotic transcription
http://en.wikipedia.org/wiki/Transfer_RNAhttp://en.wikipedia.org/wiki/Ribozymehttp://en.wikipedia.org/wiki/Upstream_and_downstream_(DNA)http://en.wikipedia.org/wiki/Five_prime_untranslated_regionhttp://en.wikipedia.org/wiki/Five_prime_untranslated_regionhttp://en.wikipedia.org/wiki/Five_prime_untranslated_regionhttp://en.wikipedia.org/wiki/Five_prime_untranslated_regionhttp://en.wikipedia.org/wiki/Upstream_and_downstream_(DNA)http://en.wikipedia.org/wiki/Three_prime_untranslated_regionhttp://en.wikipedia.org/wiki/Double_helixhttp://en.wikipedia.org/wiki/Okazaki_fragmenthttp://en.wikipedia.org/wiki/File:Transcription_label_en.jpghttp://en.wikipedia.org/wiki/Transfer_RNAhttp://en.wikipedia.org/wiki/Ribozymehttp://en.wikipedia.org/wiki/Upstream_and_downstream_(DNA)http://en.wikipedia.org/wiki/Five_prime_untranslated_regionhttp://en.wikipedia.org/wiki/Five_prime_untranslated_regionhttp://en.wikipedia.org/wiki/Upstream_and_downstream_(DNA)http://en.wikipedia.org/wiki/Three_prime_untranslated_regionhttp://en.wikipedia.org/wiki/Double_helixhttp://en.wikipedia.org/wiki/Okazaki_fragment


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A micrograph of ongoing gene transcription of ribosomal RNA illustrating the growingprimary transcripts. "Begin" indicates the3' end of the DNA template strand, where newRNA synthesis begins; "end" indicates the 5' end, where primary transcription is almostcomplete.

One major difference betweenprokaryotes and eukaryotes is the existence of membrane-bound structures within eukaryotes, including a cell nucleus with a nuclear membranethat encapsulates ng gi cellular DNA. As a result, transcription varies between thetwo, withprokaryotic transcription occurring in the cytoplasm alongside translation andeukaryotic transcription occurring only in the nucleus, where it is separated from thecytoplasmby the nuclear membrane. Following transcription, the resulting RNA istransported into the cytoplasm, where translation then occurs.

Another important difference is that eukaryotic DNA not currently in use is stored asheterochromatin around histones to form nucleosomes and must be unwound as

euchromatin to be transcribed. Chromatin, therefore, has a strong influence on theaccessibility-d b nh hng of DNA to transcription factors and the transcriptionalmachinery - b my phin m, including RNA polymerase.

A third major difference is that newly-created mRNA in eukaryotic cells is heavily processed following transcription. Several modifications take place, including RNAsplicing to remove non-coding segments and piece together coding segments and theaddition of apolyA tail and5' capto protect the mRNA from free plasma ribonuclease,aid in nuclear export, and enhance translation. In prokaryotic cells mRNA usually staysunchanged

Major steps1- Pre-initiation

In eukaryotes, RNA polymerase, and therefore the initiation of transcription,requires the presence of a corepromotersequence in the DNA y l v tr nhn ra caRNA pol n c th bt u hay l khi u qu trnh phin m. Promoters are regionsof DNA which promote transcription and are found around -10 to -35 base pairs upstreamfrom the start site of transcription. Core - hch promoters are sequences within thepromoter which are essential for transcription initiation. RNA polymerase is able to bindto core promoters in the presence of various specific transcription factorsv c mt im

c bit l RNA pol khng c kh nng lin kt vi cc promotor m chng cn c mth thng ht sc a dng ca cc yu t phin m c hiu.

Bn thn chnh hp TATA c mt trnh t DNA ngn c bit n hay c gi l vnglin kt ca cc yu t phin m TBP

The most common type of core promoter in eukaryotes is a short DNA sequenceknown as a TATA box. The TATA box, as a core promoter, is the binding site for a
http://en.wikipedia.org/wiki/Ribosomal_RNAhttp://en.wikipedia.org/wiki/Primary_transcripthttp://en.wikipedia.org/wiki/3'_endhttp://en.wikipedia.org/wiki/3'_endhttp://en.wikipedia.org/wiki/5'_endhttp://en.wikipedia.org/wiki/Prokaryotehttp://en.wikipedia.org/wiki/Eukaryotehttp://en.wikipedia.org/wiki/Organellehttp://en.wikipedia.org/wiki/Cell_nucleushttp://en.wikipedia.org/wiki/Cell_nucleushttp://en.wikipedia.org/wiki/Cell_nucleushttp://en.wikipedia.org/wiki/Nuclear_membranehttp://en.wikipedia.org/wiki/Prokaryotic_transcriptionhttp://en.wikipedia.org/wiki/Prokaryotic_transcriptionhttp://en.wikipedia.org/wiki/Cytoplasmhttp://en.wikipedia.org/wiki/Eukaryotic_transcriptionhttp://en.wikipedia.org/wiki/Cytoplasmhttp://en.wikipedia.org/wiki/Cytoplasmhttp://en.wikipedia.org/wiki/Heterochromatinhttp://en.wikipedia.org/wiki/Histonehttp://en.wikipedia.org/wiki/Histonehttp://en.wikipedia.org/wiki/Nucleosomehttp://en.wikipedia.org/wiki/Euchromatinhttp://en.wikipedia.org/wiki/Chromatinhttp://en.wikipedia.org/wiki/Transcription_factorshttp://en.wikipedia.org/wiki/Transcription_factorshttp://en.wikipedia.org/wiki/RNA_splicinghttp://en.wikipedia.org/wiki/RNA_splicinghttp://en.wikipedia.org/wiki/Intronhttp://en.wikipedia.org/wiki/Exonhttp://en.wikipedia.org/wiki/PolyA_tailhttp://en.wikipedia.org/wiki/5'_caphttp://en.wikipedia.org/wiki/5'_caphttp://en.wikipedia.org/wiki/5'_caphttp://en.wikipedia.org/wiki/Ribonucleasehttp://en.wikipedia.org/wiki/Promoterhttp://en.wikipedia.org/wiki/Transcription_factorhttp://en.wikipedia.org/wiki/Transcription_factorhttp://en.wikipedia.org/wiki/TATA_boxhttp://en.wikipedia.org/wiki/Ribosomal_RNAhttp://en.wikipedia.org/wiki/Primary_transcripthttp://en.wikipedia.org/wiki/3'_endhttp://en.wikipedia.org/wiki/5'_endhttp://en.wikipedia.org/wiki/Prokaryotehttp://en.wikipedia.org/wiki/Eukaryotehttp://en.wikipedia.org/wiki/Organellehttp://en.wikipedia.org/wiki/Cell_nucleushttp://en.wikipedia.org/wiki/Nuclear_membranehttp://en.wikipedia.org/wiki/Prokaryotic_transcriptionhttp://en.wikipedia.org/wiki/Cytoplasmhttp://en.wikipedia.org/wiki/Eukaryotic_transcriptionhttp://en.wikipedia.org/wiki/Cytoplasmhttp://en.wikipedia.org/wiki/Heterochromatinhttp://en.wikipedia.org/wiki/Histonehttp://en.wikipedia.org/wiki/Nucleosomehttp://en.wikipedia.org/wiki/Euchromatinhttp://en.wikipedia.org/wiki/Chromatinhttp://en.wikipedia.org/wiki/Transcription_factorshttp://en.wikipedia.org/wiki/RNA_splicinghttp://en.wikipedia.org/wiki/RNA_splicinghttp://en.wikipedia.org/wiki/Intronhttp://en.wikipedia.org/wiki/Exonhttp://en.wikipedia.org/wiki/PolyA_tailhttp://en.wikipedia.org/wiki/5'_caphttp://en.wikipedia.org/wiki/Ribonucleasehttp://en.wikipedia.org/wiki/Promoterhttp://en.wikipedia.org/wiki/Transcription_factorhttp://en.wikipedia.org/wiki/TATA_box


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transcription factor known as TATA binding protein (TBP), which is itself a subunit ofanother transcription factor, called Transcription Factor II D (TFIID). AfterTFIID bindsto the TATA box via the TBP, five more transcription factors and RNA polymerasecombine around the TATA box in a series of stages to form apreinitiation complex

S hnh thnh phc h phin m sy ra nh sau:

1- Hp TATA promoter lin kt vi mt nhn t phin m c gi l TBP(TATAbinding protein) n chnh l tiu n v khc ca cc yu t phin m l TFII D.

2- Sau khi TFII D bm vo hp TATA qua cc protein lin kt vi TA(TBP), nmnhn t phin m khc v RNA polymerase lin kt xung quanh hp TA nh lmt chui ca ch hnh thnh mt phc h tin phin m.

One transcription factor, DNA helicase, has helicase activity and so is involved in theseparating of opposing strands of double-stranded DNA to provide access to a single-stranded DNA template. However, only a low, or basal, rate of transcription is driven by

the preinitiation complex alone. Other proteins known asactivators and repressors, alongwith any associated coactivators or corepressors, are responsible for modulating - iuchnh, sa li cho ng transcription rate.

The transcription preinitiation in archaea, formerly adomain of prokaryote, is essentiallyhomologous to that of eukaryotes, but is much less complex. [5] The archaeal preinitiationcomplex assembles at a TATA-box binding site; however, in archaea, this complex iscomposed of only RNA polymerase II, TBP, and TFB (the archaeal homologue ofeukaryotic transcription factor II B(TFIIB)).[6][7]

Initiation

Simple diagram of transcription initiation. RNAP = RNA polymerase.

In bacteria, a domain of prokaryotes, transcription begins with the binding of RNA

polymerase to the promoter in DNA. RNA polymerase is acore enzyme consisting offive subunits: 2 subunits, 1 subunit, 1 ' subunit, and 1 subunit. At the start ofinitiation, the core enzyme is associated with a sigma factor (number 70) that aids infinding the appropriate -35 and -10 base pairs downstream ( vng 3)of promotersequences.

Transcription initiation is more complex in eukaryotes. Eukaryotic RNA polymerase doesnot directly recognize the core promoter sequences. Instead, a collection of proteins
http://en.wikipedia.org/wiki/TATA_binding_proteinhttp://en.wikipedia.org/wiki/TATA_binding_proteinhttp://en.wikipedia.org/wiki/Transcription_Factor_II_Dhttp://en.wikipedia.org/wiki/Preinitiation_complexhttp://en.wikipedia.org/wiki/Preinitiation_complexhttp://en.wikipedia.org/wiki/TATA_binding_proteinhttp://en.wikipedia.org/wiki/TATA_binding_proteinhttp://en.wikipedia.org/wiki/Helicasehttp://en.wikipedia.org/wiki/Activator_(genetics)http://en.wikipedia.org/wiki/Activator_(genetics)http://en.wikipedia.org/wiki/Repressorhttp://en.wikipedia.org/wiki/Coactivatorhttp://en.wikipedia.org/wiki/Coactivatorhttp://en.wikipedia.org/wiki/Archaeahttp://en.wikipedia.org/wiki/Domain_(biology)http://en.wikipedia.org/wiki/Domain_(biology)http://en.wikipedia.org/wiki/Transcription_(genetics)#cite_note-4%23cite_note-4http://en.wikipedia.org/wiki/Transcription_factor_II_Bhttp://en.wikipedia.org/wiki/Transcription_factor_II_Bhttp://en.wikipedia.org/wiki/Transcription_(genetics)#cite_note-5%23cite_note-5http://en.wikipedia.org/wiki/Transcription_(genetics)#cite_note-6%23cite_note-6http://en.wikipedia.org/wiki/Bacteriahttp://en.wikipedia.org/wiki/Core_enzymehttp://en.wikipedia.org/wiki/Core_enzymehttp://en.wikipedia.org/wiki/File:Simple_transcription_initiation1.svghttp://en.wikipedia.org/wiki/File:Simple_transcription_initiation1.svghttp://en.wikipedia.org/wiki/TATA_binding_proteinhttp://en.wikipedia.org/wiki/Transcription_Factor_II_Dhttp://en.wikipedia.org/wiki/Preinitiation_complexhttp://en.wikipedia.org/wiki/TATA_binding_proteinhttp://en.wikipedia.org/wiki/TATA_binding_proteinhttp://en.wikipedia.org/wiki/Helicasehttp://en.wikipedia.org/wiki/Activator_(genetics)http://en.wikipedia.org/wiki/Repressorhttp://en.wikipedia.org/wiki/Coactivatorhttp://en.wikipedia.org/wiki/Coactivatorhttp://en.wikipedia.org/wiki/Archaeahttp://en.wikipedia.org/wiki/Domain_(biology)http://en.wikipedia.org/wiki/Transcription_(genetics)#cite_note-4%23cite_note-4http://en.wikipedia.org/wiki/Transcription_factor_II_Bhttp://en.wikipedia.org/wiki/Transcription_(genetics)#cite_note-5%23cite_note-5http://en.wikipedia.org/wiki/Transcription_(genetics)#cite_note-6%23cite_note-6http://en.wikipedia.org/wiki/Bacteriahttp://en.wikipedia.org/wiki/Core_enzyme


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calledtranscription factors mediate the binding of RNA polymerase and the initiation oftranscription. Only after certain transcription factors are attached to the promoter does theRNA polymerase bind to it. The completed assembly of transcription factors and RNA polymerase bind to the promoter, forming a transcription initiation complex.Transcription in the archaea domain is similar to transcription in eukaryotes. [8]

Promoter clearance - s dn dp, dn quangclearance c ngha gn tng tnh t clear nhng chuyn qua ngha l tnh t.

After the first bond is synthesized, the RNA polymerase must clear the promoter.During this time there is a tendencyxu hng, khuynh hng to release the RNAtranscript and produce truncated-ct ct, ct ngn transcripts. This is called abortiveinitiation and is common for both eukaryotes and prokaroytes [9]. Abortive initiationcontinues to occur until the factor rearranges, resulting in the transcription elongationcomplex (which gives a 35 bp moving footprint). The factor is released before 80nucleotides of mRNA are synthesized[10]. Once the transcript reaches approximately 23

nucleotides, it no longer slips and elongation can occur. This, like most of the remainderof transcription, is an energy-dependent process, consuming adenosine triphosphate(ATP). Bn thn enzyme RNA pol c th t ko di chui m ko cn c on mi nh lDNA pol.

Promoter clearance coincides with phosphorylation of serine 5 on the carboxy terminaldomain of RNA Pol in prokaryotes, which is phosphorylated by TFIIH.

Elongation

Simple diagram of transcription elongation

One strand of DNA, the template strand(or noncoding strand), is used as a template forRNA synthesis. As transcription proceeds, RNA polymerase traverses the template strandand uses base pairing complementarily with the DNA template to create an RNA copy.Although RNA polymerase traverses the template strand from 3' 5', the coding (non-template) strand and newly-formed RNA can also be used as reference points, sotranscription can be described as occurring 5' 3'. This produces an RNA molecule

from 5' 3', an exact copy of the coding strand (except that thymines are replaced withuracils, and the nucleotides are composed of a ribose (5-carbon) sugar where DNA hasdeoxyribose (one less oxygen atom) in its sugar-phosphate backbone).

Unlike DNA replication, mRNA transcription can involve multiple RNA polymerases ona single DNA template and multiple rounds of transcription (amplification of particularmRNA), so many mRNA molecules can be rapidly produced from a single copy of agene.
http://en.wikipedia.org/wiki/Transcription_factorhttp://en.wikipedia.org/wiki/Transcription_factorhttp://en.wikipedia.org/wiki/Transcription_(genetics)#cite_note-7%23cite_note-7http://en.wikipedia.org/wiki/Transcription_(genetics)#cite_note-9%23cite_note-9http://en.wikipedia.org/wiki/Energyhttp://en.wikipedia.org/wiki/Adenosine_triphosphatehttp://en.wikipedia.org/wiki/Thyminehttp://en.wikipedia.org/wiki/Uracilhttp://en.wikipedia.org/wiki/File:Simple_transcription_elongation1.svghttp://en.wikipedia.org/wiki/Transcription_factorhttp://en.wikipedia.org/wiki/Transcription_(genetics)#cite_note-7%23cite_note-7http://en.wikipedia.org/wiki/Transcription_(genetics)#cite_note-9%23cite_note-9http://en.wikipedia.org/wiki/Energyhttp://en.wikipedia.org/wiki/Adenosine_triphosphatehttp://en.wikipedia.org/wiki/Thyminehttp://en.wikipedia.org/wiki/Uracil


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Elongation also involves a proofreading mechanism that can replace incorrectlyincorporated bases. In eukaryotes, this may correspond with short pauses duringtranscription that allow appropriate RNA editing factors to bind - bn thn qu trnh saom ny cng c nhng khong thi gian cho php chng dng li v c sa cha, khnng dng li ny cng c th l do chnh bn thn s iu khin ca RNA polymerase

hoc cng c th l do cu trc cu cc NST. These pauses may be intrinsic to the RNApolymerase or due to chromatin structure.

Termination kt thc phin m.

Simple diagram of transcription termination vi khun chng ta c hai c ch: l c ch ko ph thuc Rho tc l qu trnh sao ms dng li nu nh c s hnh thnh mt on gp kp tc giu GC theo sau bi mt snucleotide U, gip chng tho ra t khun DNA, sau l c ch ph thuc RhO, chngc kh nng lin kt theo cch ko bn vng vi khun v mRNA, v v vy, chng c khnng gii phng cc chui mRNA c tng hp mi t cc phc h ko di chui.

Bacteria use two different strategies for transcription termination: in Rho-independenttranscription termination, RNA transcription stops when the newly synthesized RNAmolecule forms a G-C rich hairpin loop followed by a run of U's, which makes it detachfrom the DNA template. In the "Rho-dependent" type of termination, a protein factor

called "Rho" destabilizes the interaction between the template and the mRNA, thusreleasing the newly synthesized mRNA from the elongation complex.

Transcription termination in eukaryotes is less understood but involves cleavage of thenew transcript followed by template-independent addition ofAs at its new 3' end, in aprocess calledpolyadenylation. S kt thc phin m thng kh hiu v v vy n clin quan n s phn tch cleavage ca cc nhn t phin m trong mt chui rt giunucleotide A c gi l polyadenylation.

Measuring and detecting transcription cc k thut s dng chonghin cu qu trnh phin m xc nh v o c mc phinm.

Transcription can be measured and detected in a variety of ways:

Nuclear Run-on assay: measures the relative abundance of newly formedtranscripts
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RNase protection assay and ChIP-Chip ofRNAP c ch kt ta min dch dng xc nh vng phin m tch cc: detect active transcription sites

RT-PCR: measures the absolute abundance of total or nuclear RNA levels, whichmay however differ from transcription rates k thut RT-PCR dng xc nhs d tha ca RNA nhn, tuy nhin chng c th khc nhau do cc t l phin

m khc nhau. DNA microarrays: measures the relative abundance of the global total or nuclearRNA levels; however, these may differ from transcription rates

In situ hybridization: detects the presence of a transcript MS2 tagging: by incorporating RNA stem loops, such as MS2, into a gene, these

become incorporated into newly synthesized RNA. The stem loops can then bedetected using a fusion of GFP and the MS2 coat protein, which has a highaffinity, sequence specific interaction with the MS2 stem loops. The recruitmentof GFP to the site of transcription is visualised as a single fluorescent spot. Thisremarkable new approach has revealed that transcription occurs in discontinuousbursts, or pulses (seeTranscriptional bursting). With the notable exception of in

situ techniques, most other methods provide cell population averages, and are notcapable of detecting this fundamental property of genes[11]. Northern blot: the traditional method, and until the advent ofRNA-Seq, the most

quantitative RNA-Seq: applies next-generation sequencing techniques to sequence whole

transcriptomes, which allows the measurement of relative abundance of RNA, aswell as the detection of additional variations such as fusion genes, post-translational edits and novel splice sites

Transcription factories cc b my ca qu trnh phin m.

Active transcription units are clustered-m, cm, b in the nucleus, in discrete sitescalled 'transcription factories' oreuchromatin (b my phim m, xng sn xut). Suchsites can be visualized by allowing engaged polymerases to extend their transcripts intagged precursors (Br-UTP or Br-U) and immuno-labeling the tagged nascent RNA.Transcription factories can also be localized using fluorescence in situ hybridization ormarked by antibodies directed against polymerases. There are ~10,000 factories in thenucleoplasm of a HeLa cell, among which are ~8,000 polymerase II factories and ~2,000polymerase III factories. Each polymerase II factor contains ~8 polymerases. As mostactive transcription units are associated with only one polymerase, each factory will beassociated with ~8 different transcription units. These units might be associated throughpromoters and/or enhancers, with loops forming a cloud around the factor.

History

A molecule which allows the genetic material to be realized as a protein was firsthypothesized byFranois Jacob andJacques Monod. RNA synthesis by RNA polymerasewas establishedin vitro by several laboratories by 1965; however, the RNA synthesizedby these enzymes had properties that suggested the existence of an additional factorneeded to terminate transcription correctly.
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In 1972, Walter Fiers became the first person to actually prove the existence of theterminating enzyme.

Roger D. Kornberg won the 2006 Nobel Prize in Chemistry "for his studies of themolecular basis of eukaryotic transcription".[12]

Reverse transcription

Scheme of reverse transcription

Some viruses (such as HIV, the cause ofAIDS), have the ability to transcribe RNA intoDNA. HIV has an RNA genome that is duplicated into DNA. The resulting DNA can bemerged with the DNA genome of the host cell. The main enzyme responsible forsynthesis of DNA from an RNA template is called reverse transcriptase. In the case of

HIV, reverse transcriptase is responsible for synthesizing a complementary DNA strand(cDNA) to the viral RNA genome. An associated enzyme, ribonuclease H, digests theRNA strand, and reverse transcriptase synthesises a complementary strand of DNA toform a double helix DNA structure. This cDNA is integrated into the host cell's genomevia another enzyme (integrase) causing the host cell to generate viral proteins whichreassemble into new viral particles. Subsequently, the host cell undergoes programmedcell death, apoptosis.

Some eukaryotic cells contain an enzyme with reverse transcription activity calledtelomerase. Telomerase is a reverse transcriptase that lengthens the ends of linearchromosomes. Telomerase carries an RNA template from which it synthesizes DNA

repeating sequence, or "junk" DNA. This repeated sequence of DNA is importantbecause every time a linear chromosome is duplicated it is shortened in length. With"junk" DNA at the ends of chromosomes, the shortening eliminates some of the non-essential, repeated sequence rather than the protein-encoding DNA sequence farther awayfrom the chromosome end. Telomerase is often activated in cancer cells to enable cancercells to duplicate their genomes indefinitely without losing important protein-codingDNA sequence. Activation of telomerase could be part of the process that allows cancer
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cells to become technically immortal. However, the true in vivo significance oftelomerase has still not been empirically proven.

See also

Genetics Molecular biology Translation - process of decoding RNA to formpolypeptides. Splicing - process of removing introns from precursor messenger RNA (pre-

mRNA) to make form messenger RNA (mRNA). Reverse transcription - process virusesuse to make DNA from RNA Crick's central dogma - DNA is transcribed to RNA which is translated to

polypeptides, never the other way around.4. Cc iu ho qu trnh phin m eukaryotes
http://en.wikipedia.org/wiki/In_vivohttp://en.wikipedia.org/wiki/Empiricalhttp://en.wikipedia.org/wiki/Geneticshttp://en.wikipedia.org/wiki/Molecular_biologyhttp://en.wikipedia.org/wiki/Translation_(genetics)http://en.wikipedia.org/wiki/Polypeptidehttp://en.wikipedia.org/wiki/Polypeptidehttp://en.wikipedia.org/wiki/Splicing_(genetics)http://en.wikipedia.org/wiki/Intronhttp://en.wikipedia.org/wiki/Pre-mRNAhttp://en.wikipedia.org/wiki/Pre-mRNAhttp://en.wikipedia.org/wiki/MRNAhttp://en.wikipedia.org/wiki/Reverse_transcriptionhttp://en.wikipedia.org/wiki/Virushttp://en.wikipedia.org/wiki/Virushttp://en.wikipedia.org/wiki/Crick's_central_dogmahttp://en.wikipedia.org/wiki/In_vivohttp://en.wikipedia.org/wiki/Empiricalhttp://en.wikipedia.org/wiki/Geneticshttp://en.wikipedia.org/wiki/Molecular_biologyhttp://en.wikipedia.org/wiki/Translation_(genetics)http://en.wikipedia.org/wiki/Polypeptidehttp://en.wikipedia.org/wiki/Splicing_(genetics)http://en.wikipedia.org/wiki/Intronhttp://en.wikipedia.org/wiki/Pre-mRNAhttp://en.wikipedia.org/wiki/Pre-mRNAhttp://en.wikipedia.org/wiki/MRNAhttp://en.wikipedia.org/wiki/Reverse_transcriptionhttp://en.wikipedia.org/wiki/Virushttp://en.wikipedia.org/wiki/Crick's_central_dogma

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