regulation of gene expression part ii molecular biology – regulation of gene expression ii
TRANSCRIPT
Figure 7-92 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
There are MULTIPLE opportunities to regulated gene expression (derivation of functional protein) after the initiation of transcription !
MOLECULAR BIOLOGY – Regulation of gene expression II
Riboswitch … short sequences of RNAthat change their conformation upon binding
small molecules such as metabolites, usually
reside in 5’ UTR
Mostly observed in bacteria but also documented in fungi and plants
Riboswitch can can activate ‘self cleaving’ ribozyme activity
MOLECULAR BIOLOGY – Regulation of gene expression II
5’AUG
STOP
H2N COOH3’ ON
AUG
H2N COOH3’ OFF
5’small molecule
Autolytic ribozyme activitySTOP
Figure 7-106c Molecular Biology of the Cell (© Garland Science 2008)
Riboswitch can affect the translation initiation from Shine-Dalgarno sequence
MOLECULAR BIOLOGY – Regulation of gene expression II
Figure 7-106b Molecular Biology of the Cell (© Garland Science 2008)
THERMOSENSOR
MOLECULAR BIOLOGY – Regulation of gene expression II
Figure 7-106d Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
Antisense RNA
Figure 7-92 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
Figure 7-94 Molecular Biology of the Cell (© Garland Science 2008)
ALTERNATIVE SPLICING
MOLECULAR BIOLOGY – Regulation of gene expression II
e.g.Drosophila Dscam
axon guidance receptors
MOLECULAR BIOLOGY – Regulation of gene expression II
Thousands of possible different functional protein sequence combinations
Figure 7-96 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
Splicing is subject to tight regulatory control
Figure 7-92 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
Figure 7-101 Molecular Biology of the Cell (© Garland Science 2008)
RNA editing
MOLECULAR BIOLOGY – Regulation of gene expression II
- specific to eukaryotes (and viruses)
Non-templated changes to the genetic information that affect the protein sequence and possibly function and are therefore not predictable from genomic DNA sequence
Deamination reactions e.g. A - I/G in RNA duplexes by ADAR:
Altered amino acid codons
C - U deaminations also possible do not rely on RNA duplexes e.g. ApoB100 mRNA
in liver and intestine
Figure 7-100 Molecular Biology of the Cell (© Garland Science 2008)
Extensive RNA editing in mitochondria of trypanosomes
MOLECULAR BIOLOGY – Regulation of gene expression II
Uracil insertions
Figure 7-92 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
Figure 6-80 Molecular Biology of the Cell (© Garland Science 2008)
Nonsense-mediated mRNA decay
MOLECULAR BIOLOGY – Regulation of gene expression II
EJC ribonucleoprotein complexes are remnants
of splicing
DNA gene
transcription
EJC displacement during translation
Premature termination of translation leaves ‘beacon’ EJC leading to abnormal mRNA
degradation
Nanos proteinBicoid protein
Some mRNAs are localized to specific regions of the cytoplasm
bicoid mRNA nanos mRNA
mRNAs for secretedproteins targeted to
ER by SRP
MOLECULAR BIOLOGY – Regulation of gene expression II
Drosophila oocyte polarity and embryo patterning
A P
bicoid and nanos proteins inhibit translation of other homogenously distributed cell fate genes which in turn affects the expression of other
cell fate mRNAs along the A-P axis as development proceeds
Figure 7-92 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
PROMOTER
AATAAA
exon 1 exon 2 exon 3
ATG TAA
AAUAAAAUG UAA
AAUAAAAUG UAA
intron intron
TRANSCRIPTION
Pre-mRNA
mRNA
DNA
RNA SPLICING
protein
TRANSLATION
coding sequence
MAPSSRGG…..
OPEN READING FRAME
5’UTR 3’UTR
CAP AAAAA
NUCLEUS
CYTOPLASM
MOLECULAR BIOLOGY – Regulation of gene expression II
Central genetic dogma
Regulation of gene expression via regulation of mature mRNAs
Figure 7-109 Molecular Biology of the Cell (© Garland Science 2008)
mRNA stability as a way to regulate gene expression
in bacteria – half life couple minutesin eukaryotes – half life minutes to tens of hours
MOLECULAR BIOLOGY – Regulation of gene expression II
poly-A tail:• participates in termination of transcription • aids mRNA nuclear export• protects from 3‘ - 5‘ exonuclease degradation in cytoplasm• targets transcripts to ribosome for translation
3’ UTR contains regulatory elements that participate in transcript stability
5‘ Cap:• aids mRNA nuclear export• protects from 5‘ - 3‘ exonuclease degradation in cytoplasm• targets transcripts to ribosome for translation
Figure 7-109 Molecular Biology of the Cell (© Garland Science 2008)
mRNA stability as a way to regulate gene expression
in bacteria – half life couple minutesin eukaryotes – half life minutes to tens of hours
MOLECULAR BIOLOGY – Regulation of gene expression II
Cytoplasmic deadenylases e.g. PARN
Figure 7-110 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
PARN binds exposed 5‘ cap of non-translated mRNAs, leading to poly-A tail deadenylation and eventual degradation
mRNA’s with longer poly-A tails more likely to be translated
Regulatory potential to influence this equilibrium
e.g. cytoplasmic polyadenylation of short poly-A tails e.g. fertilized mammalian oocytes and post-synaptic neurone sites
Figure 7-111 Molecular Biology of the Cell (© Garland Science 2008)
MOLECULAR BIOLOGY – Regulation of gene expression II
mRNA stability mechanisms in
action
e.g. ferritin/ transferrin receptor system
PROMOTER
AATAAA
exon 1 exon 2 exon 3
ATG TAA
AAUAAAAUG UAA
AAUAAAAUG UAA
intron intron
TRANSCRIPTION
Pre-mRNA
mRNA
DNA
RNA SPLICING
protein
TRANSLATION
coding sequence
MAPSSRGG…..
OPEN READING FRAME
5’UTR 3’UTR
CAP AAAAA
NUCLEUS
CYTOPLASM
MOLECULAR BIOLOGY – Regulation of gene expression II
Figure 7-112 Molecular Biology of the Cell (© Garland Science 2008)
microRNA (miRNA) ... small noncoding RNA regulators recognizing 3’UTRs
● one miRNA recognizes many mRNAs (even hundreds if they share common 3’UTRs)● more than one miRNA can bind to one mRNA (combinatorial regulation)
RNA-induced silencing complex
MOLECULAR BIOLOGY – Regulation of gene expression II
● >1000 miRNA genes targeting approx 60% of genes● estimated 16% of pre-miRNAs can be altered by ADAR mediated editing● miRNA can be derived from spliced introns in non-mammalian species, known as mirtons
Drosha & Prasha (DGCR8)
Pri-miRNA
Dicer
Pre-miRNA
RNA induced silencing complex (RISC) miRNA (imperfect duplex 22nts - guide strand
incorporated, passenger strand degraded)
3’UTR sequence homology
Figure 7-115 Molecular Biology of the Cell (© Garland Science 2008)
RNA interference (RNAi)
small interfering RNA (21-23nt)
RISC re-used
RNA-inducedtranscription silencing
MOLECULAR BIOLOGY – Regulation of gene expression II
Dicer mediated processing
dsRNA viral genomesPre-miRNA transcripts
Experimentally introduced RNA
n.b. sequence homology not limited to 3’UTR
Argonaut mediated target mRNA degradationCo-transcriptional degradation
of transcript