rna maturation transport & localization
DESCRIPTION
RNA maturation transport & localization. RNA processing: brief overview. RNA export to the cytoplasm: model systems. RNA degradation. Links between RNA processing, transport, degradation. RNA localization in the cytoplasm. All eukaryotic mRNAs are processed. Evidence for checkpoints?. - PowerPoint PPT PresentationTRANSCRIPT
RNA maturation transport & localization
RNA export to the cytoplasm: model systems
RNA degradation
Links between RNA processing, transport, degradationRNA localization in the cytoplasm
RNA processing: brief overview
Evidence for checkpoints?mRNA
transport
All eukaryotic mRNAs are processed
Specific process for Pol II transcriptsnuclear CBC binds to m7G-cap: role in splicing, transport, stability (exchanged in cytoplasm)
Function in transport, stability, translation
1. Capping
CPSF: cleavage and polyadenylation specificity factor
CStF: cleavage stimulatory factor
CF: cleavage factor
PAP: polyA polymerase
PAB: polyA binding protein
Function in transport, stability, translation
2. Polyadenylation
3. Splicing
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3. Splicing
Splicing is mediated by snRNPs
Compartments inside the nucleus
1. Nucleolus
2. Perichromatin granule clusters
Carter et al., Science (1993) 259: 1330
Balbiani Rings (Chironomus tentans)
BR RNP maturation
BR RNP translocation
BR RNP translocation
Retroviruses as mRNA export models
Gene location is influenced by gene activity
Casolari et al., 2004
SUMMARY
I. Multiple steps of mRNA biosynthesis are tightly coupled
II. Mex67/TAP is one major mRNA export factorBinding to mRNA may already occur at the site of transcription
III. Many questions remain- How are mRNA substrates released in the cytoplasm? - Are there multiple mRNA export pathways?- How is processing and transport mechanistically “coupled”?- Is mRNA export regulated?etc.
RNA half-lives vary greatly but are highly coordinated
RNA half-lives vary greatly but are highly coordinated
Wang et al., PNAS 2002
AUUUA element regulates half-life
A.
B.Casein mRNA prolactin
+
-
30,000 mRNA/cell
300 mRNA/cell
No change in transcription
Examples of regulated mRNA turnover
mRNA DEGRADATION
mRNA DECAY NMD
‘turnover’ ‘surveillance’
mRNA DECAY
AAAm7Gppp
poly A shortening Deadenylase complex
AAAAAAAAAAAAAAAAm7Gppp
Decapitation Decapping enzyme (DCP1 complex)
AAA
5’-3’ exonucleolytic cleavage Xrn1 complex
Decay factors localize to cytoplasmic processing bodies (P bodies)
Sheth et al. Science 2003
mRNA activity is regulated by multiple factors
Active mRNAs Inactive mRNAs
Storage
Decay
Transport
Translation
From Neu-Yilik et al. (2001) EMBO 20:532-540
Position of nonsense codon affects mRNA amounts
m7Gppp
Stop in penultimate exon/5’ of splicing mark
AAAAAAAAAAAAAAAA
Decapitation Decapping enzyme (DCP1 complex)
5’-3’ exonucleolytic cleavage Xrn1 complex
Nonsense Mediated Decay
AAAAAAAAAAAAAAAA
RNA localizationmRNA can be localized to subcellular compartmentsby actin or tubulin-dependent processesExamples:
Xenopus: Vg1 mRNA (TGFb) to vegetal pole
Drosophila: nanos, oskar mRNA (posterior) and bicoid (anterior)
(requires mRNA binding protein staufen)
(requires staufen and miranda)
prospero (into ganglion of mother cells; neuroblast TF)
Yeast: Ash1 mRNA to daughter cell
Examples of localized mRNAs in various systems
lamellipodia staining perinuclear staining in myotubes
3’ UTR determins localization of many mRNAs
Bertrand et al., Mol Cell (98) 2:437-445
Ash1 mRNA specifically localizes to new daughter cells
Mechanism of Ash1 mRNA localization
SUMMARY
I. mRNA decay- regulated and non-regulated turn-over but apparently coordinated- ordered pathways (e.g. deadenylation, decapping, exonucleolytic degradation)- cross-talk between translation and turnover- important regulation via non-coding RNAs- turnover occurs in specific cytoplasmic compartments- NMD: recognition of premature stop codons
II. Cytoplasmic mRNA localization- ZIP code in 3’ UTR- both actin and tubulin-mediated - yeast mating type switch as a model: Ash1 mRNA localization (via 3’ UTR, She2/3, Myo4 and actin cables)