Exon selection factor Exon selection factor U2 snRNP U1 snRNP Intron 1 Overview of mRNA Splicing Exon 1 AGGU Exon 2 A AGG Factors such as U1 and U2 snRNP identify splice sites Exons are identified by RNA sequences within the exons that are recognized by exon selection factors.
Overview of mRNA Splicing. Factors such as U1 and U2 snRNP identify splice sites. Exon selection factor. Exon selection factor. U1 snRNP. U2 snRNP. Exon 1. AGGU. Intron 1. A AGG. Exon 2. - PowerPoint PPT Presentation
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Exon selection factor
Exon selection factor
U2 snRNPU1 snRNP
Intron 1
Overview of mRNA Splicing
Exon 1 AGGU Exon 2A AGG
Factors such as U1 and U2 snRNP identify splice sites
Exons are identified by RNA sequences within the exons that are recognized by exon selection factors.
Beta globin splice mutations are one cause of beta thalassemia
EXON1 INTRON1 PHENOTYPE
AG GT AGT CONSENSUS
GCCAG GTTGGTAT NORMAL
GCCAG ATTGGTAT 0 (no beta chains)
GCCAG TTTGGTAT 0 (no beta chains)
GCCAG GTTGTTAT + (some beta chains)
GCCAG GTTGCTAT + (some beta chains)
GCCAG GTTGGCAT + (some beta chains)
AG
Beta globin splice mutations:creation of a new acceptor site
Normal site used 10% of the time:normal protein from these RNAs
New site used 90% of the time: no protein from these RNAs (note the shift in reading frame).
10%
10%
90%
100%
Net result: this allele shows a 90% reduction in β-globin production
19 nucleotides
Nonsense Mediated Decay
Exon/Exon junction
Normal stop codon is downstream or <50 bases upstream from splice junction
Premature stop codon >50 bases upstream from splice junction
>50 bases
mRNA Decay
Translation
A.
B.
Last exon
Last exon
Nonsense Mediated DecayOrigin of premature stop codons
- Improper splicing- intron retained- frameshift
- Mutation
Possible consequences of premature stop codons:
- non functional protein- formation of amyloid- loss of a regulatory region from a protein that regulates growth cancer
Nonsense Mediated Decay
Exon/Exon junctions
Normal Stop Codon
1st round of Translation
Spliceosomes
Protein complexes (Exon-junction-complexes; EJC)
Nucleus
Cytoplasm
More translation
Complexes removed by ribosome transit
Nonsense Mediated Decay
Exon/Exon junctions
Normal stop codonPremature stop codon
mRNA Decay
1st round of Translation
Spliceosomes
Protein complexes (Exon-junction-complexes; EJC)
Nucleus
Cytoplasm
Stopped ribosome
Complex not removed
• Some drugs that affect the accuracy of codon recognition by ribosomes (such as gentamicin) decrease Nonsense mediated decay.
• Treatment with these drugs allows a low level of expression from genes with premature stop codons.
• Possible treatment for several disorders including some alleles of cystic fibrosis.
Reference: Holbrook et al Nature Genetics 36:801-808 (2004)
Nonsense mediated DecayClinical applications (in trials)
For most (but not all) promoters, a complex of proteins is assembled around the TATA box, located about 25-30 b.p. upstream from the start site. The consensus sequence of the TATA box is TATAAA
The core promoter
-30 start of transcription +30
TATA box
DNA with TATA box binding protein
DNA
Protein
The TATA binding protein binds to the TATA box
The core promoter
-30 start of transcription +30
TATA binding protein
-30 start of transcription +30
The TATA binding protein is one subunit of a large complex: TFII-D.
The core promoter
TFII-D
-30 start of transcription +30
Several other complexes bind to TFII-D.
The core promoter
TFII-DTFII-B
TFII-ATFII-F
-30 start of transcription +30
RNA polymerase is recruited to the promoter.
The core promoter
TFII-DTFII-B
TFII-ATFII-F
RNA pol II
-30 start of transcription +30
The factor TFII-H plays a key role in initiating transcription by phosphorylating the C-terminal domain of the large subunit of RNA pol II.
The core promoter
TFII-DTFII-B
TFII-ATFII-F
RNA pol IITFII-H
…...(Tyr-Ser-Pro-Thr-Ser-Pro-Ser)52COOH
CTD: a pol II switchCTD: The COOH Terminal Domain of the RNA pol II large subunit
…...(Tyr-Ser-Pro-Thr-Ser-Pro-Ser)52COOH
TFIIH
…...(Tyr-Ser-Pro-Thr-Ser-Pro-Ser)52COOH
PO3 phosphorylated Ser 5 of the repeats
Other kinases
More phosphorylation of the CTD
CTD: a pol II switchCTD: The COOH Terminal Domain of the RNA pol II large subunit
ATP
ADP
ATP
ADP
TFIIH controls the start of transcription
Unphosphorylated CTD:Involved in initiation:
Binding of initiation factors
Phosphorylated CTD:Involved in elongation & RNA processing
Binds components involved in RNA cappingBinds components involved in RNA splicingBinds components involved in 3’ end formation
CTD: a pol II switchCTD: The COOH Terminal Domain of the RNA pol II large subunit
From Orphanadies & Reinberg (2002) Cell 108:439-51
The CTD ties elongation to capping, splicing and 3’-end formation
A model promoter
TGACTCA GACGTC GGGCGG
SP-1
CREBFos Jun CREB
AP-1 (Fos-Jun binding site)Regulation bygrowth factors,stress, and varioustransmembranesignals
CRE (Cyclic AMPResponse Element)Regulation by cAMP,and by Ca+. Interacts withcore promoter (through CREB Binding Protein)and modifies chromatin structure (through HAT).
SP-1 SiteProvides basalunregulatedtranscriptionalactivity. Manygenes have multiple SP-1 sites