Regulated Unproductive Splicing

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Regulated Unproductive Splicing

• Liana Lareau
• Brenner Group
• Labs arent carpeted. Groups are. Or so Im told.

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Alternative Splicing
Genomic DNA Sequence
Transcription
pre-mRNA
Intron
Intron
Intron
Exon
Exon
Exon
Exon
Exon
RNA Processing
Gm
AAAAA
Gm
AAAAA
mRNA
mRNA
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How much alternative splicing occurs in
humans?What is its role?
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Alternative Isoform Inference
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Inferred Isoforms
0
10000
2000
4000
6000
8000
5970
Alternative isoforms
9527
All isoforms, including canonical
3557 genes with alternative spicing, from 12,000
mRNAs
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Inferred Isoforms
0
10000
2000
4000
6000
8000
5970
Alternative isoforms
9527
All isoforms, including canonical
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Nonsense-Mediated mRNA Decay
Translated normally
ORF
Gm
mRNA
AAAAAAAAA
Degraded by NMD
ORF
Gm
mRNA
AAAAAAAAA
gt50 nt
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Alternative Splicing Can Yield Isoforms
Differentially Subjected to Decay
DNA
DNA
pre-mRNA
pre-mRNA
mRNA
mRNA
Nonsense mediated decay
Premature termination codon
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Eukaryota
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Eukaryota
human, mouse, fly
yeast
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Eukaryote sequencing projects
1
3
6
1
16
1
8
5
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The Players
Upf1 aka RENT1 (human), SMG-2 (C. elegans) Binds
to downstream Upf2 and Upf3 during translation
termination Promotes mRNA decapping and
degradation
Upf2 aka SMG-3 (C. elegans) Binds to Upf3 after
nuclear export
Upf3 aka SMG-4 (C. elegans) Associates with exon
junction complex in nucleus
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Upf1
14
Upf2
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Upf3
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Eukaryota
Plasmodium, Cryptosporidium
human, mouse, fly, mosquito, worm
yeast, S. pombe, Aspergillus, Neurospora
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Upf3 Yeast vs. Human
BLAST results Score 26.9 bits (58), Expect
9.8 Identities 30/131 (22), Positives
48/131 (36), Gaps 16/131 (12)
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transcriptional regulation
Gene locus
transcription
pre-mRNA
productive splicing
productive mRNA
regulated unproductive splicing
translation
Protein
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SC35 Auto-regulation
Sureau et al. (2001) EMBO J 201785-96
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SC35 Auto-regulation
Sureau et al. (2001) EMBO J 201785-96
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SC35 Auto-regulation
Sureau et al. (2001) EMBO J 201785-96
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SC35 Auto-regulation
Sureau et al. (2001) EMBO J 201785-96
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SC35 Auto-regulation
SC35 mRNA (with premature termination codon)
Sureau et al. (2001) EMBO J 201785-96
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SC35 Auto-regulation
SC35 mRNA (with premature termination codon)
Sureau et al. (2001) EMBO J 201785-96
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SC35 Auto-regulation
SC35 Locus
transcription
SC35 pre-mRNA
splicing
alternative splicing
Productive SC35 mRNA
translation
SC35 protein