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Regulated Unproductive Splicing. Liana Lareau Brenner Group* *Labs aren’t carpeted. Groups are. Or so I’m told. Alternative Splicing. Genomic DNA Sequence. Transcription. pre-mRNA. Intron. Intron. Intron. Exon. Exon. Exon. Exon. Exon. RNA Processing. G m. AAAAA. G m. AAAAA.

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regulated unproductive splicing

Regulated Unproductive Splicing

Liana Lareau

Brenner Group*

*Labs aren’t carpeted. Groups are. Or so I’m told.

alternative splicing
Alternative Splicing

Genomic DNA Sequence

Transcription

pre-mRNA

Intron

Intron

Intron

Exon

Exon

Exon

Exon

Exon

RNA Processing

Gm

AAAAA

Gm

AAAAA

mRNA

mRNA

inferred isoforms
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

inferred isoforms1

Premature

stop codon

2078 (35 % of 5970)

Inferred Isoforms

0

10000

2000

4000

6000

8000

5970

Alternative isoforms

9527

All isoforms, including canonical

nonsense mediated mrna decay
Nonsense-Mediated mRNA Decay

Translated normally

ORF

Gm

mRNA

AAAAAAAAA

Degraded by NMD

ORF

Gm

mRNA

AAAAAAAAA

>50 nt

alternative splicing can yield isoforms differentially subjected to decay
Alternative Splicing Can Yield Isoforms Differentially Subjected to Decay

DNA

DNA

pre-mRNA

pre-mRNA

mRNA

mRNA

Nonsense

mediated

decay

Premature

termination

codon

eukaryota1
Eukaryota

human, mouse,

fly

yeast

the players
The Players

Upf1aka RENT1 (human), SMG-2 (C. elegans)

Binds to downstream Upf2 and Upf3 during translation termination

Promotes mRNA decapping and degradation

Upf2aka SMG-3 (C. elegans)

Binds to Upf3 after nuclear export

Upf3aka SMG-4 (C. elegans)

Associates with exon junction complex in nucleus

eukaryota2
Eukaryota

Plasmodium,

Cryptosporidium

human, mouse,

fly, mosquito,

worm

yeast, S. pombe,

Aspergillus, Neurospora

upf3 yeast vs human
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%)

slide18

transcriptional

regulation

Gene locus

transcription

pre-mRNA

productive

splicing

productive

mRNA

regulated

unproductive splicing

translation

Protein

slide19

ORF

SC35 pre-mRNA

SC35 Auto-regulation

Sureau et al. (2001) EMBO J20:1785-96

slide20

ORF

SC35 pre-mRNA

Gm

AAAAA

SC35 mRNA

SC35 Auto-regulation

Sureau et al. (2001) EMBO J20:1785-96

slide21

ORF

SC35 pre-mRNA

Gm

AAAAA

SC35 mRNA

SC35

SC35

protein

SC35 Auto-regulation

Sureau et al. (2001) EMBO J20:1785-96

slide22

ORF

SC35 pre-mRNA

Gm

AAAAA

SC35 mRNA

SC35

SC35

SC35

protein

SC35 pre-mRNA

SC35 Auto-regulation

Sureau et al. (2001) EMBO J20:1785-96

slide23

ORF

SC35 pre-mRNA

Gm

AAAAA

SC35 mRNA

SC35

SC35

SC35

protein

SC35 pre-mRNA

Gm

AAAAA

SC35 Auto-regulation

SC35 mRNA

(with premature termination codon)

Sureau et al. (2001) EMBO J20:1785-96

slide24

ORF

SC35 pre-mRNA

Gm

AAAAA

SC35 mRNA

SC35

SC35

SC35

protein

SC35 pre-mRNA

Gm

AAAAA

SC35 Auto-regulation

SC35 mRNA

(with premature termination codon)

Sureau et al. (2001) EMBO J20:1785-96

sc35 auto regulation
SC35 Auto-regulation

SC35 Locus

transcription

SC35 pre-mRNA

alternative

splicing

splicing

Productive SC35 mRNA

translation

SC35 protein

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