SRSF3 and SRSF7 modulate 3'UTR length through suppression or activation of proximal polyadenylation sites and regulation of CFIm levels.
3' Untranslated Regions
Alternative Splicing
Animals
Base Sequence
Cleavage And Polyadenylation Specificity Factor
/ genetics
Gene Expression Regulation
Mice
Models, Biological
Monomeric GTP-Binding Proteins
/ metabolism
Neurons
Phosphorylation
Poly A
Poly(A)-Binding Proteins
/ metabolism
Polyadenylation
Protein Binding
Protein Interaction Domains and Motifs
RNA, Messenger
/ genetics
Serine-Arginine Splicing Factors
/ metabolism
3′UTR length
APA
CFIm
FIP1
MACE-seq
SRSF3
SRSF7
dPAS
iCLIP
pPAS
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
11 03 2021
11 03 2021
Historique:
received:
16
06
2020
accepted:
11
02
2021
entrez:
12
3
2021
pubmed:
13
3
2021
medline:
12
1
2022
Statut:
epublish
Résumé
Alternative polyadenylation (APA) refers to the regulated selection of polyadenylation sites (PASs) in transcripts, which determines the length of their 3' untranslated regions (3'UTRs). We have recently shown that SRSF3 and SRSF7, two closely related SR proteins, connect APA with mRNA export. The mechanism underlying APA regulation by SRSF3 and SRSF7 remained unknown. Here we combine iCLIP and 3'-end sequencing and find that SRSF3 and SRSF7 bind upstream of proximal PASs (pPASs), but they exert opposite effects on 3'UTR length. SRSF7 enhances pPAS usage in a concentration-dependent but splicing-independent manner by recruiting the cleavage factor FIP1, generating short 3'UTRs. Protein domains unique to SRSF7, which are absent from SRSF3, contribute to FIP1 recruitment. In contrast, SRSF3 promotes distal PAS (dPAS) usage and hence long 3'UTRs directly by counteracting SRSF7, but also indirectly by maintaining high levels of cleavage factor Im (CFIm) via alternative splicing. Upon SRSF3 depletion, CFIm levels decrease and 3'UTRs are shortened. The indirect SRSF3 targets are particularly sensitive to low CFIm levels, because here CFIm serves a dual function; it enhances dPAS and inhibits pPAS usage by binding immediately downstream and assembling unproductive cleavage complexes, which together promotes long 3'UTRs. We demonstrate that SRSF3 and SRSF7 are direct modulators of pPAS usage and show how small differences in the domain architecture of SR proteins can confer opposite effects on pPAS regulation.
Sections du résumé
BACKGROUND
Alternative polyadenylation (APA) refers to the regulated selection of polyadenylation sites (PASs) in transcripts, which determines the length of their 3' untranslated regions (3'UTRs). We have recently shown that SRSF3 and SRSF7, two closely related SR proteins, connect APA with mRNA export. The mechanism underlying APA regulation by SRSF3 and SRSF7 remained unknown.
RESULTS
Here we combine iCLIP and 3'-end sequencing and find that SRSF3 and SRSF7 bind upstream of proximal PASs (pPASs), but they exert opposite effects on 3'UTR length. SRSF7 enhances pPAS usage in a concentration-dependent but splicing-independent manner by recruiting the cleavage factor FIP1, generating short 3'UTRs. Protein domains unique to SRSF7, which are absent from SRSF3, contribute to FIP1 recruitment. In contrast, SRSF3 promotes distal PAS (dPAS) usage and hence long 3'UTRs directly by counteracting SRSF7, but also indirectly by maintaining high levels of cleavage factor Im (CFIm) via alternative splicing. Upon SRSF3 depletion, CFIm levels decrease and 3'UTRs are shortened. The indirect SRSF3 targets are particularly sensitive to low CFIm levels, because here CFIm serves a dual function; it enhances dPAS and inhibits pPAS usage by binding immediately downstream and assembling unproductive cleavage complexes, which together promotes long 3'UTRs.
CONCLUSIONS
We demonstrate that SRSF3 and SRSF7 are direct modulators of pPAS usage and show how small differences in the domain architecture of SR proteins can confer opposite effects on pPAS regulation.
Identifiants
pubmed: 33706811
doi: 10.1186/s13059-021-02298-y
pii: 10.1186/s13059-021-02298-y
pmc: PMC7948361
doi:
Substances chimiques
3' Untranslated Regions
0
Cleavage And Polyadenylation Specificity Factor
0
Poly(A)-Binding Proteins
0
RNA, Messenger
0
Srsf3 protein, mouse
0
Serine-Arginine Splicing Factors
170974-22-8
Poly A
24937-83-5
FiP1 protein, mouse
EC 3.6.1.-
Monomeric GTP-Binding Proteins
EC 3.6.5.2
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
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