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PLoS Genet. 2015 Apr 23;11(4):e1005166. doi: 10.1371/journal.pgen.1005166. eCollection 2015 Apr.

Systematic profiling of poly(A)+ transcripts modulated by core 3' end processing and splicing factors reveals regulatory rules of alternative cleavage and polyadenylation.

Author information

1
Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America; Rutgers Cancer Institute of New Jersey, Newark, New Jersey, United States of America.
2
Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America.
3
Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America; Rutgers Graduate School of Biomedical Sciences, Newark, New Jersey, United States of America.
4
Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America.
5
Departments of Biochemistry and Medical Biochemistry, University of Illinois, Urbana, Illinois, United States of America.
6
Department of Biological Sciences, Columbia University, New York, New York, United Staes of America.
7
Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America; Rutgers Cancer Institute of New Jersey, Newark, New Jersey, United States of America; Rutgers Graduate School of Biomedical Sciences, Newark, New Jersey, United States of America.

Abstract

Alternative cleavage and polyadenylation (APA) results in mRNA isoforms containing different 3' untranslated regions (3'UTRs) and/or coding sequences. How core cleavage/polyadenylation (C/P) factors regulate APA is not well understood. Using siRNA knockdown coupled with deep sequencing, we found that several C/P factors can play significant roles in 3'UTR-APA. Whereas Pcf11 and Fip1 enhance usage of proximal poly(A) sites (pAs), CFI-25/68, PABPN1 and PABPC1 promote usage of distal pAs. Strong cis element biases were found for pAs regulated by CFI-25/68 or Fip1, and the distance between pAs plays an important role in APA regulation. In addition, intronic pAs are substantially regulated by splicing factors, with U1 mostly inhibiting C/P events in introns near the 5' end of gene and U2 suppressing those in introns with features for efficient splicing. Furthermore, PABPN1 inhibits expression of transcripts with pAs near the transcription start site (TSS), a property possibly related to its role in RNA degradation. Finally, we found that groups of APA events regulated by C/P factors are also modulated in cell differentiation and development with distinct trends. Together, our results support an APA code where an APA event in a given cellular context is regulated by a number of parameters, including relative location to the TSS, splicing context, distance between competing pAs, surrounding cis elements and concentrations of core C/P factors.

PMID:
25906188
PMCID:
PMC4407891
DOI:
10.1371/journal.pgen.1005166
[Indexed for MEDLINE]
Free PMC Article

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