title: Systematic profiling of poly(A)+ transcripts modulated by core 3' end processing and splicing factors reveals regulatory rules of alternative cleavage and polyadenylation.
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.
authors.affiliation: 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.
authors.forename: Wencheng
authors.initials: W
authors.lastname: Li
authors.affiliation: Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America.
authors.forename: Bei
authors.initials: B
authors.lastname: You
authors.affiliation: Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America.
authors.forename: Mainul
authors.initials: M
authors.lastname: Hoque
authors.affiliation: 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.
authors.forename: Dinghai
authors.initials: D
authors.lastname: Zheng
authors.affiliation: 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.
authors.forename: Wenting
authors.initials: W
authors.lastname: Luo
authors.affiliation: 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.
authors.forename: Zhe
authors.initials: Z
authors.lastname: Ji
authors.affiliation: Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America.
authors.forename: Ji Yeon
authors.initials: JY
authors.lastname: Park
authors.affiliation: Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America.
authors.forename: Samuel I
authors.initials: SI
authors.lastname: Gunderson
authors.affiliation: Departments of Biochemistry and Medical Biochemistry, University of Illinois, Urbana, Illinois, United States of America.
authors.forename: Auinash
authors.initials: A
authors.lastname: Kalsotra
authors.affiliation: Department of Biological Sciences, Columbia University, New York, New York, United Staes of America.
authors.forename: James L
authors.initials: JL
authors.lastname: Manley
authors.affiliation: 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.
authors.forename: Bin
authors.initials: B
authors.lastname: Tian
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D002454:Cell Differentiation / Q000235:genetics*; D005091:Exons; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007438:Introns / Q000235:genetics; D039122:Poly(A)-Binding Protein I / Q000096:biosynthesis / Q000235:genetics*; D026723:Polyadenylation / Q000235:genetics*; D012326:RNA Splicing / Q000235:genetics*; D020871:RNA Stability / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics
chemical_list: D020413:3' Untranslated Regions; C576588:PABPN1 protein, human; D039122:Poly(A)-Binding Protein I; D012333:RNA, Messenger