title: PAF Complex Plays Novel Subunit-Specific Roles in Alternative Cleavage and Polyadenylation.
abstract: The PAF complex (Paf1C) has been shown to regulate chromatin modifications, gene transcription, and RNA polymerase II (PolII) elongation. Here, we provide the first genome-wide profiles for the distribution of the entire complex in mammalian cells using chromatin immunoprecipitation and high throughput sequencing. We show that Paf1C is recruited not only to promoters and gene bodies, but also to regions downstream of cleavage/polyadenylation (pA) sites at 3' ends, a profile that sharply contrasted with the yeast complex. Remarkably, we identified novel, subunit-specific links between Paf1C and regulation of alternative cleavage and polyadenylation (APA) and upstream antisense transcription using RNAi coupled with deep sequencing of the 3' ends of transcripts. Moreover, we found that depletion of Paf1C subunits resulted in the accumulation of PolII over gene bodies, which coincided with APA. Depletion of specific Paf1C subunits led to global loss of histone H2B ubiquitylation, although there was little impact of Paf1C depletion on other histone modifications, including tri-methylation of histone H3 on lysines 4 and 36 (H3K4me3 and H3K36me3), previously associated with this complex. Our results provide surprising differences with yeast, while unifying observations that link Paf1C with PolII elongation and RNA processing, and indicate that Paf1C subunits could play roles in controlling transcript length through suppression of PolII accumulation at transcription start site (TSS)-proximal pA sites and regulating pA site choice in 3'UTRs.
authors.affiliation: Department of Pathology, New York University (NYU) School of Medicine, New York, New York, United States of America.
authors.forename: Yan
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, 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: Mainul
authors.initials: M
authors.lastname: Hoque
authors.affiliation: Department of Pathology, New York University (NYU) School of Medicine, New York, New York, United States of America.
authors.forename: Liming
authors.initials: L
authors.lastname: Hou
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, Genome Technology Center, New York University (NYU) School of Medicine, New York, New York, United States of America.
authors.forename: Steven
authors.initials: S
authors.lastname: Shen
authors.affiliation: Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America.
authors.forename: Bin
authors.initials: B
authors.lastname: Tian
authors.affiliation: Department of Pathology, New York University (NYU) School of Medicine, New York, New York, United States of America.
authors.forename: Brian D
authors.initials: BD
authors.lastname: Dynlacht
mesh_terms: D000818:Animals; D002352:Carrier Proteins / Q000235:genetics*; D002843:Chromatin / Q000235:genetics; D048749:Cytokinesis; D019175:DNA Methylation / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000235:genetics; D051379:Mice; D026723:Polyadenylation / Q000235:genetics*; D012319:RNA Polymerase II / Q000235:genetics*; D024363:Transcription Initiation Site; D014158:Transcription, Genetic; D054875:Ubiquitination
chemical_list: D002352:Carrier Proteins; D002843:Chromatin; D006657:Histones; C547921:RNA polymerase II associated factor 1, mouse; D012319:RNA Polymerase II