Transcriptomics,Genomics

Dataset Information

300

Paf1C 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 PolII elongation. Here, we provide the first genome-wide analysis of chromatin occupancy by the entire PAF complex in mammalian cells. 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, our studies identified novel, subunit-specific links between Paf1C and regulation of alternative cleavage and polyadenylation (APA) and upstream antisense transcription. Moreover, we found that depletion of Paf1C subunits also resulted in the accumulation of RNA polymerase II (PolII) over gene bodies, which coincided with APA. Depletion of specific Paf1C subunits leads to global loss of histone H2B ubiquitylation, but surprisingly, there is little impact of Paf1C depletion on other histone modifications, including the 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 suggest that Paf1C could play a role in protecting transcripts from premature cleavage by preventing PolII accumulation at TSS-proximal pA sites. ChIP-seq, RNA-seq and 3'READS of Paf1C factors in mouse C2C12 myoblast cells

ORGANISM(S): Mus musculus  

SUBMITTER: Bin Tian   Mainul Hoque  Brian D Dynlacht  Wencheng Li  Yan Yang  Liming Hou  Steven Shen 

PROVIDER: E-GEOD-72574 | ArrayExpress | 2016-01-15

SECONDARY ACCESSION(S): GSE72574SRP063051PRJNA294381

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

PAF Complex Plays Novel Subunit-Specific Roles in Alternative Cleavage and Polyadenylation.

Yang Yan Y   Li Wencheng W   Hoque Mainul M   Hou Liming L   Shen Steven S   Tian Bin B   Dynlacht Brian D BD  

PLoS genetics 20160114 1


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 contrast  ...[more]

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