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

Area of Science:

• Molecular Biology
• Genetics
• Epigenetics

Background:

• The PAF complex (Paf1C) is known to influence chromatin modifications, gene transcription, and RNA polymerase II (PolII) elongation.
• Previous studies have linked Paf1C to histone modifications, particularly H2B ubiquitylation, H3K4me3, and H3K36me3.

Purpose of the Study:

• To determine the genome-wide distribution of the entire Paf1C in mammalian cells.
• To investigate the role of Paf1C in alternative cleavage and polyadenylation (APA) and upstream antisense transcription.
• To elucidate the function of Paf1C subunits in regulating transcript length and PolII elongation.

Main Methods:

• Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) for genome-wide Paf1C profiling.
• RNA interference (RNAi) coupled with deep sequencing of transcript 3' ends to study APA and antisense transcription.
• Analysis of histone modifications and PolII accumulation upon Paf1C subunit depletion.

Main Results:

• Paf1C is recruited to promoters, gene bodies, and regions downstream of cleavage/polyadenylation (pA) sites.
• Novel subunit-specific links between Paf1C and APA, and upstream antisense transcription were identified.
• Depletion of Paf1C subunits caused PolII accumulation and coincided with APA, alongside a global loss of H2Bub1.

Conclusions:

• Mammalian Paf1C exhibits distinct genomic distribution compared to its yeast counterpart.
• Paf1C plays a crucial role in regulating transcript length by influencing PolII accumulation and APA.
• Paf1C subunits are involved in suppressing PolII accumulation at TSS-proximal pA sites and regulating 3'UTR pA site choice.