A Chromatin-Based Mechanism for Limiting Divergent Noncoding Transcription

Abstract

In addition to their annotated transcript, many eukaryotic mRNA promoters produce divergent noncoding transcripts. To define determinants of divergent promoter directionality we used genomic replacement experiments. Sequences within non-coding transcripts specified their degradation pathways, and functional protein-coding transcripts could be produced in the divergent direction. To screen for mutants affecting the ratio of transcription in each direction, a bi-directional fluorescent protein reporter construct was introduced into the yeast non-essential gene deletion collection. We identified chromatin assembly as an important regulator of divergent transcription. Mutations in the CAF-I complex caused genome-wide de-repression of nascent divergent non-coding transcription. In opposition to the CAF-I chromatin assembly pathway, H3K56 hyperacetylation together with the nucleosome remodeler SWI/SNF facilitated divergent transcription by promoting rapid nucleosome turnover. We propose that these chromatin-mediated effects control divergent transcription initiation, complementing downstream pathways linked to early termination and degradation of the non-coding RNAs.

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

“…Many chromatin modifiers control antisense transcription (Churchman and Weissman, 2011; DeGennaro et al, 2013; Kim et al, 2012; Marquardt et al, 2014; Whitehouse et al, 2007), and we asked how promoter-proximal transcriptional activity relates to local chromatin structure. We used DNase-seq to map regions of open chromatin and highly positioned nucleosomes in the same HeLa S3 cells used for NET-seq (Thurman et al, 2012).…”

The functions and unique features of long intergenic non-coding RNA

“…Divergent transcription produces approximately 13% of the annotated lincRNAs located within 10 kb of coding gene promoters, of which 65% are within 1 kb of transcription start sites 28 . Divergent transcription is associated with histone H3 Lys56 (H3K56) acetylation and Pol II Tyr1 phosphorylation, is promoted by SWI/SNF chromatin remodellers and is repressed by the RNA deadenylase CAF1 ( 17,58,59 ), features that may indicate distinct divergent RNA transcription and RNA processing mechanisms.…”

Emerging roles of the histone chaperone CAF-1 in cellular plasticity

“…It is plausible that CAF-1 scores more frequently and strongly in cell transition assays because it acts as a general chromatin factor affecting both nucleosome assembly and heterochromatin organization. Moreover, CAF-1 is proposed to affect a wide range of activating and repressive histone marks including H3K56ace, H3K9ace, H3K27ace, H3K9me3 and H3K4me2/3 [62,63,82]. It also remains poorly understood how CAF-1 interacts with alternative histone deposition pathways.…”