A Chromatin-Based Mechanism for Limiting Divergent Noncoding Transcription

• Published in: Cell 2014-06, Vol.157 (7), p.1712-1723
• Main Authors: Marquardt, Sebastian, Escalante-Chong, Renan, Pho, Nam, Wang, Jue, Churchman, L. Stirling, Springer, Michael, Buratowski, Stephen
• Format: Article
• Language: English
• Subjects: Chromatin - metabolism; Chromatin Assembly and Disassembly; Chromatin Assembly Factor-1 - metabolism; fluorescent proteins; gene deletion; Gene Expression Regulation, Fungal; messenger RNA; mutants; non-coding RNA; nucleosomes; Nucleosomes - metabolism; Promoter Regions, Genetic; RNA Stability; RNA, Fungal - genetics; RNA, Fungal - metabolism; RNA, Untranslated - genetics; RNA, Untranslated - metabolism; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - metabolism; Transcription Termination, Genetic; Transcription, Genetic; yeasts
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2014.04.036

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 noncoding 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 bidirectional fluorescent protein reporter construct was introduced into the yeast nonessential gene deletion collection. We identified chromatin assembly as an important regulator of divergent transcription. Mutations in the CAF-I complex caused genome-wide derepression of nascent divergent noncoding 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 noncoding RNAs. [Display omitted] •Divergent promoters can produce functional mRNAs in the “noncoding” direction•Divergent transcription is suppressed by chromatin assembly factors•CAF-I and histones repress divergent ncRNA transcription•Divergent transcription is stimulated by H3K56 acetylation and Swi/Snf An unbiased genetic screen in yeast reveals that CAF-I and other chromatin assembly factors suppress transcription in the noncoding RNA direction of divergent promoters.