General Regulatory Factors control the fidelity of transcription by restricting non-coding and ectopic initiation

Abstract

The fidelity of transcription initiation is essential for accurate gene expression, but the determinants of start site selection are not fully understood. Rap1 and other General Regulatory Factors (GRFs) control the expression of many genes in yeast. We show that depletion of these factors induces widespread ectopic transcription initiation within promoters. This generates many novel non-coding RNAs and transcript isoforms with diverse stability, profoundly altering the coding potential of the transcriptome. Ectopic transcription initiation strongly correlates with altered nucleosome positioning. We show that Rap1 sterically constrains nucleosomes as its mere binding to the DNA can be sufficient for restoration normal nucleosome positioning, transcription initiation and gene expression. These results demonstrate an essential role for GRFs in the fidelity of transcription initiation and in the suppression of pervasive transcription, redefining current models of their function. They have general implications for the mechanism of transcription initiation and the control of gene expression.

Termination of non‐coding transcription in yeast relies on both an RNA Pol II CTD interaction domain and a CTD‐mimicking region in Sen1

“…For mRNAs, we used the annotations in Challal et al (). For the 5′ and the 3′ end of mature snoRNAs, we used the annotations in Xu et al ().…”

Ruler elements in chromatin remodelers set nucleosome array spacing and phasing

“…A combination of both in vivo studies (Ganapathi et al, 2011;Hartley and Madhani, 2009;Kubik et al, 2018;Tsankov et al, 2011;van Bakel et al, 2013;Yan et al, 2018;Yarragudi et al, 2004) and in vitro reconstitutions indicated that these 6 Senior author 7 These authors contributed equally. This organization is important for transcription fidelity as mutants with impaired array phasing show aberrant transcription initiation (Challal et al, 2018;Hennig et al, 2012;Kubik et al, 2019;Pointner et al, 2012;Smolle et al, 2012). Throughout eukaryotes, phased arrays are prominent at active promoters.…”