Hda1C restricts the transcription initiation frequency to limit divergent non-coding RNA transcription

Abstract

Nucleosome-depleted regions (NDRs) at gene promoters support initiation of RNA Polymerase II transcription. Interestingly, transcription often initiates in both directions, resulting in an mRNA, and a divergent non-coding (DNC) transcript with an unclear purpose. Here, we characterized the genetic architecture and molecular mechanism of DNC transcription in budding yeast. We identified the Hda1 histone deacetylase complex (Hda1C) as a repressor of DNC in high-throughput reverse genetic screens based on quantitative single-cell fluorescence measurements. Nascent transcription profiling showed a genome-wide role of Hda1C in DNC repression. Live-cell imaging of transcription revealed that Hda1C reduced the frequency of DNC transcription. Hda1C contributed to decreased acetylation of histone H3 in DNC regions, supporting DNC repression by histone deacetylation. Our data support the interpretation that DNC results as a consequence of the NDR-based architecture of eukaryotic promoters, but that it is governed by locus-specific repression to maintain genome fidelity.

Multimodal regulatory elements within a hormone-specific super enhancer control a heterogeneous transcriptional response

“…Image analysis smFISH spot segmentation was performed on the maximum intensity projections. RNA smFISH spots were identified by fitting to a 2D Gaussian mask and performing local background subtraction using custom python code adapted from Donovan et al (2019) and Gowthaman et al (2021). Cytoplasmic and nuclear masks were generated using Cellprofiler (Carpenter et al, 2006).…”

RSC and GRFs confer promoter directionality by restricting divergent noncoding transcription

“…Here, we showed that RSC is important to position nucleosomes and to ensure that cryptic divergent promoters are “protected” and transcriptionally repressed. Conversely, opening of chromatin because of increased histone lysine 56 acetylation (H3K56ac) leads to more divergent transcription in yeast, whereas deacetylation of histone H3 by Hda1 deacetylase complex (Hda1C) facilitates repression of divergent transcription ( Marquardt et al, 2014 ; Gowthaman et al, 2021 Preprint ). The GRF Rap1 can repress divergent transcription at gene promoters by occupying cryptic divergent promoters ( Wu et al, 2018 ).…”

“…Divergent transcription units are also typically short, because of enrichment in transcription termination signals ( Schulz et al, 2013 ). In addition, divergent transcription can be repressed by chromatin remodellers and histone-modifying enzymes ( Marquardt et al, 2014 ; Gowthaman et al, 2021 Preprint ). Lastly, general regulatory factors (GRFs) can repress initiation of aberrant noncoding transcription events ( Challal et al, 2018 ; Wu et al, 2018 ).…”

RSC and GRFs confer promoter directionality by limiting divergent noncoding transcription

“…For example, increased histone lysine 56 acetylation (H3K56ac) leads to more divergent transcription in yeast (Marquardt et al, 2014). Conversely, deacetylation of histone H3 by Hda1 deacetylase complex (Hda1C) facilitates repression of divergent transcription (Gowthaman et al, 2021). The role of RSC at promoters is likely different from CAF-I, H3K56ac, and Hda1C.…”

“…Divergent transcription units are also typically short, due to enrichment in transcription termination signals (Schulz et al 2013). Additionally, divergent transcription can be repressed by chromatin remodellers and histone modifying enzymes (Gowthaman et al 2021, Marquardt et al 2014). Lastly, general regulatory factors (GRFs) can repress initiation of aberrant noncoding transcription events (Challal et al 2018, Wu et al 2018).…”