Author response: The nucleosome DNA entry-exit site is important for transcription termination and prevention of pervasive transcription

Compared to other stages in the RNA polymerase II transcription cycle, the role of chromatin in transcription termination is poorly understood. We performed a genetic screen in Saccharomyces cerevisiae to identify histone mutants that exhibit transcriptional readthrough of terminators. Amino acid substitutions identified by the screen map to the nucleosome DNA entry-exit site. The strongest H3 mutants revealed widespread genomic changes, including increased sense-strand transcription upstream and downstream of genes, increased antisense transcription overlapping gene bodies, and reduced nucleosome occupancy particularly at the 3’ ends of genes. Replacement of the native sequence downstream of a gene with a sequence that increases nucleosome occupancy in vivo reduced readthrough transcription and suppressed the effect of a DNA entry-exit site substitution. Our results suggest that nucleosomes can facilitate termination by serving as a barrier to transcription and highlight the importance of the DNA entry-exit site in broadly maintaining the integrity of the transcriptome.

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Pervasive transcription-dependent chromatin remodeling influences the replication initiation program

10.1101/272666 ◽

2018 ◽

Author(s):

Julien Soudet ◽

Jatinder Kaur ◽

Françoise Stutz

Keyword(s):

Chromatin Remodeling ◽

Noncoding Rna ◽

Transcription Termination ◽

Replication Timing ◽

Replication Initiation ◽

Late Replication ◽

H3k36 Methylation ◽

Rna Transcription ◽

Eukaryotic Organisms ◽

Pervasive Transcription

ABSTRACTIn Eukaryotic organisms, replication initiation follows a temporal program. Among the parameters that regulate this program in Saccharomyces cerevisiae, chromatin structure has been at the center of attention without considering the contribution of transcription. Here, we revisit the replication initiation program in the light of pervasive transcription. We find that noncoding RNA transcription termination in the vicinity of replication origins or ARS (Autonomously Replicating Sequences) maximizes replication initiation by restricting transcriptional readthrough into ARS. Consistently, high natural nascent transcription correlates with low ARS efficiency and late replication timing. High readthrough transcription is also linked to chromatin features such as high levels of H3K36me3 and deacetylated nucleosomes. Moreover, forcing ARS readthrough transcription promotes these histone modifications. Finally, replication initiation defects induced by increased transcriptional readthrough are partially rescued in the absence of H3K36 methylation. Altogether, these observations indicate that natural pervasive transcription into ARS influences replication initiation through chromatin remodeling.

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Modulated termination of non-coding transcription partakes in the regulation of gene expression

10.1101/2021.01.06.425579 ◽

2021 ◽

Author(s):

Nouhou Haidara ◽

Odil Porrua

Keyword(s):

Catalytic Domain ◽

Transcription Termination ◽

Regulation Of Gene Expression ◽

Gene Encoding ◽

Genome Expression ◽

Zn Homeostasis ◽

Regulatory Capacity ◽

Gene Regulatory ◽

Non Coding Rnas ◽

Pervasive Transcription

Pervasive transcription is a universal phenomenon leading to the production of a plethora of non-coding RNAs. If left uncontrolled, pervasive transcription can be harmful for genome expression and stability. However, non-coding transcription can also play important regulatory roles, for instance by promoting the repression of specific genes by a mechanism of transcriptional interference. The efficiency of transcription termination can strongly influence the regulatory capacity of non-coding transcription events, yet very little is known about the mechanisms modulating the termination of non-coding transcription in response to environmental cues. Here, we address this question by investigating the mechanisms that regulate the activity of the main actor in termination of non-coding transcription in budding yeast, the helicase Sen1. We identify a phosphorylation at a conserved threonine of the catalytic domain of Sen1 and we provide evidence that phosphorylation at this site reduces the efficiency of Sen1-mediated termination. Interestingly, we find that this phosphorylation impairs termination at an unannotated non-coding gene, thus repressing the expression of a downstream gene encoding the master regulator of Zn homeostasis, Zap1. Consequently, many additional genes exhibit an expression pattern mimicking conditions of Zn excess, where ZAP1 is naturally repressed. Our findings provide a novel paradigm of gene regulatory mechanism relying on the direct modulation of non-coding transcription termination.

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Author response: Transcription termination and antitermination of bacterial CRISPR arrays

10.7554/elife.58182.sa2 ◽

2020 ◽

Author(s):

Anne M Stringer ◽

Gabriele Baniulyte ◽

Erica Lasek-Nesselquist ◽

Kimberley D Seed ◽

Joseph T Wade

Keyword(s):

Transcription Termination ◽

Author Response

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The nucleosome DNA entry-exit site is important for transcription termination in Saccharomyces cerevisiae

10.1101/2020.05.03.075200 ◽

2020 ◽

Author(s):

A. Elizabeth Hildreth ◽

Mitchell A. Ellison ◽

Alex M. Francette ◽

Julia M. Seraly ◽

Lauren M. Lotka ◽

...

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Nucleosome Occupancy ◽

Transcription Termination ◽

Antisense Transcription ◽

Exit Site ◽

A Genome ◽

Sense Strand ◽

Native Sequence

AbstractCompared to other stages in the RNA polymerase II transcription cycle, the role of chromatin in transcription termination is poorly understood. Through a genetic screen, we identified histone mutant strains that exhibit transcriptional readthrough of terminators in vivo. Amino acid subtitutions map to the nucleosome DNA entry-exit site. On a genome-wide scale, the strongest H3 mutants revealed increased sense-strand transcription upstream and downstream of Pol II transcribed genes, increased antisense transcription overlapping gene bodies, and reduced nucleosome occupancy particularly at the 3’ ends of genes. Replacement of the native sequence downstream of a gene with a sequence that increases nucleosome occupancy in vivo reduced readthrough transcription and suppressed the effect of a DNA entry-exit site substitution. Our results suggest that nucleosomes can facilitate termination by serving as a barrier to RNA polymerase II progression and highlight the importance of the DNA entry-exit site in maintaining the integrity of the transcriptome.

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