Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration

mRNA homoeostasis is favoured by crosstalk between transcription and degradation machineries. Both the Ccr4-Not and the Xrn1-decaysome complexes have been described to influence transcription. While Ccr4-Not has been shown to directly stimulate transcription elongation, the information available on how Xrn1 influences transcription is scarce and contradictory. In this study we have addressed this issue by mapping RNA polymerase II (RNA pol II) at high resolution, using CRAC and BioGRO-seq techniques in Saccharomyces cerevisiae. We found significant effects of Xrn1 perturbation on RNA pol II profiles across the genome. RNA pol II profiles at 5ʹ exhibited significant alterations that were compatible with decreased elongation rates in the absence of Xrn1. Nucleosome mapping detected altered chromatin configuration in the gene bodies. We also detected accumulation of RNA pol II shortly upstream of polyadenylation sites by CRAC, although not by BioGRO-seq, suggesting higher frequency of backtracking before pre-mRNA cleavage. This phenomenon was particularly linked to genes with poorly positioned nucleosomes at this position. Accumulation of RNA pol II at 3ʹ was also detected in other mRNA decay mutants. According to these and other pieces of evidence, Xrn1 seems to influence transcription elongation at least in two ways: by directly favouring elongation rates and by a more general mechanism that connects mRNA decay to late elongation.Ministerio de Economía y Competitividad BFU2016-77728- C3-1-P, BFU2016-77728-C3-3-P, BFU2016- 77728-C3-2-P, RED2018-102467-TJunta de Andalucía BIO271, US-1256285, BIO258, UJA 1260360Generalitat Valenciana AICO/2019/08

Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration

mRNA homoeostasis is favoured by crosstalk between transcription and degradation machineries. Both the Ccr4-Not and the Xrn1-decaysome complexes have been described to influence transcription. While Ccr4-Not has been shown to directly stimulate transcription elongation, the information available on how Xrn1 influences transcription is scarce and contradictory. In this study we have addressed this issue by mapping RNA polymerase II (RNA pol II) at high resolution, using CRAC and BioGRO-seq techniques in Saccharomyces cerevisiae. We found significant effects of Xrn1 perturbation on RNA pol II profiles across the genome. RNA pol II profiles at 5ʹ exhibited significant alterations that were compatible with decreased elongation rates in the absence of Xrn1. Nucleosome mapping detected altered chromatin configuration in the gene bodies. We also detected accumulation of RNA pol II shortly upstream of polyadenylation sites by CRAC, although not by BioGRO-seq, suggesting higher frequency of backtracking before pre-mRNA cleavage. This phenomenon was particularly linked to genes with poorly positioned nucleosomes at this position. Accumulation of RNA pol II at 3ʹ was also detected in other mRNA decay mutants. According to these and other pieces of evidence, Xrn1 seems to influence transcription elongation at least in two ways: by directly favouring elongation rates and by a more general mechanism that connects mRNA decay to late elongation.This work has been supported by grants from the Ministerio de Economía, Industria y Competitividad – Agencia Estatal de Investigación, and European Union funds (FEDER) [BFU2016-77728-C3-1-P to S. C.],[BFU2016-77728-C3-3-P to J.E.P-O & P.A], [BFU2016-77728-C3-2-P to F.N.] and RED2018‐102467‐T to J.E.P-O, F.N. and S.C.; by FPI grants from the Spanish Government to V.B and A.C-B; by the Regional Andalusian Government [BIO271 and US-1256285 to S. C.], [BIO258 and FEDER-UJA 1260360 to F.N.] and from the Regional Valencian Government [AICO/2019/088 to J.E.P-O]. Funding for open access charge: [BFU2016-77728-C3-1-P]

Rôle des facteurs de transcription dans le contrôle de l'expression des gènes et de la fidélité de la transcription

The last decades have been marked by the discovery of pervasive transcription. Indeed, many studies have shown that transcription by RNA polymerase II is not restricted to annotated regions but is widespread in eukaryotic genomes, leading to the production of a plethora of non-coding RNAs. Precise delimitation of transcriptional units appears to be essential to ensure robust fidelity of gene expression and to maintain the integrity of DNA-associated events by preventing the occurrence of conflicts with transcription. In this respect, accurate transcription initiation and termination represent crucial mechanisms to partition the genome and define the correct processing of RNA molecules. Here, we show that yeast general regulatory factors (GRFs), a class of highly expressed transcription regulators, control pervasive transcription at the level of initiation and termination and are also involved in the fidelity of initiation of mRNA-coding genes. We demonstrate that GRFs bound at promoter regions can elicit transcription termination by physically impeding the progression of polymerases mainly deriving from readthrough transcription at upstream canonical termination sites. We provide evidence that this termination pathway named roadblock is widespread throughout the yeast genome and protects promoter regions from transcriptional interference. Furthermore, we establish that the presence of general regulatory factors also limits pervasive transcription at the level of initiation, notably by occluding spurious transcription start sites present in the vicinity of their binding sites. We also unveil the importance of these factors in promoting correct transcription start site selection at mRNA-coding genes thus favouring the synthesis of transcripts with an appropriate coding potential. Finally, we determine that the role of GRFs in controlling proper initiation is intimately linked to their ability to correctly position nucleosomes in promoters, a role that occurs independently from but in cooperation with chromatin remodelers.Ces dernières décennies ont été marquées par la découverte de la transcription dite « cachée » ou « pervasive ». Il a été en effet montré que la majeure partie du génome des eucaryotes est transcrite, donnant naissance à la formation de nombreux ARNs non-codants. La délimitation des unités de transcription apparait essentielle dans le contrôle de l’expression des gènes mais également dans le maintien de l’intégrité des processus associés à l’ADN en limitant notamment l’apparition de conflits avec la transcription. Dans ce contexte, l’initiation et la terminaison de la transcription représentent des étapes clés dans le partitionnement du génome et le métabolisme des ARNs. Nous avons montré que certains facteurs de transcription, appelés GRFs (General Regulatory Factors) chez la levure S. cerevisiae, jouent un rôle important dans le contrôle de la transcription pervasive à la fois au niveau de l’initiation mais également de la terminaison de la transcription et sont également requis pour assurer la fidélité de la transcription des gènes codant les ARN messagers. Nous avons prouvé que les GRFs liés au niveau des régions promotrices sont capables d’induire la terminaison de la transcription en bloquant physiquement la progression d’ARN polymérases issues de la translecture des terminateurs situés en amont. D’après nos études, cette voie de terminaison appelée « roadblock » est très répandue à l’échelle du génome et joue un rôle important dans la protection des promoteurs contre l’interférence transcriptionnelle. Nous avons également découvert que les GRFs limitent la transcription pervasive en obstruant les sites d’initiations ectopiques situés à proximité de leur site de fixation sur l’ADN. Ces facteurs sont aussi impliqués dans le contrôle de l’expression des gènes codants en favorisant l’utilisation de sites d’initiations les plus appropriés, c’est-à-dire, permettant la synthèse d’ARNs ayant un fort potentiel codant. Le rôle des GRFs dans le contrôle de l’initiation apparait intimement lié à leur capacité à correctement positionner les nucléosomes au niveau des promoteurs en collaboration avec les facteurs de remodelage de la chromatine

A dual, catalytic role for the fission yeast Ccr4-Not complex in gene silencing and heterochromatin spreading

Heterochromatic gene silencing relies on combinatorial control by specific histone modifications, the occurrence of transcription, and/or RNA degradation. Once nucleated, heterochromatin propagates within defined chromosomal regions and is maintained throughout cell divisions to warrant proper genome expression and integrity. In the fission yeast Schizosaccharomyces pombe, the Ccr4-Not complex partakes in gene silencing, but its relative contribution to distinct heterochromatin domains and its role in nucleation versus spreading have remained elusive. Here, we unveil major functions for Ccr4-Not in silencing and heterochromatin spreading at the mating type locus and subtelomeres. Mutations of the catalytic subunits Caf1 or Mot2, involved in RNA deadenylation and protein ubiquitinylation, respectively, result in impaired propagation of H3K9me3 and massive accumulation of nucleation-distal heterochromatic transcripts. Both silencing and spreading defects are suppressed upon disruption of the heterochromatin antagonizing factor Epe1. Overall, our results position the Ccr4-Not complex as a critical, dual regulator of heterochromatic gene silencing and spreading

High-resolution transcription maps reveal the widespread impact of roadblock termination in yeast

International audienceTranscription termination delimits transcription units but also plays important roles in limiting pervasive transcription. We have previously shown that transcription termination occurs when elongating RNA polymerase II (RNAPII) collides with the DNA-bound general transcription factor Reb1. We demonstrate here that many different DNA-binding proteins can induce termination by a similar roadblock (RB) mechanism. We generated high-resolution transcription maps by the direct detection of RNAPII upon nuclear depletion of two essential RB factors or when the canonical termination pathways for coding and non-coding RNAs are defective. We show that RB termination occurs genomewide and functions independently of (and redundantly with) the main transcription termination pathways. We provide evidence that transcriptional readthrough at canonical terminators is a significant source of pervasive transcription, which is controlled to a large extent by RB termination. Finally, we demonstrate the occurrence of RB termination around centromeres and tRNA genes, which we suggest shields these regions from RNAPII to preserve their functional integrity

General Regulatory Factors Control the Fidelity of Transcription by Restricting Non-coding and Ectopic Initiation

International audienceThe 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, drastically altering the coding potential of the transcriptome. Ectopic transcription initiation strongly correlates with altered nucleosome positioning. We provide evidence that Rap1 can suppress ectopic initiation by a "place-holder" mechanism whereby it physically occludes inappropriate sites for pre-initiation complex formation. These results reveal an essential role for GRFs in the fidelity of transcription initiation and in the suppression of pervasive transcription, profoundly redefining current models for their function. They have important implications for the mechanism of transcription initiation and the control of gene expression

Binding to RNA regulates Set1 function

International audienceThe Set1 family of histone H3 lysine 4 (H3K4) methyltransferases is highly conserved from yeast to human. Here we show that the Set1 complex (Set1C) directly binds RNA in vitro through the regions that comprise the double RNA recognition motifs (dRRM) and N-SET domain within Set1 and its subunit Spp1. To investigate the functional relevance of RNA binding, we performed UV RNA crosslinking (CRAC) for Set1 and RNA polymerase II in parallel with ChIP-seq experiments. Set1 binds nascent transcripts through its dRRM. RNA binding is important to define the appropriate topology of Set1C distribution along transcription units and correlates with the efficient deposition of the H3K4me3 mark. In addition, we uncovered that Set1 binds to different classes of RNAs to levels that largely exceed the levels of binding to the general population of transcripts, suggesting the Set1 persists on these RNAs after transcription. This class includes RNAs derived from SET1, Ty1 retrotransposons, specific transcription factors genes and snRNAs (small nuclear RNAs). We propose that Set1 modulates adaptive responses, as exemplified by the post-transcriptional inhibition of Ty1 retrotransposition

The Chromatin Remodeler ISW1 Is a Quality Control Factor that Surveys Nuclear mRNP Biogenesis

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Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration.

mRNA homoeostasis is favoured by crosstalk between transcription and degradation machineries. Both the Ccr4-Not and the Xrn1-decaysome complexes have been described to influence transcription. While Ccr4-Not has been shown to directly stimulate transcription elongation, the information available on how Xrn1 influences transcription is scarce and contradictory. In this study we have addressed this issue by mapping RNA polymerase II (RNA pol II) at high resolution, using CRAC and BioGRO-seq techniques in Saccharomyces cerevisiae. We found significant effects of Xrn1 perturbation on RNA pol II profiles across the genome. RNA pol II profiles at 5' exhibited significant alterations that were compatible with decreased elongation rates in the absence of Xrn1. Nucleosome mapping detected altered chromatin configuration in the gene bodies. We also detected accumulation of RNA pol II shortly upstream of polyadenylation sites by CRAC, although not by BioGRO-seq, suggesting higher frequency of backtracking before pre-mRNA cleavage. This phenomenon was particularly linked to genes with poorly positioned nucleosomes at this position. Accumulation of RNA pol II at 3' was also detected in other mRNA decay mutants. According to these and other pieces of evidence, Xrn1 seems to influence transcription elongation at least in two ways: by directly favouring elongation rates and by a more general mechanism that connects mRNA decay to late elongation