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

Candelli, Tito; Challal, Drice; Briand, Jean-Baptiste; Boulay, Jocelyne; Porrúa, Odil; Colin, Jessie; Libri, Domenico

doi:10.15252/embj.201797490

Cited by 63 publications

(117 citation statements)

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“…For these reasons, we relied on high-resolution transcription 163 maps derived from the direct detection of RNAPII by the sequencing of the nascent transcript (RNAPII 164 PAR-CLIP, Photo-Activable Ribonucleoside-enhanced UV-Crosslink and Immunoprecipitation) 165 (Schaughency et al, 2014). We also generated additional datasets using the analogous RNAPII 166 CRAC, (Crosslinking Analysis of cDNAs, Granneman et al, 2009;Candelli et al, 2018). Both methods 167 detect significant levels of transcription in many regions that lack annotations (data not shown; 168 Candelli et al, 2018).…”

Section: Rnapii Pausing and Transcription Termination Occur At Ars Bomentioning

confidence: 99%

Pervasive Transcription Fine-tunes Replication Origin Activity

Candelli

Gros

Libri

2018

Preprint

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RNA polymerase (RNAPII) transcription occurs pervasively, which raises the important question of its functional impact on other DNA-associated processes, including replication. In budding yeast, replication originates from Autonomously Replicating Sequences (ARSs), generally located in intergenic regions. The influence of transcription on ARSs function has been studied for decades, but these earlier studies have necessarily neglected the role of non-annotated transcription. We studied the relationships between pervasive transcription and replication origin activity using high-resolution transcription maps. We show that ARSs alter the pervasive transcription landscape by pausing and terminating neighboring RNAPII transcription, thus limiting the occurrence of pervasive transcription within origins. We provide evidence that quasi-symmetrical binding of the ORC complex to ARS borders is responsible for pausing/termination. We also show that low, physiological levels of pervasive transcription impact the function of replication origins. Overall, our results have important implications for understanding the impact of genomic location on origin function.

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Section: Rnapii Pausing and Transcription Termination Occur At Ars Bomentioning

confidence: 99%

Pervasive Transcription Fine-tunes Replication Origin Activity

Candelli

Gros

Libri

2018

Preprint

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“…Another component of transcriptional interference may be the physical eviction of the sense PIC by the RNAPII travelling in antisense direction. However, we think this is unlikely since many DNA-binding proteins behave as roadblocking factors in front of which RNAPII stalls (Colin et al 2014;Mayer et al 2015;Candelli et al 2018). Nevertheless, the possibility of RNAPII removing DNA-binding factors remains to be thoroughly tested.…”

Section: A Chromatin-driven Transcription Interference Model Derived mentioning

confidence: 98%

Fine chromatin-driven mechanism of transcription interference by antisense noncoding transcription

Gill

Maffioletti

García-Molinero

et al. 2019

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AbstractEukaryotic genomes are almost entirely transcribed by RNA polymerase II (RNAPII). Consequently, the transcription of long noncoding RNAs (lncRNAs) often overlaps with coding gene promoters triggering potential gene repression through a poorly characterized mechanism of transcription interference. In this study, we propose a global model of chromatin-based transcription interference in Saccharomyces cerevisiae (S. cerevisiae). By using a noncoding transcription inducible strain, we analyzed the relationship between antisense elongation and coding sense repression, nucleosome occupancy and transcription-associated histone modifications using near-base pair resolution techniques. We show that antisense noncoding transcription leads to the deaceylation of a subpopulation of −1/+1 nucleosomes associated with increased H3K36 trimethylation (H3K36me3). Reduced acetylation results in decreased binding of the RSC chromatin remodeler at −1/+1 nucleosomes and subsequent sliding into the Nucleosome-Depleted Region (NDR) hindering Pre-Initiation Complex (PIC) association. Finally, we extend our model by showing that natural antisense noncoding transcription significantly represses around 20% of S. cerevisiae genes through this chromatin-based transcription interference mechanism.HighlightsInduction of antisense noncoding transcription leads to −1/+1 nucleosome sliding that competes with sense transcription PIC deposition.Antisense induction leads to a subpopulation of H3K36me3 nucleosomes differently positioned compared to H3K18ac nucleosomes.RSC chromatin remodeler recruitment to −1/+1 nucleosomes is modulated by histone acetylation levels.20% of S. cerevisiae genes are significantly repressed by this antisense-dependent chromatin-based transcription interference mechanism.

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“…To detect the binding of Nab3 and Nrd1 in vivo, we employed an improved version of the crosslinking and cDNA analysis protocol (CRAC) (Granneman et al, 2009;Candelli et al, 2018;Challal et al, 2018). The proteins of interest are purified after a step of in vivo UV crosslinking and the covalently associated transcripts are sequenced, which provides a read-out of the extent and position of RNA binding.…”

Section: Rna Degradation Is Required For Releasing Nrd1 and Nab3 Frommentioning

confidence: 99%

“…CRAC signals can have two components: one, post-transcriptional, deriving from the binding of proteins to RNAs that have been released from the site of transcription; a second, co-transcriptional, due to proteins binding to the nascent RNA. Because the CRAC signal depends on the levels of transcription, which might differ in wild type (wt) and exosome-defective rrp6∆ cells, we also measured transcription by RNAPII CRAC (Milligan et al, 2016;Candelli et al, 2018;Challal et al, 2018) in the two genetic backgrounds.…”

Section: Rna Degradation Is Required For Releasing Nrd1 and Nab3 Frommentioning

confidence: 99%

“…To extend these findings to a genomewide perspective, we focused on a manually curated representative subset of 329 CUTs. We chose to generate a reannotated model set of CUTs (see STAR Methods; Table S1) because early annotations, mainly based on the automated detection of microarray signals , do not generally take into account novel and more accurate datasets defining the TSS, the termination region and the RNAPII occupancy (Malabat et al, 2015;Roy et al, 2016;Challal et al, 2018) Also, we took into account the NNS dependency (Roy et al, 2016;Candelli et al, 2018), for a better distinction of CUTs that are NNS targets from other non-coding RNAs.…”

Section: Rna Degradation Is Required For Releasing Nrd1 and Nab3 Frommentioning

confidence: 99%

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Degradation of non-coding RNAs promotes recycling of termination factors at sites of transcription

Villa

Barucco

Martin-Niclos

et al. 2019

Preprint

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A large share of the non-coding transcriptome in yeast is controlled by the Nrd1-Nab3-Sen1 (NNS) complex, which promotes transcription termination of noncoding RNA (ncRNA) genes, and by the nuclear exosome, which limits the steady state levels of the transcripts produced. How global ncRNA levels impinge on cellular functions is a longstanding and important question. Here we show that degradation of ncRNAs by the exosome is required for freeing Nrd1 and Nab3 from the released transcript after termination. In exosome mutants, these factors are sequestered by ncRNAs and cannot be efficiently recycled to sites of transcription, which induces termination defects genome-wide. ncRNA-dependent, genome-wide termination defects can be recapitulated by the expression of a degradationresistant, circular RNA containing a natural NNS target in exosome proficient cells.Our results have important implications for the mechanism of termination, the general impact of ncRNAs on cellular physiology and the importance of nuclear ncRNA degradation.Government through its "Investments for the Future" program.This work has benefited from the facilities and expertise of the high throughput sequencing core facility of I2BC (Centre de Recherche de Gif -http://www.i2bc-saclay.fr/). AUTHORS CONTRIBUTION Conceptualization, D.L., T.V., and A.J.; Methodology, T.V., M.B., and M-J.M.N.; Software, M.B.; Formal Analysis, M.B., T.V., and D.L.; Investigation, T.V., M-J.M.N., and D.L.; Writing -Original Draft, T.V. and D.L.; Writing -Review and Editing, T.V. and D.L.; Funding Acquisition, D.L.; Supervision, D.L.

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

Cited by 63 publications

References 64 publications

Pervasive Transcription Fine-tunes Replication Origin Activity

Pervasive Transcription Fine-tunes Replication Origin Activity

Fine chromatin-driven mechanism of transcription interference by antisense noncoding transcription

Degradation of non-coding RNAs promotes recycling of termination factors at sites of transcription

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