ARN non-codant, épigénétique et fluidité du génome

Publications de l’équipe

Année de publication : 2015

Marc Descrimes, Yousra Ben Zouari, Maxime Wery, Rachel Legendre, Daniel Gautheret, Antonin Morillon (2015 Sep 9)

VING: a software for visualization of deep sequencing signals.

BMC research notes : 419 : DOI : 10.1186/s13104-015-1404-5 En savoir plus
Résumé

Next generation sequencing (NGS) data treatment often requires mapping sequenced reads onto a reference genome for further analysis. Mapped data are commonly visualized using genome browsers. However, such software are not suited for a publication-ready and versatile representation of NGS data coverage, especially when multiple experiments are simultaneously treated.

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Flore Sinturel, Albertas Navickas, Maxime Wery, Marc Descrimes, Antonin Morillon, Claire Torchet, Lionel Benard (2015 Sep 8)

Cytoplasmic Control of Sense-Antisense mRNA Pairs.

Cell reports : 1853-64 : DOI : 10.1016/j.celrep.2015.08.016 En savoir plus
Résumé

Transcriptome analyses have revealed that convergent gene transcription can produce many 3′-overlapping mRNAs in diverse organisms. Few studies have examined the fate of 3′-complementary mRNAs in double-stranded RNA-dependent nuclear phenomena, and nothing is known about the cytoplasmic destiny of 3′-overlapping messengers or their impact on gene expression. Here, we demonstrate that the complementary tails of 3′-overlapping mRNAs can interact in the cytoplasm and promote post-transcriptional regulatory events including no-go decay (NGD) in Saccharomyces cerevisiae. Genome-wide experiments confirm that these messenger-interacting mRNAs (mimRNAs) form RNA duplexes in wild-type cells and thus have potential roles in modulating the mRNA levels of their convergent gene pattern under different growth conditions. We show that the post-transcriptional fate of hundreds of mimRNAs is controlled by Xrn1, revealing the extent to which this conserved 5′-3′ cytoplasmic exoribonuclease plays an unexpected but key role in the post-transcriptional control of convergent gene expression.

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Nicola Manfrini, Michela Clerici, Maxime Wery, Chiara Vittoria Colombo, Marc Descrimes, Antonin Morillon, Fabrizio d'Adda di Fagagna, Maria Pia Longhese (2015 Aug 1)

Resection is responsible for loss of transcription around a double-strand break in Saccharomyces cerevisiae.

eLife : DOI : 10.7554/eLife.08942 En savoir plus
Résumé

Emerging evidence indicate that the mammalian checkpoint kinase ATM induces transcriptional silencing in cis to DNA double-strand breaks (DSBs) through a poorly understood mechanism. Here we show that in Saccharomyces cerevisiae a single DSB causes transcriptional inhibition of proximal genes independently of Tel1/ATM and Mec1/ATR. Since the DSB ends undergo nucleolytic degradation (resection) of their 5′-ending strands, we investigated the contribution of resection in this DSB-induced transcriptional inhibition. We discovered that resection-defective mutants fail to stop transcription around a DSB, and the extent of this failure correlates with the severity of the resection defect. Furthermore, Rad9 and generation of γH2A reduce this DSB-induced transcriptional inhibition by counteracting DSB resection. Therefore, the conversion of the DSB ends from double-stranded to single-stranded DNA, which is necessary to initiate DSB repair by homologous recombination, is responsible for loss of transcription around a DSB in S. cerevisiae.

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Hung-Fu Liao, Chu-Fan Mo, Shinn-Chih Wu, Dai-Han Cheng, Chih-Yun Yu, Kai-Wei Chang, Tzu-Hao Kao, Chia-Wei Lu, Marina Pinskaya, Antonin Morillon, Shih-Shun Lin, Winston T K Cheng, Déborah Bourc'his, Timothy Bestor, Li-Ying Sung, Shau-Ping Lin (2015 Jul 11)

Dnmt3l-knockout donor cells improve somatic cell nuclear transfer reprogramming efficiency.

Reproduction (Cambridge, England) : 245-56 : DOI : 10.1530/REP-15-0031 En savoir plus
Résumé

Nuclear transfer (NT) is a technique used to investigate the development and reprogramming potential of a single cell. DNA methyltransferase-3-like, which has been characterized as a repressive transcriptional regulator, is expressed in naturally fertilized egg and morula/blastocyst at pre-implantation stages. In this study, we demonstrate that the use of Dnmt3l-knockout (Dnmt3l-KO) donor cells in combination with Trichostatin A treatment improved the developmental efficiency and quality of the cloned embryos. Compared with the WT group, Dnmt3l-KO donor cell-derived cloned embryos exhibited increased cell numbers as well as restricted OCT4 expression in the inner cell mass (ICM) and silencing of transposable elements at the blastocyst stage. In addition, our results indicate that zygotic Dnmt3l is dispensable for cloned embryo development at pre-implantation stages. In Dnmt3l-KO mouse embryonic fibroblasts, we observed reduced nuclear localization of HDAC1, increased levels of the active histone mark H3K27ac and decreased accumulation of the repressive histone marks H3K27me3 and H3K9me3, suggesting that Dnmt3l-KO donor cells may offer a more permissive epigenetic state that is beneficial for NT reprogramming.

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Marta Kwapisz, Myriam Ruault, Erwin van Dijk, Stephanie Gourvennec, Marc Descrimes, Angela Taddei and Antonin Morillon (2015 Jul 3)

Expression of Subtelomeric lncRNAs Links Telomeres Dynamics to RNA Decay in S. cerevisiae

Non-coding RNA : 1 : 94-126 : DOI : 10.3390/ncrna1020094 En savoir plus
Résumé

Long non-coding RNAs (lncRNAs) have been shown to regulate gene expression, chromatin domains and chromosome stability in eukaryotic cells. Recent observations have reported the existence of telomeric repeats containing long ncRNAs – TERRA in mammalian and yeast cells. However, their functions remain poorly characterized. Here, we report the existence in S. cerevisiae of several lncRNAs within Y′ subtelomeric regions. We have called them subTERRA. These belong to Cryptic Unstable Transcripts (CUTs) and Xrn1p-sensitive Unstable Transcripts (XUTs) family. subTERRA transcription, carried out mainly by RNAPII, is initiated within the subtelomeric Y’ element and occurs in both directions, towards telomeres as well as centromeres. We show that subTERRA are distinct from TERRA and are mainly degraded by the general cytoplasmic and nuclear 5′- and 3′- RNA decay pathways in a transcription-dependent manner. subTERRA accumulates preferentially during the G1/S transition and in C-terminal rap1 mutant but independently of Rap1p function in silencing. The accumulation of subTERRA in RNA decay mutants coincides with telomere misregulation: shortening of telomeres, loss of telomeric clustering in mitotic cells and changes in silencing of subtelomeric regions. Our data suggest that subtelomeric RNAs expression links telomere maintenance to RNA degradation pathways.

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Dat Tran, Kundan Verma, Kristin Ward, Dolores Diaz, Esha Kataria, Alireza Torabi, Anna Almeida, Bernard Malfoy, Eva W Stratford, Dianne C Mitchell, Brad A Bryan (2015 Jan 28)

Functional genomics analysis reveals a MYC signature associated with a poor clinical prognosis in liposarcomas.

The American journal of pathology : 717-28 : DOI : 10.1016/j.ajpath.2014.11.024 En savoir plus
Résumé

Liposarcomas, which are malignant fatty tumors, are the second most common soft-tissue sarcomas. Several histologically defined liposarcoma subtypes exist, yet little is known about the molecular pathology that drives the diversity in these tumors. We used functional genomics to classify a panel of diverse liposarcoma cell lines based on hierarchical clustering of their gene expression profiles, indicating that liposarcoma gene expression profiles and histologic classification are not directly correlated. Boolean probability approaches based on cancer-associated properties identified differential expression in multiple genes, including MYC, as potentially affecting liposarcoma signaling networks and cancer outcome. We confirmed our method with a large panel of lipomatous tumors, revealing that MYC protein expression is correlated with patient survival. These data encourage increased reliance on genomic features in conjunction with histologic features for liposarcoma clinical characterization and lay the groundwork for using Boolean-based probabilities to identify prognostic biomarkers for clinical outcome in tumor patients.

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Année de publication : 2014

Nicola Manfrini, Camilla Trovesi, Maxime Wery, Marina Martina, Daniele Cesena, Marc Descrimes, Antonin Morillon, Fabrizio d'Adda di Fagagna, Maria Pia Longhese (2014 Dec 19)

RNA-processing proteins regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA.

EMBO reports : 221-31 : DOI : 10.15252/embr.201439458 En savoir plus
Résumé

Eukaryotic cells respond to DNA double-strand breaks (DSBs) by activating a checkpoint that depends on the protein kinases Tel1/ATM and Mec1/ATR. Mec1/ATR is activated by RPA-coated single-stranded DNA (ssDNA), which arises upon nucleolytic degradation (resection) of the DSB. Emerging evidences indicate that RNA-processing factors play critical, yet poorly understood, roles in genomic stability. Here, we provide evidence that the Saccharomyces cerevisiae RNA decay factors Xrn1, Rrp6 and Trf4 regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA. The lack of Xrn1 inhibits ssDNA generation at the DSB by preventing the loading of the MRX complex. By contrast, DSB resection is not affected in the absence of Rrp6 or Trf4, but their lack impairs the recruitment of RPA, and therefore of Mec1, to the DSB. Rrp6 and Trf4 inactivation affects neither Rad51/Rad52 association nor DSB repair by homologous recombination (HR), suggesting that full Mec1 activation requires higher amount of RPA-coated ssDNA than HR-mediated repair. Noteworthy, deep transcriptome analyses do not identify common misregulated gene expression that could explain the observed phenotypes. Our results provide a novel link between RNA processing and genome stability.

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Marina Pinskaya, Yad Ghavi-Helm, Sylvie Mariotte-Labarre, Antonin Morillon, Julie Soutourina, Michel Werner (2014 Jul 17)

PHD and TFIIS-Like domains of the Bye1 transcription factor determine its multivalent genomic distribution.

PloS one : e102464 : DOI : 10.1371/journal.pone.0102464 En savoir plus
Résumé

The BYpass of Ess1 (Bye1) protein is a putative S. cerevisiae transcription factor homologous to the human cancer-associated PHF3/DIDO family of proteins. Bye1 contains a Plant Homeodomain (PHD) and a TFIIS-like domain. The Bye1 PHD finger interacts with tri-methylated lysine 4 of histone H3 (H3K4me3) while the TFIIS-like domain binds to RNA polymerase (Pol) II. Here, we investigated the contribution of these structural features to Bye1 recruitment to chromatin as well as its function in transcriptional regulation. Genome-wide analysis of Bye1 distribution revealed at least two distinct modes of association with actively transcribed genes: within the core of Pol II- and Pol III-transcribed genes concomitant with the presence of the TFIIS transcription factor and, additionally, with promoters of a subset of Pol II-transcribed genes. Specific loss of H3K4me3 abolishes Bye1 association to gene promoters, but doesn’t affect its binding within gene bodies. Genetic interactions suggested an essential role of Bye1 in cell fitness under stress conditions compensating the absence of TFIIS. Furthermore, BYE1 deletion resulted in the attenuation of GAL genes expression upon galactose-mediated induction indicating its positive role in transcription regulation. Together, these findings point to a bimodal role of Bye1 in regulation of Pol II transcription. It is recruited via its PHD domain to H3K4 tri-methylated promoters at early steps of transcription. Once Pol II is engaged into elongation, Bye1 binds directly to the transcriptional machinery, modulating its progression along the gene.

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Année de publication : 2013

Antonin Morillon, Jean-Christophe Andrau (2013 Sep 10)

Editorial for « Diversity of the non-coding transcriptomes revealed by RNA-seq technologies ».

Methods (San Diego, Calif.) : 1-2 : DOI : 10.1016/j.ymeth.2013.08.030 En savoir plus
Résumé

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Maxime Wery, Marc Descrimes, Claude Thermes, Daniel Gautheret, Antonin Morillon (2012 Sep 18)

Zinc-mediated RNA fragmentation allows robust transcript reassembly upon whole transcriptome RNA-Seq.

Methods (San Diego, Calif.) : 25-31 : DOI : 10.1016/j.ymeth.2013.03.009 En savoir plus
Résumé

Whole transcriptome RNA-Seq has emerged as a powerful tool in transcriptomics, enabling genome-wide quantitative analysis of gene expression and qualitative identification of novel coding or non-coding RNA species through transcriptome reassembly. Common protocols for preparation of RNA-Seq libraries include an RNA fragmentation step for which several RNA sizing techniques are commercially available. To date, there is no global information about their putative bias on transcriptome analysis. Here we compared the effects of RNase III- and zinc-mediated RNA fragmentation on transcript expression measurement and transcriptome reassembly in the budding yeast Saccharomyces cerevisiae. We observed that RNA cleavage by RNase III is heterogeneous along transcripts with a striking decrease of autocorrelation between adjacent nucleotides along the transcriptome. This had little impact on mRNA expression measurement, but specific classes of transcripts such as abundant non-coding RNAs were underrepresented in the libraries constructed using RNase III. Furthermore, zinc-mediated fragmentation allows proper reassembly of more transcripts, with more precise 5′ and 3′ ends. Together, our results show that transcriptome reassembly from RNA-Seq data is very sensitive to the RNA fragmentation technique, and that zinc-mediated fragmentation provides more robust and accurate transcript identification than cleavage by RNase III.

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Année de publication : 2011

Michael B Clark, Paulo P Amaral, Felix J Schlesinger, Marcel E Dinger, Ryan J Taft, John L Rinn, Chris P Ponting, Peter F Stadler, Kevin V Morris, Antonin Morillon, Joel S Rozowsky, Mark B Gerstein, Claes Wahlestedt, Yoshihide Hayashizaki, Piero Carninci, Thomas R Gingeras, John S Mattick (2011 Jul 19)

The reality of pervasive transcription.

PLoS biology : e1000625; discussion e1001102 : DOI : 10.1371/journal.pbio.1000625 En savoir plus
Résumé

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Bruno Cosnier, Marta Kwapisz, Isabelle Hatin, Olivier Namy, Sylvie Hermann-Le Denmat, Antonin Morillon, Jean-Pierre Rousset, Céline Fabret (2011 May 12)

A viable hypomorphic allele of the essential IMP3 gene reveals novel protein functions in Saccharomyces cerevisiae.

PloS one : e19500 : DOI : 10.1371/journal.pone.0019500 En savoir plus
Résumé

In Saccharomyces cerevisiae, the essential IMP3 gene encodes a component of the SSU processome, a large ribonucleoprotein complex required for processing of small ribosomal subunit RNA precursors. Mutation of the IMP3 termination codon to a sense codon resulted in a viable mutant allele producing a C-terminal elongated form of the Imp3 protein. A strain expressing the mutant allele displayed ribosome biogenesis defects equivalent to IMP3 depletion. This hypomorphic allele represented a unique opportunity to investigate and better understand the Imp3p functions. We demonstrated that the +1 frameshifting was increased in the mutant strain. Further characterizations revealed involvement of the Imp3 protein in DNA repair and telomere length control, pointing to a functional relationship between both pathways and ribosome biogenesis.

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Mathieu Tisseur, Marta Kwapisz, Antonin Morillon (2011 May 3)

Pervasive transcription – Lessons from yeast.

Biochimie : 1889-96 : DOI : 10.1016/j.biochi.2011.07.001 En savoir plus
Résumé

Pervasive transcription is now accepted to be a general feature of eukaryotic genomes, generating short and long non-coding RNAs (ncRNAs). Growing number of examples have shown that regulatory ncRNAs can control gene expression and chromatin domain formation. In this review, we discuss recent reports that show that Saccharomyces cerevisiae’s genome also supports pervasive transcription, which is strongly controlled by RNA decay pathways and nucleosome positioning. We therefore propose that S. cerevisiae is an excellent model for studying large ncRNAs, which has already provided important examples of antisense-mediated transcriptional silencing.

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Année de publication : 2010

E L van Dijk, C L Chen, Y d'Aubenton-Carafa, S Gourvennec, M Kwapisz, V Roche, C Bertrand, M Silvain, P Legoix-Né, S Loeillet, A Nicolas, C Thermes, A Morillon (2010 Dec 31)

XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast.

Nature : 114-7 : DOI : 10.1038/nature10118 En savoir plus
Résumé

Non-coding (nc)RNAs are key players in numerous biological processes such as gene regulation, chromatin domain formation and genome stability. Large ncRNAs interact with histone modifiers and are involved in cancer development, X-chromosome inactivation and autosomal gene imprinting. However, despite recent evidence showing that pervasive transcription is more widespread than previously thought, only a few examples mediating gene regulation in eukaryotes have been described. In Saccharomyces cerevisiae, the bona-fide regulatory ncRNAs are destabilized by the Xrn1 5′-3′ RNA exonuclease (also known as Kem1), but the genome-wide characterization of the entire regulatory ncRNA family remains elusive. Here, using strand-specific RNA sequencing (RNA-seq), we identify a novel class of 1,658 Xrn1-sensitive unstable transcripts (XUTs) in which 66% are antisense to open reading frames. These transcripts are polyadenylated and RNA polymerase II (RNAPII)-dependent. The majority of XUTs strongly accumulate in lithium-containing media, indicating that they might have a role in adaptive responses to changes in growth conditions. Notably, RNAPII chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) analysis of Xrn1-deficient strains revealed a significant decrease of RNAPII occupancy over 273 genes with antisense XUTs. These genes show an unusual bias for H3K4me3 marks and require the Set1 histone H3 lysine 4 methyl-transferase for silencing. Furthermore, abolishing H3K4me3 triggers the silencing of other genes with antisense XUTs, supporting a model in which H3K4me3 antagonizes antisense ncRNA repressive activity. Our results demonstrate that antisense ncRNA-mediated regulation is a general regulatory pathway for gene expression in S. cerevisiae.

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Année de publication : 2009

Julia Berretta, Antonin Morillon (2009 Aug 15)

Pervasive transcription constitutes a new level of eukaryotic genome regulation.

EMBO reports : 973-82 : DOI : 10.1038/embor.2009.181 En savoir plus
Résumé

During the past few years, it has become increasingly evident that the expression of eukaryotic genomes is far more complex than had been previously noted. The idea that the transcriptome is derived exclusively from protein-coding genes and some specific non-coding RNAs–such as snRNAs, snoRNAs, tRNAs or rRNAs–has been swept away by numerous studies indicating that RNA polymerase II can be found at almost any genomic location. Pervasive transcription is widespread and, far from being a futile process, has a crucial role in controlling gene expression and genomic plasticity. Here, we review recent findings that point to cryptic transcription as a fundamental component of the regulation of eukaryotic genomes.

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