Publications by authors named "Antonin Morillon"

50 Publications

A Role for the Mre11-Rad50-Xrs2 Complex in Gene Expression and Chromosome Organization.

Mol Cell 2021 01 4;81(1):183-197.e6. Epub 2020 Dec 4.

Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labéllisée Ligue contre le Cancer, 34396 Montpellier, France; University of Basel and Friedrich Miescher Institute for Biomedical Research, Faculty of Natural Sciences, Klingelbergstrasse 50, 4056 Basel, Switzerland. Electronic address:

Mre11-Rad50-Xrs2 (MRX) is a highly conserved complex with key roles in various aspects of DNA repair. Here, we report a new function for MRX in limiting transcription in budding yeast. We show that MRX interacts physically and colocalizes on chromatin with the transcriptional co-regulator Mediator. MRX restricts transcription of coding and noncoding DNA by a mechanism that does not require the nuclease activity of Mre11. MRX is required to tether transcriptionally active loci to the nuclear pore complex (NPC), and it also promotes large-scale gene-NPC interactions. Moreover, MRX-mediated chromatin anchoring to the NPC contributes to chromosome folding and helps to control gene expression. Together, these findings indicate that MRX has a role in transcription and chromosome organization that is distinct from its known function in DNA repair.
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http://dx.doi.org/10.1016/j.molcel.2020.11.010DOI Listing
January 2021

Transient DNMT3L Expression Reinforces Chromatin Surveillance to Halt Senescence Progression in Mouse Embryonic Fibroblast.

Front Cell Dev Biol 2020 4;8:103. Epub 2020 Mar 4.

Institute of Biotechnology, National Taiwan University, Taipei, Taiwan.

Global heterochromatin reduction, which is one of the hallmarks of senescent cells, is associated with reduced transposable element repression and increased risk of chromatin instability. To ensure genomic integrity, the irreparable cells in a population exit permanently from the cell cycle, and this process is termed "senescence." However, senescence only blocks the expansion of unwanted cells, and the aberrant chromatin of senescent cells remains unstable. Serendipitously, we found that the transient ectopic expression of a repressive epigenetic modulator, DNA methyltransferase 3-like (DNMT3L) was sufficient to delay the premature senescence progression of late-passage mouse embryonic fibroblasts (MEFs) associated with a tightened global chromatin structure. DNMT3L induces more repressive H3K9 methylation on endogenous retroviruses and downregulates the derepressed transposons in aging MEFs. In addition, we found that a pulse of ectopic DNMT3L resulted in the reestablishment of H3K27me3 on polycomb repressive complex 2 (PRC2)-target genes that were derepressed in old MEFs. We demonstrated that ectopic DNMT3L interacted with PRC2 in MEFs. Our data also suggested that ectopic DNMT3L might guide PRC2 to redress deregulated chromatin regions in cells undergoing senescence. This study might lead to an epigenetic reinforcement strategy for overcoming aging-associated epimutation and senescence.
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http://dx.doi.org/10.3389/fcell.2020.00103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7064442PMC
March 2020

Subtelomeric Transcription and its Regulation.

J Mol Biol 2020 07 6;432(15):4199-4219. Epub 2020 Feb 6.

ncRNA, Epigenetic and Genome Fluidity, CNRS UMR 3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, 26 rue d'Ulm, 75248, Paris, France. Electronic address:

The subtelomeres, highly heterogeneous repeated sequences neighboring telomeres, are transcribed into coding and noncoding RNAs in a variety of organisms. Telomereproximal subtelomeric regions produce non-coding transcripts i.e., ARRET, αARRET, subTERRA, and TERRA, which function in telomere maintenance. The role and molecular mechanisms of the majority of subtelomeric transcripts remain unknown. This review depicts the current knowledge and puts into perspective the results obtained in different models from yeasts to humans.
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http://dx.doi.org/10.1016/j.jmb.2020.01.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7374410PMC
July 2020

GC content shapes mRNA storage and decay in human cells.

Elife 2019 12 19;8. Epub 2019 Dec 19.

Sorbonne Université, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire de Biologie du Développement, Paris, France.

mRNA translation and decay appear often intimately linked although the rules of this interplay are poorly understood. In this study, we combined our recent P-body transcriptome with transcriptomes obtained following silencing of broadly acting mRNA decay and repression factors, and with available CLIP and related data. This revealed the central role of GC content in mRNA fate, in terms of P-body localization, mRNA translation and mRNA stability: P-bodies contain mostly AU-rich mRNAs, which have a particular codon usage associated with a low protein yield; AU-rich and GC-rich transcripts tend to follow distinct decay pathways; and the targets of sequence-specific RBPs and miRNAs are also biased in terms of GC content. Altogether, these results suggest an integrated view of post-transcriptional control in human cells where most translation regulation is dedicated to inefficiently translated AU-rich mRNAs, whereas control at the level of 5' decay applies to optimally translated GC-rich mRNAs.
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http://dx.doi.org/10.7554/eLife.49708DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6944446PMC
December 2019

Reference-free transcriptome exploration reveals novel RNAs for prostate cancer diagnosis.

Life Sci Alliance 2019 12 15;2(6). Epub 2019 Nov 15.

ncRNA, Epigenetic and Genome Fluidity, Université Paris Sciences & Lettres (PSL), Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Institut Curie, Research Center, Paris, France

The use of RNA-sequencing technologies held a promise of improved diagnostic tools based on comprehensive transcript sets. However, mining human transcriptome data for disease biomarkers in clinical specimens are restricted by the limited power of conventional reference-based protocols relying on unique and annotated transcripts. Here, we implemented a blind reference-free computational protocol, DE-kupl, to infer yet unreferenced RNA variations from total stranded RNA-sequencing datasets of tissue origin. As a bench test, this protocol was powered for detection of RNA subsequences embedded into putative long noncoding (lnc)RNAs expressed in prostate cancer. Through filtering of 1,179 candidates, we defined 21 lncRNAs that were further validated by NanoString for robust tumor-specific expression in 144 tissue specimens. Predictive modeling yielded a restricted probe panel enabling more than 90% of true-positive detections of cancer in an independent The Cancer Genome Atlas cohort. Remarkably, this clinical signature made of only nine unannotated lncRNAs largely outperformed PCA3, the only used prostate cancer lncRNA biomarker, in detection of high-risk tumors. This modular workflow is highly sensitive and can be applied to any pathology or clinical application.
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http://dx.doi.org/10.26508/lsa.201900449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6858606PMC
December 2019

Endogenous RNAi pathway evolutionarily shapes the destiny of the antisense lncRNAs transcriptome.

Life Sci Alliance 2019 10 28;2(5). Epub 2019 Aug 28.

ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR 3244, Paris, France

Antisense long noncoding (aslnc)RNAs are extensively degraded by the nuclear exosome and the cytoplasmic exoribonuclease Xrn1 in the budding yeast , lacking RNAi. Whether the ribonuclease III Dicer affects aslncRNAs in close RNAi-capable relatives remains unknown. Using genome-wide RNA profiling, here we show that aslncRNAs are primarily targeted by the exosome and Xrn1 in the RNAi-capable budding yeast , Dicer only affecting Xrn1-sensitive aslncRNAs levels in Xrn1-deficient cells. The and mutants display synergic growth defects, indicating that Dicer becomes critical in the absence of Xrn1. Small RNA sequencing showed that Dicer processes aslncRNAs into small RNAs, with a preference for Xrn1-sensitive aslncRNAs. Consistently, Dicer localizes into the cytoplasm. Finally, we observed an expansion of the exosome-sensitive antisense transcriptome in compared with , suggesting that the presence of cytoplasmic RNAi has reinforced the nuclear RNA surveillance machinery to temper aslncRNAs expression. Our data provide fundamental insights into aslncRNAs metabolism and open perspectives into the possible evolutionary contribution of RNAi in shaping the aslncRNAs transcriptome.
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http://dx.doi.org/10.26508/lsa.201900407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6713810PMC
October 2019

Bridging the gap between reference and real transcriptomes.

Genome Biol 2019 06 3;20(1):112. Epub 2019 Jun 3.

Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette, France.

Genetic, transcriptional, and post-transcriptional variations shape the transcriptome of individual cells, rendering establishing an exhaustive set of reference RNAs a complicated matter. Current reference transcriptomes, which are based on carefully curated transcripts, are lagging behind the extensive RNA variation revealed by massively parallel sequencing. Much may be missed by ignoring this unreferenced RNA diversity. There is plentiful evidence for non-reference transcripts with important phenotypic effects. Although reference transcriptomes are inestimable for gene expression analysis, they may turn limiting in important medical applications. We discuss computational strategies for retrieving hidden transcript diversity.
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http://dx.doi.org/10.1186/s13059-019-1710-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6545731PMC
June 2019

Transcription-dependent spreading of the Dal80 yeast GATA factor across the body of highly expressed genes.

PLoS Genet 2019 02 28;15(2):e1007999. Epub 2019 Feb 28.

Metabolism of Model Microorganisms, Labiris, Brussels, Belgium.

GATA transcription factors are highly conserved among eukaryotes and play roles in transcription of genes implicated in cancer progression and hematopoiesis. However, although their consensus binding sites have been well defined in vitro, the in vivo selectivity for recognition by GATA factors remains poorly characterized. Using ChIP-Seq, we identified the Dal80 GATA factor targets in yeast. Our data reveal Dal80 binding to a large set of promoters, sometimes independently of GATA sites, correlating with nitrogen- and/or Dal80-sensitive gene expression. Strikingly, Dal80 was also detected across the body of promoter-bound genes, correlating with high expression. Mechanistic single-gene experiments showed that Dal80 spreading across gene bodies requires active transcription. Consistently, Dal80 co-immunoprecipitated with the initiating and post-initiation forms of RNA Polymerase II. Our work suggests that GATA factors could play dual, synergistic roles during transcription initiation and post-initiation steps, promoting efficient remodeling of the gene expression program in response to environmental changes.
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http://dx.doi.org/10.1371/journal.pgen.1007999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6413948PMC
February 2019

The anti-cancer drug 5-fluorouracil affects cell cycle regulators and potential regulatory long non-coding RNAs in yeast.

RNA Biol 2019 06 20;16(6):727-741. Epub 2019 Mar 20.

a Univ Rennes , Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)- UMR_S 1085 , Rennes , France.

5-fluorouracil (5-FU) was isolated as an inhibitor of thymidylate synthase, which is important for DNA synthesis. The drug was later found to also affect the conserved 3'-5' exoribonuclease EXOSC10/Rrp6, a catalytic subunit of the RNA exosome that degrades and processes protein-coding and non-coding transcripts. Work on 5-FU's cytotoxicity has been focused on mRNAs and non-coding transcripts such as rRNAs, tRNAs and snoRNAs. However, the effect of 5-FU on long non-coding RNAs (lncRNAs), which include regulatory transcripts important for cell growth and differentiation, is poorly understood. RNA profiling of synchronized 5-FU treated yeast cells and protein assays reveal that the drug specifically inhibits a set of cell cycle regulated genes involved in mitotic division, by decreasing levels of the paralogous Swi5 and Ace2 transcriptional activators. We also observe widespread accumulation of different lncRNA types in treated cells, which are typically present at high levels in a strain lacking EXOSC10/Rrp6. 5-FU responsive lncRNAs include potential regulatory antisense transcripts that form double-stranded RNAs (dsRNAs) with overlapping sense mRNAs. Some of these transcripts encode proteins important for cell growth and division, such as the transcription factor Ace2, and the RNA exosome subunit EXOSC6/Mtr3. In addition to revealing a transcriptional effect of 5-FU action via DNA binding regulators involved in cell cycle progression, our results have implications for the function of putative regulatory lncRNAs in 5-FU mediated cytotoxicity. The data raise the intriguing possibility that the drug deregulates lncRNAs/dsRNAs involved in controlling eukaryotic cell division, thereby highlighting a new class of promising therapeutical targets.
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http://dx.doi.org/10.1080/15476286.2019.1581596DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6546400PMC
June 2019

Expanding heterochromatin reveals discrete subtelomeric domains delimited by chromatin landscape transitions.

Genome Res 2018 12 24;28(12):1867-1881. Epub 2018 Oct 24.

Institut Curie, PSL Research University, CNRS, UMR3664, F-75005 Paris, France.

The eukaryotic genome is divided into chromosomal domains of heterochromatin and euchromatin. Transcriptionally silent heterochromatin is found at subtelomeric regions, leading to the telomeric position effect (TPE) in yeast, fly, and human. Heterochromatin generally initiates and spreads from defined loci, and diverse mechanisms prevent the ectopic spread of heterochromatin into euchromatin. Here, we overexpressed the silencing factor Sir3 at varying levels in yeast and found that Sir3 spreads into extended silent domains (ESDs), eventually reaching saturation at subtelomeres. We observed the spread of Sir3 into subtelomeric domains associated with specific histone marks in wild-type cells, and stopping at zones of histone mark transitions including H3K79 trimethylation levels. Our study shows that the conserved H3K79 methyltransferase Dot1 is essential in restricting Sir3 spread beyond ESDs, thus ensuring viability upon overexpression of Sir3. Last, our analyses of published data demonstrate how ESDs unveil uncharacterized discrete domains isolating structural and functional subtelomeric features from the rest of the genome. Our work offers a new approach on how to separate subtelomeres from the core chromosome.
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http://dx.doi.org/10.1101/gr.236554.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6280759PMC
December 2018

Bases of antisense lncRNA-associated regulation of gene expression in fission yeast.

PLoS Genet 2018 07 5;14(7):e1007465. Epub 2018 Jul 5.

ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie,Paris, France.

Antisense (as)lncRNAs can regulate gene expression but the underlying mechanisms and the different cofactors involved remain unclear. Using Native Elongating Transcript sequencing, here we show that stabilization of antisense Exo2-sensitivite lncRNAs (XUTs) results in the attenuation, at the nascent transcription level, of a subset of highly expressed genes displaying prominent promoter-proximal nucleosome depletion and histone acetylation. Mechanistic investigations on the catalase gene ctt1 revealed that its induction following oxidative stress is impaired in Exo2-deficient cells, correlating with the accumulation of an asXUT. Interestingly, expression of this asXUT was also activated in wild-type cells upon oxidative stress, concomitant to ctt1 induction, indicating a potential attenuation feedback. This attenuation correlates with asXUT abundance, it is transcriptional, characterized by low RNAPII-ser5 phosphorylation, and it requires an histone deacetylase activity and the conserved Set2 histone methyltransferase. Finally, we identified Dicer as another RNA processing factor acting on ctt1 induction, but independently of Exo2. We propose that asXUTs could modulate the expression of their paired-sense genes when it exceeds a critical threshold, using a conserved mechanism independent of RNAi.
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http://dx.doi.org/10.1371/journal.pgen.1007465DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6049938PMC
July 2018

Correction to: Stage-dependent piRNAs in chicken implicated roles in modulating male germ cell development.

BMC Genomics 2018 06 19;19(1):480. Epub 2018 Jun 19.

Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan.

Following publication of the original article [1], the authors reported that one of the authors' names is spelled incorrectly.
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http://dx.doi.org/10.1186/s12864-018-4863-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6006743PMC
June 2018

Stage-dependent piRNAs in chicken implicated roles in modulating male germ cell development.

BMC Genomics 2018 Jun 1;19(1):425. Epub 2018 Jun 1.

Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan.

Background: The PIWI/piRNA pathway is a conserved machinery important for germ cell development and fertility. This piRNA-guided molecular machinery is best known for repressing derepressed transposable elements (TE) during epigenomic reprogramming. The extent to which piRNAs are involved in modulating transcripts beyond TEs still need to be clarified, and it may be a stage-dependent event. We chose chicken germline as a study model because of the significantly lower TE complexity in the chicken genome compared to mammalian species.

Results: We generated high-confidence piRNA candidates in various stages across chicken germline development by 3'-end-methylation-enriched small RNA sequencing and in-house bioinformatics analysis. We observed a significant developmental stage-dependent loss of TE association and a shifting of the ping-pong cycle signatures. Moreover, the stage-dependent reciprocal abundance of LINE retrotransposons, CR1-C, and its associated piRNAs implicated the developmental stage-dependent role of piRNA machinery. The stage dependency of piRNA expression and its potential functions can be better addressed by analyzing the piRNA precursors/clusters. Interestingly, the new piRNA clusters identified from embryonic chicken testes revealed evolutionary conservation between chickens and mammals, which was previously thought to not exist.

Conclusions: In this report, we provided an original chicken RNA resource and proposed an analytical methodology that can be used to investigate stage-dependent changes in piRNA compositions and their potential roles in TE regulation and beyond, and also revealed possible conserved functions of piRNAs in developing germ cells.
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http://dx.doi.org/10.1186/s12864-018-4820-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5984780PMC
June 2018

Histone deacetylation promotes transcriptional silencing at facultative heterochromatin.

Nucleic Acids Res 2018 06;46(11):5426-5440

Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.

It is important to accurately regulate the expression of genes involved in development and environmental response. In the fission yeast Schizosaccharomyces pombe, meiotic genes are tightly repressed during vegetative growth. Despite being embedded in heterochromatin these genes are transcribed and believed to be repressed primarily at the level of RNA. However, the mechanism of facultative heterochromatin formation and the interplay with transcription regulation is not understood. We show genome-wide that HDAC-dependent histone deacetylation is a major determinant in transcriptional silencing of facultative heterochromatin domains. Indeed, mutation of class I/II HDACs leads to increased transcription of meiotic genes and accumulation of their mRNAs. Mechanistic dissection of the pho1 gene where, in response to phosphate, transient facultative heterochromatin is established by overlapping lncRNA transcription shows that the Clr3 HDAC contributes to silencing independently of SHREC, but in an lncRNA-dependent manner. We propose that HDACs promote facultative heterochromatin by establishing alternative transcriptional silencing.
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http://dx.doi.org/10.1093/nar/gky232DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6009587PMC
June 2018

Diversification of human plasmacytoid predendritic cells in response to a single stimulus.

Nat Immunol 2018 Jan 4;19(1):63-75. Epub 2017 Dec 4.

Institut Curie, Centre de Recherche, PSL Research University, Paris, France.

Innate immune cells adjust to microbial and inflammatory stimuli through a process termed environmental plasticity, which links a given individual stimulus to a unique activated state. Here, we report that activation of human plasmacytoid predendritic cells (pDCs) with a single microbial or cytokine stimulus triggers cell diversification into three stable subpopulations (P1-P3). P1-pDCs (PD-L1CD80) displayed a plasmacytoid morphology and specialization for type I interferon production. P3-pDCs (PD-L1CD80) adopted a dendritic morphology and adaptive immune functions. P2-pDCs (PD-L1CD80) displayed both innate and adaptive functions. Each subpopulation expressed a specific coding- and long-noncoding-RNA signature and was stable after secondary stimulation. P1-pDCs were detected in samples from patients with lupus or psoriasis. pDC diversification was independent of cell divisions or preexisting heterogeneity within steady-state pDCs but was controlled by a TNF autocrine and/or paracrine communication loop. Our findings reveal a novel mechanism for diversity and division of labor in innate immune cells.
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http://dx.doi.org/10.1038/s41590-017-0012-zDOI Listing
January 2018

Native elongating transcript sequencing reveals global anti-correlation between sense and antisense nascent transcription in fission yeast.

RNA 2018 02 7;24(2):196-208. Epub 2017 Nov 7.

ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France.

Antisense transcription can regulate sense gene expression. However, previous annotations of antisense transcription units have been based on detection of mature antisense long noncoding (aslnc)RNAs by RNA-seq and/or microarrays, only giving a partial view of the antisense transcription landscape and incomplete molecular bases for antisense-mediated regulation. Here, we used native elongating transcript sequencing to map genome-wide nascent antisense transcription in fission yeast. Strikingly, antisense transcription was detected for most protein-coding genes, correlating with low sense transcription, especially when overlapping the mRNA start site. RNA profiling revealed that the resulting aslncRNAs mainly correspond to cryptic Xrn1/Exo2-sensitive transcripts (XUTs). ChIP-seq analyses showed that antisense (as)XUT's expression is associated with specific histone modification patterns. Finally, we showed that asXUTs are controlled by the histone chaperone Spt6 and respond to meiosis induction, in both cases anti-correlating with levels of the paired-sense mRNAs, supporting physiological significance to antisense-mediated gene attenuation. Our work highlights that antisense transcription is much more extended than anticipated and might constitute an additional nonpromoter determinant of gene regulation complexity.
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http://dx.doi.org/10.1261/rna.063446.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769747PMC
February 2018

History, Discovery, and Classification of lncRNAs.

Adv Exp Med Biol 2017 ;1008:1-46

ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University and Université Pierre et Marie Curie, Paris, France.

The RNA World Hypothesis suggests that prebiotic life revolved around RNA instead of DNA and proteins. Although modern cells have changed significantly in 4 billion years, RNA has maintained its central role in cell biology. Since the discovery of DNA at the end of the nineteenth century, RNA has been extensively studied. Many discoveries such as housekeeping RNAs (rRNA, tRNA, etc.) supported the messenger RNA model that is the pillar of the central dogma of molecular biology, which was first devised in the late 1950s. Thirty years later, the first regulatory non-coding RNAs (ncRNAs) were initially identified in bacteria and then in most eukaryotic organisms. A few long ncRNAs (lncRNAs) such as H19 and Xist were characterized in the pre-genomic era but remained exceptions until the early 2000s. Indeed, when the sequence of the human genome was published in 2001, studies showed that only about 1.2% encodes proteins, the rest being deemed "non-coding." It was later shown that the genome is pervasively transcribed into many ncRNAs, but their functionality remained controversial. Since then, regulatory lncRNAs have been characterized in many species and were shown to be involved in processes such as development and pathologies, revealing a new layer of regulation in eukaryotic cells. This newly found focus on lncRNAs, together with the advent of high-throughput sequencing, was accompanied by the rapid discovery of many novel transcripts which were further characterized and classified according to specific transcript traits.In this review, we will discuss the many discoveries that led to the study of lncRNAs, from Friedrich Miescher's "nuclein" in 1869 to the elucidation of the human genome and transcriptome in the early 2000s. We will then focus on the biological relevance during lncRNA evolution and describe their basic features as genes and transcripts. Finally, we will present a non-exhaustive catalogue of lncRNA classes, thus illustrating the vast complexity of eukaryotic transcriptomes.
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http://dx.doi.org/10.1007/978-981-10-5203-3_1DOI Listing
January 2018

LncRNAs, lost in translation or licence to regulate?

Curr Genet 2017 Feb 26;63(1):29-33. Epub 2016 May 26.

ncRNA, Epigenetic and Genome Fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248, Paris Cedex 05, France.

Over the last decade, advances in transcriptomics have revealed that the pervasive transcription of eukaryotic genomes produces plethora of long noncoding RNAs (lncRNAs), which are now recognized as major regulators of multiple cellular processes. Although they have been thought to lack any protein-coding potential, recent ribosome-profiling data indicate that lncRNAs can interact with the translation machinery, leading to the production of functional peptides in some cases. In this perspective, we have explored the idea that translation can be part of the fate of cytoplasmic lncRNAs, raising the possibility for them to work as bifunctional RNAs, endowed with dual coding and regulatory functions.
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http://dx.doi.org/10.1007/s00294-016-0615-1DOI Listing
February 2017

Prognostic value of a newly identified MALAT1 alternatively spliced transcript in breast cancer.

Br J Cancer 2016 06 12;114(12):1395-404. Epub 2016 May 12.

Department of Genetics, Unit of Pharmacogenetics, Institut Curie, 26 rue d'Ulm, Paris Cedex F-75248, France.

Background: Epigenetic deregulation is considered as a new hallmark of cancer. The long non-coding RNA MALAT1 has been implicated in several cancers; however, its role in breast cancer is still little known.

Methods: We used RT-PCR, in situ hybridisation, and RPPA methods to quantify (i) the full-length (FL) and an alternatively spliced variant (Δsv) of MALAT1, and (ii) a panel of transcripts and proteins involved in MALAT1 pathways, in a large series of breast tumours from patients with known clinical/pathological status and long-term outcome.

Results: MALAT1 was overexpressed in 14% (63/446) of the breast tumours. MALAT1-overexpressed tumour epithelial cells showed marked diffuse nuclear signals and numerous huge nuclear speckles. Screening of the dbEST database led to the identification of Δsv-MALAT1, a major alternatively spliced MALAT1 transcript, with a very different expression pattern compared with FL-MALAT1. This alternative Δsv-MALAT1 transcript was mainly underexpressed (18.8%) in our breast tumour series. Multivariate analysis showed that alternative Δsv-MALAT1 transcript is an independent prognostic factor. Δsv-MALAT1 expression was associated with alterations of the pre-mRNAs alternative splicing machinery, and of the Drosha-DGCR8 complex required for non-coding RNA biogenesis. Alternative Δsv-MALAT1 transcript expression was associated to YAP protein status and with an activation of the PI3K-AKT pathway.

Conclusions: Our results reveal a complex expression pattern of various MALAT1 transcript variants in breast tumours, and suggest that this pattern of expressions should be taken into account to evaluate MALAT1 as predictive biomarker and therapeutic target.
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http://dx.doi.org/10.1038/bjc.2016.123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4984455PMC
June 2016

Nonsense-Mediated Decay Restricts LncRNA Levels in Yeast Unless Blocked by Double-Stranded RNA Structure.

Mol Cell 2016 Feb 21;61(3):379-392. Epub 2016 Jan 21.

ncRNA, Epigenetic, and Genome Fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France. Electronic address:

Antisense long non-coding (aslnc)RNAs represent a substantial part of eukaryotic transcriptomes that are, in yeast, controlled by the Xrn1 exonuclease. Nonsense-Mediated Decay (NMD) destabilizes the Xrn1-sensitive aslncRNAs (XUT), but what determines their sensitivity remains unclear. We report that 3' single-stranded (3'-ss) extension mediates XUTs degradation by NMD, assisted by the Mtr4 and Dbp2 helicases. Single-gene investigation, genome-wide RNA analyses, and double-stranded (ds)RNA mapping revealed that 3'-ss extensions discriminate the NMD-targeted XUTs from stable lncRNAs. Ribosome profiling showed that XUT are translated, locking them for NMD activity. Interestingly, mutants of the Mtr4 and Dbp2 helicases accumulated XUTs, suggesting that dsRNA unwinding is a critical step for degradation. Indeed, expression of anticomplementary transcripts protects cryptic intergenic lncRNAs from NMD. Our results indicate that aslncRNAs form dsRNA that are only translated and targeted to NMD if dissociated by Mtr4 and Dbp2. We propose that NMD buffers genome expression by discarding pervasive regulatory transcripts.
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http://dx.doi.org/10.1016/j.molcel.2015.12.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4747904PMC
February 2016

A Dual Model for Prioritizing Cancer Mutations in the Non-coding Genome Based on Germline and Somatic Events.

PLoS Comput Biol 2015 Nov 20;11(11):e1004583. Epub 2015 Nov 20.

Institute for Integrative Biology of the Cell, CNRS, CEA, Université Paris-Sud, Gif-sur-Yvette, France.

We address here the issue of prioritizing non-coding mutations in the tumoral genome. To this aim, we created two independent computational models. The first (germline) model estimates purifying selection based on population SNP data. The second (somatic) model estimates tumor mutation density based on whole genome tumor sequencing. We show that each model reflects a different set of constraints acting either on the normal or tumor genome, and we identify the specific genome features that most contribute to these constraints. Importantly, we show that the somatic mutation model carries independent functional information that can be used to narrow down the non-coding regions that may be relevant to cancer progression. On this basis, we identify positions in non-coding RNAs and the non-coding parts of mRNAs that are both under purifying selection in the germline and protected from mutation in tumors, thus introducing a new strategy for future detection of cancer driver elements in the expressed non-coding genome.
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http://dx.doi.org/10.1371/journal.pcbi.1004583DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654583PMC
November 2015

Long Noncoding RNAs as New Architects in Cancer Epigenetics, Prognostic Biomarkers, and Potential Therapeutic Targets.

Biomed Res Int 2015 13;2015:320214. Epub 2015 Sep 13.

UMR 3244, Non-Coding RNA, Epigenetics and Genome Fluidity, Institute Curie, 75248 Paris, France.

Recent advances in genome-wide analysis have revealed that 66% of the genome is actively transcribed into noncoding RNAs (ncRNAs) while less than 2% of the sequences encode proteins. Among ncRNAs, high-resolution microarray and massively parallel sequencing technologies have identified long ncRNAs (>200 nucleotides) that lack coding protein function. LncRNAs abundance, nuclear location, and diversity allow them to create in association with protein interactome, a complex regulatory network orchestrating cellular phenotypic plasticity via modulation of all levels of protein-coding gene expression. Whereas lncRNAs biological functions and mechanisms of action are still not fully understood, accumulating data suggest that lncRNAs deregulation is pivotal in cancer initiation and progression and metastatic spread through various mechanisms, including epigenetic effectors, alternative splicing, and microRNA-like molecules. Mounting data suggest that several lncRNAs expression profiles in malignant tumors are associated with prognosis and they can be detected in biological fluids. In this review, we will briefly discuss characteristics and functions of lncRNAs, their role in carcinogenesis, and their potential usefulness as diagnosis and prognosis biomarkers and novel therapeutic targets.
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http://dx.doi.org/10.1155/2015/320214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4584070PMC
August 2016

VING: a software for visualization of deep sequencing signals.

BMC Res Notes 2015 Sep 7;8:419. Epub 2015 Sep 7.

ncRNA, Epigenetics and Genome Fluidity, Institut Curie, PSL Research University, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248, Paris Cedex 05, France.

Background: 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.

Results: We developed 'VING', a stand-alone R script that takes as input NGS mapping files and genome annotations to produce accurate snapshots of the NGS coverage signal for any specified genomic region. VING offers multiple viewing options, including strand-specific views and a special heatmap mode for representing multiple experiments in a single figure.

Conclusions: VING produces high-quality figures for NGS data representation in a genome region of interest. It is available at http://vm-gb.curie.fr/ving/. We also developed a Galaxy wrapper, available in the Galaxy tool shed with installation and usage instructions.
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http://dx.doi.org/10.1186/s13104-015-1404-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4562374PMC
September 2015

Cytoplasmic Control of Sense-Antisense mRNA Pairs.

Cell Rep 2015 Sep 3;12(11):1853-64. Epub 2015 Sep 3.

Sorbonne Universités, UPMC Paris 06, CNRS UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, 75005 Paris, France. Electronic address:

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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http://dx.doi.org/10.1016/j.celrep.2015.08.016DOI Listing
September 2015

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

Elife 2015 Jul 31;4. Epub 2015 Jul 31.

Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy.

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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http://dx.doi.org/10.7554/eLife.08942DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4541074PMC
July 2015

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

Reproduction 2015 Oct 9;150(4):245-56. Epub 2015 Jul 9.

Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, T

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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http://dx.doi.org/10.1530/REP-15-0031DOI Listing
October 2015

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

Noncoding RNA 2015 Jul 3;1(2):94-126. Epub 2015 Jul 3.

RNA, epigenetics and genome fluidity, Institut Curie, PSL Research University, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France.

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 ⁻ in mammalian and yeast cells. However, their functions remain poorly characterized. Here, we report the existence in of several lncRNAs within Y' subtelomeric regions. We have called them These belong to Cryptic Unstable Transcripts (CUTs) and Xrn1p-sensitive Unstable Transcripts (XUTs) family. 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 are distinct from and are mainly degraded by the general cytoplasmic and nuclear 5'- and 3'- RNA decay pathways in a transcription-dependent manner. accumulates preferentially during the G1/S transition and in C-terminal mutant but independently of Rap1p function in silencing. The accumulation of 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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http://dx.doi.org/10.3390/ncrna1020094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5932542PMC
July 2015

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

EMBO Rep 2015 Feb 19;16(2):221-31. Epub 2014 Dec 19.

Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy

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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http://dx.doi.org/10.15252/embr.201439458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4328749PMC
February 2015

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

PLoS One 2014 16;9(7):e102464. Epub 2014 Jul 16.

iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France; CNRS, FRE3377, Gif-sur-Yvette, France; Université Paris-Sud, FRE3377, Gif-sur-Yvette, France.

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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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0102464PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4100922PMC
November 2015