Publications by authors named "Didier Auboeuf"

61Publications

Intragenic recruitment of NF-κB drives splicing modifications upon activation by the oncogene Tax of HTLV-1.

Nat Commun 2020 06 16;11(1):3045. Epub 2020 Jun 16.

Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, 69007, Lyon, France.

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http://dx.doi.org/10.1038/s41467-020-16853-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7298006PMC
June 2020

Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces.

Authors:
Didier Auboeuf

Life (Basel) 2020 Jan 21;10(2). Epub 2020 Jan 21.

Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie, Site Jacques Monod, F-69007, Lyon, France.

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http://dx.doi.org/10.3390/life10020007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7175370PMC
January 2020

Characterizing the interplay between gene nucleotide composition bias and splicing.

Genome Biol 2019 11 29;20(1):259. Epub 2019 Nov 29.

Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France.

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http://dx.doi.org/10.1186/s13059-019-1869-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6883713PMC
November 2019

Interplay between coding and exonic splicing regulatory sequences.

Genome Res 2019 05 8;29(5):711-722. Epub 2019 Apr 8.

Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, F-69007, Lyon, France.

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http://genome.cshlp.org/lookup/doi/10.1101/gr.241315.118
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http://dx.doi.org/10.1101/gr.241315.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499313PMC
May 2019

The RNA helicase DDX17 controls the transcriptional activity of REST and the expression of proneural microRNAs in neuronal differentiation.

Nucleic Acids Res 2018 09;46(15):7686-7700

Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, INSERM U1210, CNRS UMR 5239, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France.

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http://dx.doi.org/10.1093/nar/gky545DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125624PMC
September 2018

Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data.

Sci Rep 2018 03 9;8(1):4307. Epub 2018 Mar 9.

Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622, Villeurbanne, EPI ERABLE - Inria Grenoble, Rhône-Alpes, France.

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http://dx.doi.org/10.1038/s41598-018-21770-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5844962PMC
March 2018

Alternative mRNA processing sites decrease genetic variability while increasing functional diversity.

Authors:
Didier Auboeuf

Transcription 2018 3;9(2):75-87. Epub 2017 Nov 3.

a Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell , 46 Allée d'Italie Site Jacques Monod, Lyon , France.

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http://dx.doi.org/10.1080/21541264.2017.1373891DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5834221PMC
November 2018

The RNA helicase DDX5 is a reprogramming roadblock.

Stem Cell Investig 2017 27;4:79. Epub 2017 Sep 27.

Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France.

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http://dx.doi.org/10.21037/sci.2017.09.04DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5639033PMC
September 2017

Genome evolution is driven by gene expression-generated biophysical constraints through RNA-directed genetic variation: A hypothesis.

Authors:
Didier Auboeuf

Bioessays 2017 10 8;39(10). Epub 2017 Sep 8.

Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Site Jacques Monod, Lyon, France.

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http://dx.doi.org/10.1002/bies.201700069DOI Listing
October 2017

Putative RNA-directed adaptive mutations in cancer evolution.

Authors:
Didier Auboeuf

Transcription 2016 Oct;7(5):164-187

Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France.

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http://dx.doi.org/10.1080/21541264.2016.1221491DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066521PMC
October 2016

The multiple functions of RNA helicases as drivers and regulators of gene expression.

Nat Rev Mol Cell Biol 2016 07 2;17(7):426-38. Epub 2016 Jun 2.

Université de Lyon, École Normale Supérieure de Lyon, Université Claude Bernard, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 5239, Institut National de la Santé et de la Recherche Médicale (INSERM) U1210, Laboratory of Biology and Modelling of the Cell, 46 allée d'Italie Site Jacques Monod, F-69007, Lyon, France.

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http://dx.doi.org/10.1038/nrm.2016.50DOI Listing
July 2016

The proto-oncogenic protein TAL1 controls TGF-β1 signaling through interaction with SMAD3.

Biochim Open 2016 Jun 14;2:69-78. Epub 2016 May 14.

Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France.

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https://linkinghub.elsevier.com/retrieve/pii/S22140085163000
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http://dx.doi.org/10.1016/j.biopen.2016.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5889486PMC
June 2016

Candidate gene prioritization with Endeavour.

Nucleic Acids Res 2016 07 30;44(W1):W117-21. Epub 2016 Apr 30.

Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics Department, KU Leuven, B-3001 Leuven, Belgium iMinds Future Health Department, KU Leuven, B-3001 Leuven, Belgium.

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http://dx.doi.org/10.1093/nar/gkw365DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987917PMC
July 2016

HTLV-1-infected CD4+ T-cells display alternative exon usages that culminate in adult T-cell leukemia.

Retrovirology 2014 Dec 18;11:119. Epub 2014 Dec 18.

Université de Lyon 1, CNRS UMR5239, Oncovirologie et Biothérapies, Laboratoire de Biologie Moléculaire de la Cellule, Faculté de Médecine Lyon Sud, Pierre Bénite, France.

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http://dx.doi.org/10.1186/s12977-014-0119-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4293115PMC
December 2014

RNA helicases DDX5 and DDX17 dynamically orchestrate transcription, miRNA, and splicing programs in cell differentiation.

Cell Rep 2014 Jun 6;7(6):1900-13. Epub 2014 Jun 6.

INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.05.010DOI Listing
June 2014

A recently evolved class of alternative 3'-terminal exons involved in cell cycle regulation by topoisomerase inhibitors.

Nat Commun 2014 Feb 28;5:3395. Epub 2014 Feb 28.

1] INSERM U1052, 28 rue Laennec, Lyon F-69000, France [2] CNRS UMR5286, 28 rue Laennec, Lyon F-69000, France [3] Centre Léon Bérard, 28 rue Laennec, Lyon F-69000, France [4] Centre de Recherche en Cancérologie de Lyon, 28 rue Laennec, Lyon F-69000, France [5] Université de Lyon, Lyon 69007, France.

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http://dx.doi.org/10.1038/ncomms4395DOI Listing
February 2014

The Ddx5 and Ddx17 RNA helicases are cornerstones in the complex regulatory array of steroid hormone-signaling pathways.

Nucleic Acids Res 2014 Feb 25;42(4):2197-207. Epub 2013 Nov 25.

Université de Paris Diderot-Paris 7, F-75013 Paris, France, Inserm U1052, F-69008 Lyon, France, CNRS UMR5286, F-69008 Lyon, France, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France and Université de Lyon 1, F-69100 Villeurbanne, France.

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http://dx.doi.org/10.1093/nar/gkt1216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3936752PMC
February 2014

The RNA helicase DDX5/p68 is a key factor promoting c-fos expression at different levels from transcription to mRNA export.

Nucleic Acids Res 2013 Jan 11;41(1):554-64. Epub 2012 Nov 11.

Université de Lyon, Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Centre Léon Bérard, 28 Rue Laennec, F-69008 Lyon, France.

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http://nar.oxfordjournals.org/content/early/2012/11/10/nar.g
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gks1046
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http://dx.doi.org/10.1093/nar/gks1046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3592390PMC
January 2013

Splicing switch of an epigenetic regulator by RNA helicases promotes tumor-cell invasiveness.

Nat Struct Mol Biol 2012 Nov 30;19(11):1139-46. Epub 2012 Sep 30.

Institut National de la Santé et de la Recherche Médicale, U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.

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http://dx.doi.org/10.1038/nsmb.2390DOI Listing
November 2012

Alternative splicing and cancer.

J Nucleic Acids 2012 20;2012:363809. Epub 2012 May 20.

Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, 69008 Lyon, France.

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http://dx.doi.org/10.1155/2012/363809DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3364008PMC
August 2012

Splicing programs and cancer.

J Nucleic Acids 2012 24;2012:269570. Epub 2011 Oct 24.

Université de Lyon, 28 rue Laënnec, 69008 Lyon, France.

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http://dx.doi.org/10.1155/2012/269570DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202119PMC
August 2012

Analysis of co-transcriptional RNA processing by RNA-ChIP assay.

Methods Mol Biol 2012 ;809:563-77

Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.

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http://dx.doi.org/10.1007/978-1-61779-376-9_36DOI Listing
March 2012

Cotranscriptional exon skipping in the genotoxic stress response.

Nat Struct Mol Biol 2010 Nov 24;17(11):1358-66. Epub 2010 Oct 24.

Institut National de Santé et de Recherche Médicale U590, Centre Léon Bérard, Lyon, France.

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http://dx.doi.org/10.1038/nsmb.1912DOI Listing
November 2010

Alternative splicing and breast cancer.

RNA Biol 2010 Jul-Aug;7(4):403-11. Epub 2010 Jul 1.

Institut National de la Santé et de la Recherche Médicale (INSERM) U590, Centre Léon Bérard, Lyon, France.

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http://dx.doi.org/10.4161/rna.7.4.12152DOI Listing
January 2011

Estrogen regulation and physiopathologic significance of alternative promoters in breast cancer.

Cancer Res 2010 May 20;70(9):3760-70. Epub 2010 Apr 20.

Institut National de la Sante et de la Recherche Medicale, U590, Centre Léon Bérard, Lyon, France.

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http://dx.doi.org/10.1158/0008-5472.CAN-09-3988DOI Listing
May 2010

Splicing factor and exon profiling across human tissues.

Nucleic Acids Res 2010 May 27;38(9):2825-38. Epub 2010 Jan 27.

GenoSplice technology, Centre Hayem, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010, Paris, France.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkq008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875023PMC
May 2010

Widespread estrogen-dependent repression of micrornas involved in breast tumor cell growth.

Cancer Res 2009 Nov 13;69(21):8332-40. Epub 2009 Oct 13.

Institut National de la Sante et de la Recherche Medicale U563, Institut Claudius Regaud, and Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan, Toulouse, France.

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http://dx.doi.org/10.1158/0008-5472.CAN-09-2206DOI Listing
November 2009

Coupled alteration of transcription and splicing by a single oncogene: boosting the effect on cyclin D1 activity.

Cell Cycle 2008 Aug 17;7(15):2299-305. Epub 2008 Jun 17.

INSERM U685, Institut Universitaire d'Hématologie, Paris, France.

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http://dx.doi.org/10.4161/cc.6445DOI Listing
August 2008

Cotranscriptional splicing potentiates the mRNA production from a subset of estradiol-stimulated genes.

Mol Cell Biol 2008 Sep 21;28(18):5811-24. Epub 2008 Jul 21.

INSERM U685, Institut Universitaire d'Hematologie, Hopital Saint-Louis, 1 Avenue Claude Vellefaux, 75010 Paris, France.

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http://dx.doi.org/10.1128/MCB.02231-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2546936PMC
September 2008

Alteration of cyclin D1 transcript elongation by a mutated transcription factor up-regulates the oncogenic D1b splice isoform in cancer.

Proc Natl Acad Sci U S A 2008 Apr 14;105(16):6004-9. Epub 2008 Apr 14.

Institut National de la Santé et de la Recherche Médicale, Unité 685, Institut Universitaire d'Hématologie, 1, Avenue Claude Vellefaux, 75010 Paris, France.

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http://dx.doi.org/10.1073/pnas.0710748105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2329709PMC
April 2008

Regulation of H-ras splice variant expression by cross talk between the p53 and nonsense-mediated mRNA decay pathways.

Mol Cell Biol 2007 Oct 20;27(20):7315-33. Epub 2007 Aug 20.

INSERM U685, Equipe AVENIR, Hopital Saint-Louis, 1 Avenue Claude Vellefaux, Paris 75010, France.

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http://dx.doi.org/10.1128/MCB.00272-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168895PMC
October 2007

Coregulators: transducing signal from transcription to alternative splicing.

Trends Endocrinol Metab 2007 Apr 21;18(3):122-9. Epub 2007 Feb 21.

INSERM, U685/AVENIR, Centre G. Hayem, Hôpital Saint Louis, 1 Avenue Claude Vellefaux, 75010 Paris, France.

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http://dx.doi.org/10.1016/j.tem.2007.02.003DOI Listing
April 2007

ASEtrap: a biological method for speeding up the exploration of spliceomes.

Genome Res 2006 Jun 8;16(6):776-86. Epub 2006 May 8.

Genoscope-Centre National de Séquençage and Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-8030, 91000 Evry, France.

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http://dx.doi.org/10.1101/gr.5063306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1479860PMC
June 2006

FAST DB: a website resource for the study of the expression regulation of human gene products.

Nucleic Acids Res 2005 28;33(13):4276-84. Epub 2005 Jul 28.

INSERM U685/AVENIR, Centre G. Hayem, Institut Universitaire d'Hématologiem, Hôpital Saint Louis, 1 Avenue Claude Vellefaux, 75010 Paris, France.

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http://dx.doi.org/10.1093/nar/gki738DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1181862PMC
August 2005

Steroid hormone receptor coactivation and alternative RNA splicing by U2AF65-related proteins CAPERalpha and CAPERbeta.

Mol Cell 2005 Feb;17(3):429-39

Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/j.molcel.2004.12.025DOI Listing
February 2005

Differential recruitment of nuclear receptor coactivators may determine alternative RNA splice site choice in target genes.

Proc Natl Acad Sci U S A 2004 Feb;101(8):2270-4

Department of Molecular and Cellular Biology, Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC356940PMC
http://dx.doi.org/10.1073/pnas.0308133100DOI Listing
February 2004

CoAA, a nuclear receptor coactivator protein at the interface of transcriptional coactivation and RNA splicing.

Mol Cell Biol 2004 Jan;24(1):442-53

Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC303353PMC
http://dx.doi.org/10.1128/mcb.24.1.442-453.2004DOI Listing
January 2004

Coordinate regulation of transcription and splicing by steroid receptor coregulators.

Science 2002 Oct;298(5592):416-9

Department of Molecular and Cellular Biology, Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1073734
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http://dx.doi.org/10.1126/science.1073734DOI Listing
October 2002

Regulation of alternative splicing by the ATP-dependent DEAD-box RNA helicase p72.

Mol Cell Biol 2002 Aug;22(16):5698-707

Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC133985PMC
http://dx.doi.org/10.1128/mcb.22.16.5698-5707.2002DOI Listing
August 2002

Coactivator/corepressor ratios modulate PR-mediated transcription by the selective receptor modulator RU486.

Proc Natl Acad Sci U S A 2002 Jun 4;99(12):7940-4. Epub 2002 Jun 4.

Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

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http://dx.doi.org/10.1073/pnas.122225699DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC122999PMC
June 2002