Robert Lab | Publications

PUBLICATIONS

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The complete list of publications from François Robert can also be found on PubMed here.

Robert F, Jeronimo C (2023) Transcription-coupled nucleosome assembly. Trends Biochem Sci. 2023 Nov;48(11):978-992. doi: 10.1016/j.tibs.2023.08.003. Epub 2023 Aug 30. PMID: 37657993

Robert F (2023) When the +1 nucleosome gets in the way, TFIIH fails but does not fall. Mol Cell. 2023 Jun 1;83(11):1763-1764. doi: 10.1016/j.molcel.2023.05.003.

González L, Kolbin D, Trahan C, Jeronimo C, Robert F, Oeffinger M, Bloom K, Michnick SW (2023) Adaptive partitioning of a gene locus to the nuclear envelope in Saccharomyces cerevisiae is driven by polymer-polymer phase separation. Nat Commun. Feb 28;14(1):1135. doi: 10.1038/s41467-023-36391-6.

Neumann H, Jeronimo C, Lucier JF, Pasquier E, Robert F, Wellinger RJ, Gaudreau L (2023) The Histone Variant H2A.Z C-Terminal Domain Has Locus-Specific Differential Effects on H2A.Z Occupancy and Nucleosome Localization. Microbiol Spectr. Feb 23;11(2):e0255022. doi: 10.1128/spectrum.02550-22.

Jeronimo C, Robert F (2022) The histone chaperone FACT: a guardian of chromatin structure integrity. Transcription. Apr 29;1-23. doi: 10.1080/21541264.2022.2069995.

Lambert É, Puwakdandawa K, Tao YF, Robert F. (2021) From structure to molecular condensates: emerging mechanisms for Mediator function. FEBS J. 2021 Oct 26. doi: 10.1111/febs.16250.

Jeronimo C, Angel A, Nguyen VQ, Kim JM, Poitras C, Lambert E, Collin P, Mellor J, Wu C, Robert F. (2021) FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner. Mol Cell. 2021 Sep 2;81(17):3542-3559.e11.

Saleh MM, Jeronimo C, Robert F, Zentner GE (2021) Connection of core and tail Mediator modules restrains transcription from TFIID-dependent promoters. PLoS Genet. 2021 Aug 12;17(8):e1009529.

Eyboulet F, Jeronimo C, Côté J, Robert F (2020) The deubiquitylase Ubp15 couples transcription to mRNA export. Elife. 2020 Nov 23;9:e61264.

Jeronimo C, Poitras C, Robert F. (2019) Histone Recycling by FACT and Spt6 during Transcription Prevents the Scrambling of Histone Modifications. Cell Rep. 2019 Jul 30;28(5):1206-1218.

Collin P, Jeronimo C, Poitras C, Robert F. (2019) RNA Polymerase II CTD Tyrosine 1 Is Required for Efficient Termination by the Nrd1-Nab3-Sen1 Pathway. Mol Cell. 2019 Feb 21;73(4):655-669.

Robert F. Bidirectional terminators: an underestimated aspect of gene regulation. Curr Genet. 2018 Apr;64(2):389-391.

Robert F. Spt6 Gets in the Way of Polycomb to Promote ESC Pluripotency. Mol Cell. 2017 Oct 19;68(2):263-264.

Jeronimo C, Robert F. The Mediator Complex: At the Nexus of RNA Polymerase II Transcription. Trends Cell Biol. 2017 Oct;27(10):765-783.

Uwimana N, Collin P, Jeronimo C, Haibe-Kains B, Robert F. Bidirectional terminators in Saccharomyces cerevisiae prevent cryptic transcription from invading neighboring genes. Nucleic Acids Res. 2017 Jun 20;45(11):6417-6426.

Jeronimo C, Robert F. A Spiking Strategy for ChIP-chip Data Normalization in S. cerevisiae. Methods Mol Biol. 2017;1528:211-227.

Steunou AL, Cramet M, Rossetto D, Aristizabal MJ, Lacoste N, Drouin S, Côté V, Paquet E, Utley RT, Krogan N, Robert F, Kobor MS, Côté J. Combined Action of Histone Reader Modules Regulates NuA4 Local Acetyltransferase Function but Not Its Recruitment on the Genome. Mol Cell Biol. 2016 Oct 28;36(22):2768-2781.

Jeronimo C, Langelier MF, Bataille AR, Pascal JM, Pugh BF, Robert F. Tail and Kinase Modules Differently Regulate Core Mediator Recruitment and Function In Vivo. Mol Cell. 2016 Nov 3;64(3):455-466.

Botezatu L, Michel LC, Helness A, Vadnais C, Makishima H, Hönes JM, Robert F, Vassen L, Thivakaran A, Al-Matary Y, Lams RF, Schütte J, Giebel B, Görgens A, Heuser M, Medyouf H, Maciejewski J, Dührsen U, Möröy T, Khandanpour C. Epigenetic therapy as a novel approach for GFI136N-associated murine/human AML. Exp Hematol. 2016 Aug;44(8):713-726.e14.

Fraszczak J, Helness A, Chen R, Vadnais C, Robert F, Khandanpour C, Möröy T. Threshold Levels of Gfi1 Maintain E2A Activity for B Cell Commitment via Repression of Id1. PLoS One. 2016 Jul 28;11(7):e0160344.

Jeronimo C, Collin P, Robert F. The RNA Polymerase II CTD: The Increasing Complexity of a Low-Complexity Protein Domain. J Mol Biol. 2016 Jun 19;428(12):2607-2622.

Gaudreau MC, Grapton D, Helness A, Vadnais C, Fraszczak J, Shooshtarizadeh P, Wilhelm B, Robert F, Heyd F, Möröy T. Heterogeneous Nuclear Ribonucleoprotein L is required for the survival and functional integrity of murine hematopoietic stem cells. Sci Rep. 2016 Jun 7;6:27379.

Hönes JM, Botezatu L, Helness A, Vadnais C, Vassen L, Robert F, Hergenhan SM, Thivakaran A, Schütte J, Al-Matary YS, Lams RF, Fraszscak J, Makishima H, Radivoyevitch T, Przychodzen B, da Conceição Castro SV, Görgens A, Giebel B, Klein-Hitpass L, Lennartz K, Heuser M, Thiede C, Ehninger G, Dührsen U, Maciejewski JP, Möröy T, Khandanpour C. GFI1 as a novel prognostic and therapeutic factor for AML/MDS. Leukemia. 2016 Jun;30(6):1237-45.

Jeronimo C, Robert F. Histone chaperones FACT and Spt6 prevent histone variants from turning into histone deviants. Bioessays. 2016 May;38(5):420-6.

Jeronimo C, Watanabe S, Kaplan CD, Peterson CL, Robert F. The Histone Chaperones FACT and Spt6 Restrict H2A.Z from Intragenic Locations. Mol Cell. 2015 Jun 18;58(6):1113-23.

Cheng X, Auger A, Altaf M, Drouin S, Paquet E, Utley RT, Robert F, Côté J. Eaf1 Links the NuA4 Histone Acetyltransferase Complex to Htz1 Incorporation and Regulation of Purine Biosynthesis. Eukaryot Cell. 2015 Jun;14(6):535-44.

Burugula BB, Jeronimo C, Pathak R, Jones JW, Robert F, Govind CK. Histone deacetylases and phosphorylated polymerase II C-terminal domain recruit Spt6 for cotranscriptional histone reassembly. Mol Cell Biol. 2014 Nov 15;34(22):4115-29.

Gasmi N, Jacques PE, Klimova N, Guo X, Ricciardi A, Robert F, Turcotte B. The switch from fermentation to respiration in Saccharomyces cerevisiae is regulated by the Ert1 transcriptional activator/repressor. Genetics. 2014 Oct;198(2):547-60.

Shahbabian K, Jeronimo C, Forget A, Robert F, Chartrand P. Co-transcriptional recruitment of Puf6 by She2 couples translational repression to mRNA localization. Nucleic Acids Res. 2014 Jul;42(13):8692-704.

Coulombe C, Poitras C, Nordell-Markovits A, Brunelle M, Lavoie MA, Robert F, Jacques PÉ. VAP: a versatile aggregate profiler for efficient genome-wide data representation and discovery. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W485-93.

Jeronimo C, Robert F. Kin28 regulates the transient association of Mediator with core promoters. Nat Struct Mol Biol. 2014 May;21(5):449-55.

Praktiknjo SD, Llamas B, Scott-Boyer MP, Picard S, Robert F, Langlais D, Haibe-Kains B, Faubert D, Silversides DW, Deschepper CF. Novel effects of chromosome Y on cardiac regulation, chromatin remodeling, and neonatal programming in male mice. Endocrinology. 2013 Dec;154(12):4746-56.

Jeronimo C, Bataille AR, Robert F. The writers, readers, and functions of the RNA polymerase II C-terminal domain code. Chem Rev. 2013 Nov 13;113(11):8491-522.

Woo S, Zhang X, Sauteraud R, Robert F, Gottardo R. PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data. Bioinformatics. 2013 Aug 15;29(16):2049-50.

Sansó M, Lee KM, Viladevall L, Jacques PÉ, Pagé V, Nagy S, Racine A, St Amour CV, Zhang C, Shokat KM, Schwer B, Robert F, Fisher RP, Tanny JC. A positive feedback loop links opposing functions of P-TEFb/Cdk9 and histone H2B ubiquitylation to regulate transcript elongation in fission yeast. PLoS Genet. 2012;8(8):e1002822.

Soontorngun N, Baramee S, Tangsombatvichit C, Thepnok P, Cheevadhanarak S, Robert F, Turcotte B. Genome-wide location analysis reveals an important overlap between the targets of the yeast transcriptional regulators Rds2 and Adr1. Biochem Biophys Res Commun. 2012 Jul 13;423(4):632-7.

Bataille AR, Jeronimo C, Jacques PÉ, Laramée L, Fortin MÈ, Forest A, Bergeron M, Hanes SD, Robert F. A universal RNA polymerase II CTD cycle is orchestrated by complex interplays between kinase, phosphatase, and isomerase enzymes along genes. Mol Cell. 2012 Jan 27;45(2):158-70.

Poschmann J, Drouin S, Jacques PE, El Fadili K, Newmarch M, Robert F, Ramotar D. The peptidyl prolyl isomerase Rrd1 regulates the elongation of RNA polymerase II during transcriptional stresses. PLoS One. 2011;6(8):e23159.

Ivanovska I, Jacques PÉ, Rando OJ, Robert F, Winston F. Control of chromatin structure by spt6: different consequences in coding and regulatory regions. Mol Cell Biol. 2011 Feb;31(3):531-41.

Gonsalves SE, Moses AM, Razak Z, Robert F, Westwood JT. Whole-genome analysis reveals that active heat shock factor binding sites are mostly associated with non-heat shock genes in Drosophila melanogaster. PLoS One. 2011 Jan 14;6(1):e15934.

Drouin S, Laramée L, Jacques PÉ, Forest A, Bergeron M, Robert F. DSIF and RNA polymerase II CTD phosphorylation coordinate the recruitment of Rpd3S to actively transcribed genes. PLoS Genet. 2010 Oct 28;6(10):e1001173.

Hardy S, Robert F. Random deposition of histone variants: A cellular mistake or a novel regulatory mechanism? Epigenetics. 2010 Jul 1;5(5):368-72.

Szilard RK, Jacques PE, Laramée L, Cheng B, Galicia S, Bataille AR, Yeung M, Mendez M, Bergeron M, Robert F, Durocher D. Systematic identification of fragile sites via genome-wide location analysis of gamma-H2AX. Nat Struct Mol Biol. 2010 Mar;17(3):299-305.

Turcotte B, Liang XB, Robert F, Soontorngun N. Transcriptional regulation of nonfermentable carbon utilization in budding yeast. FEMS Yeast Res. 2010 Feb;10(1):2-13.

Hardy S, Jacques PE, Gévry N, Forest A, Fortin ME, Laflamme L, Gaudreau L, Robert F. The euchromatic and heterochromatic landscapes are shaped by antagonizing effects of transcription on H2A.Z deposition. PLoS Genet. 2009 Oct;5(10):e1000687.

Ghazal G, Gagnon J, Jacques PE, Landry JR, Robert F, Elela SA. Yeast RNase III triggers polyadenylation-independent transcription termination. Mol Cell. 2009 Oct 9;36(1):99-109.

Gévry N, Hardy S, Jacques PE, Laflamme L, Svotelis A, Robert F, Gaudreau L. Histone H2A.Z is essential for estrogen receptor signaling. Genes Dev. 2009 Jul 1;23(13):1522-33.

Bataille AR, Robert F. Profiling genome-wide histone modifications and variants by ChIP-chip on tiling microarrays in S. cerevisiae. Methods Mol Biol. 2009;543:267-79.

Truscott M, Harada R, Vadnais C, Robert F, Nepveu A. p110 CUX1 cooperates with E2F transcription factors in the transcriptional activation of cell cycle-regulated genes. Mol Cell Biol. 2008 May;28(10):3127-38.

Znaidi S, Weber S, Al-Abdin OZ, Bomme P, Saidane S, Drouin S, Lemieux S, De Deken X, Robert F, Raymond M. Genomewide location analysis of Candida albicans Upc2p, a regulator of sterol metabolism and azole drug resistance. Eukaryot Cell. 2008 May;7(5):836-47.

Harada R, Vadnais C, Sansregret L, Leduy L, Bérubé G, Robert F, Nepveu A. Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes. Nucleic Acids Res. 2008 Jan;36(1):189-202.

Soontorngun N, Larochelle M, Drouin S, Robert F, Turcotte B. Regulation of gluconeogenesis in Saccharomyces cerevisiae is mediated by activator and repressor functions of Rds2. Mol Cell Biol. 2007 Nov;27(22):7895-905.

Rufiange A, Jacques PE, Bhat W, Robert F, Nourani A. Genome-wide replication-independent histone H3 exchange occurs predominantly at promoters and implicates H3 K56 acetylation and Asf1. Mol Cell. 2007 Aug 3;27(3):393-405.

Sonoda J, Laganière J, Mehl IR, Barish GD, Chong LW, Li X, Scheffler IE, Mock DC, Bataille AR, Robert F, Lee CH, Giguère V, Evans RM. Nuclear receptor ERR alpha and coactivator PGC-1 beta are effectors of IFN-gamma-induced host defense. Genes Dev. 2007 Aug 1;21(15):1909-20.

Ferretti V, Poitras C, Bergeron D, Coulombe B, Robert F, Blanchette M. PReMod: a database of genome-wide mammalian cis-regulatory module predictions. Nucleic Acids Res. 2007 Jan;35(Database issue):D122-6.

Larochelle M, Drouin S, Robert F, Turcotte B. Oxidative stress-activated zinc cluster protein Stb5 has dual activator/repressor functions required for pentose phosphate pathway regulation and NADPH production. Mol Cell Biol. 2006 Sep;26(17):6690-701.

Blanchette M, Bataille AR, Chen X, Poitras C, Laganière J, Lefèbvre C, Deblois G, Giguère V, Ferretti V, Bergeron D, Coulombe B, Robert F. Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res. 2006 May;16(5):656-68.

Nourani A, Robert F, Winston F. Evidence that Spt2/Sin1, an HMG-like factor, plays roles in transcription elongation, chromatin structure, and genome stability in Saccharomyces cerevisiae. Mol Cell Biol. 2006 Feb;26(4):1496-509.

Guillemette B, Bataille AR, Gévry N, Adam M, Blanchette M, Robert F, Gaudreau L. Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning. PLoS Biol. 2005 Dec;3(12):e384.

Laganière J, Deblois G, Lefebvre C, Bataille AR, Robert F, Giguère V. From the Cover: Location analysis of estrogen receptor alpha target promoters reveals that FOXA1 defines a domain of the estrogen response. Proc Natl Acad Sci U S A. 2005 Aug 16;102(33):11651-6.

Robert F, Pokholok DK, Hannett NM, Rinaldi NJ, Chandy M, Rolfe A, Workman JL, Gifford DK, Young RA. Global position and recruitment of HATs and HDACs in the yeast genome. Mol Cell. 2004 Oct 22;16(2):199-209.

Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, Gifford DK. Computational discovery of gene modules and regulatory networks. Nat Biotechnol. 2003 Nov;21(11):1337-42.

Ng HH, Robert F, Young RA, Struhl K. Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol Cell. 2003 Mar;11(3):709-19.

Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 2002 Oct 25;298(5594):799-804.

Ng HH, Robert F, Young RA, Struhl K. Genome-wide location and regulated recruitment of the RSC nucleosome-remodeling complex. Genes Dev. 2002 Apr 1;16(7):806-19.

Robert F, Blanchette M, Maes O, Chabot B, Coulombe B. A human RNA polymerase II-containing complex associated with factors necessary for spliceosome assembly. J Biol Chem. 2002 Mar 15;277(11):9302-6.

Adam M, Robert F, Larochelle M, Gaudreau L. H2A.Z is required for global chromatin integrity and for recruitment of RNA polymerase II under specific conditions. Mol Cell Biol. 2001 Sep;21(18):6270-9.

Robert F, Coulombe B. Use of site-specific protein-DNA photocrosslinking to analyze the molecular organization of the RNA polymerase II initiation complex. Methods Mol Biol. 2001;148:383-93.

Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP, Young RA. Genome-wide location and function of DNA binding proteins. Science. 2000 Dec 22;290(5500):2306-9.

Robert F, Douziech M, Forget D, Egly JM, Greenblatt J, Burton ZF, Coulombe B. Wrapping of promoter DNA around the RNA polymerase II initiation complex induced by TFIIF. Mol Cell. 1998 Sep;2(3):341-51.

Forget D, Robert F, Grondin G, Burton ZF, Greenblatt J, Coulombe B. RAP74 induces promoter contacts by RNA polymerase II upstream and downstream of a DNA bend centered on the TATA box. Proc Natl Acad Sci U S A. 1997 Jul 8;94(14):7150-5.

Robert F, Forget D, Li J, Greenblatt J, Coulombe B. Localization of subunits of transcription factors IIE and IIF immediately upstream of the transcriptional initiation site of the adenovirus major late promoter. J Biol Chem. 1996 Apr 12;271(15):8517-20.