Epigenetics
Publications
2020
A non-canonical monovalent zinc finger stabilizes the integration of Cfp1 into the H3K4 methyltransferase complex COMPASS. Yang Y, Joshi M, Takahashi YH, Ning Z, Qu Q, Brunzelle JS, Skiniotis G, Figeys D, Shilatifard A, Couture JF. Nucleic Acids Res 48: 421-431.
Nucleosome positioning sequence patterns as packing or regulatory. Pranckeviciene E, Hosid S, Liang N, Ioshikhes I. PLoS Comput Biol. 16: e1007365.
Maternal folic acid supplementation and infant birthweight in low- and middle-income countries: A systematic review. Jonker H, Capelle N, Lanes A, Wen SW, Walker M, Corsi DJ. Matern Child Nutr. 16: e12895.
2019
ATXR5/6 Forms Alternative Protein Complexes with PCNA and the Nucleosome Core Particle. Davarinejad H, Joshi M, Ait-Hamou N, Munro K, Couture JF. J Mol Biol 431: 1370-1379.
Polycomb/Trithorax Antagonism: Cellular Memory in Stem Cell Fate and Function. Brand M, Nakka K, Zhu J, Dilworth FJ. Cell Stem Cell 24: 518-533.
Single-Cell Proteomics Reveal that Quantitative Changes in Co-expressed Lineage-Specific Transcription Factors Determine Cell Fate. Palii CG, Cheng Q, Gillespie MA, Shannon P, Mazurczyk M, Napolitani G, Price ND, Ranish JA, Morrissey E, Higgs DR, Brand M. Cell Stem Cell 24: 812-820.
Transcriptomically Guided Mesendoderm Induction of Human Pluripotent Stem Cells Using a Systematically Defined Culture Scheme. Carpenedo RL, Kwon SY, Tanner RM, Yockell-Lelièvre J, Choey C, Doré C, Ho M, Stewart DJ, Perkins TJ, Stanford WL. Stem Cell Reports 13: 1111-1125.
MLL1 is required for PAX7 expression and satellite cell self-renewal in mice. Addicks GC, Brun CE, Sincennes MC, Saber J, Porter CJ, Francis Stewart A, Ernst P, Rudnicki MA. Nat Commun. 10: 4256.
Gene expression profiling of skeletal myogenesis in human embryonic stem cells reveals a potential cascade of transcription factors regulating stages of myogenesis, including quiescent/activated satellite cell-like gene expression. Shelton M, Ritso M, Liu J, O'Neil D, Kocharyan A, Rudnicki MA, Stanford WL, Skerjanc IS, Blais A. PLoS One 14:e0222946.
Snf2h Drives Chromatin Remodeling to Prime Upper Layer Cortical Neuron Development. Alvarez-Saavedra M, Yan K, De Repentigny Y, Hashem LE, Chaudary N, Sarwar S, Yang D, Ioshikhes I, Kothary R, Hirayama T, Yagi T, Picketts DJ. Front Mol Neurosci. 12: 243.
A synthetic non-histone substrate to study substrate targeting by the Gcn5 HAT and sirtuin HDACs. Rössl A, Denoncourt A, Lin MS, Downey M. J Biol Chem. 294: 6227-6239.
Delivery of MicroRNAs by Chitosan Nanoparticles to Functionally Alter Macrophage Cholesterol Efflux in Vitro and in Vivo. Nguyen MA, Wyatt H, Susser L, Geoffrion M, Rasheed A, Duchez AC, Cottee ML, Afolayan E, Farah E, Kahiel Z, Côté M, Gadde S, Rayner KJ. ACS Nano 13: 6491-6505.
PRMT7 methylates eukaryotic translation initiation factor 2α and regulates its role in stress granule formation. Haghandish N, Baldwin RM, Morettin A, Dawit HT, Adhikary H, Masson JY, Mazroui R, Trinkle-Mulcahy L, Côté J. Mol Biol Cell. 30:778-793.
2018
Structural Analysis of the Ash2L/Dpy-30 Complex Reveals a Heterogeneity in H3K4 Methylation. Haddad JF, Yang Y, Takahashi YH, Joshi M, Chaudhary N, Woodfin AR, Benyoucef A, Yeung S, Brunzelle JS, Skiniotis G, Brand M, Shilatifard A, Couture JF. Structure. 26: 1594-1603.
A complex of C9ORF72 and p62 uses arginine methylation to eliminate stress granules by autophagy.Chitiprolu M, Jagow C, Tremblay V, Bondy-Chorney E, Paris G, Savard A, Palidwor G, Barry FA, Zinman L, Keith J, Rogaeva E, Robertson J, Lavallée-Adam M, Woulfe J, Couture JF, Côté J, Gibbings D. Nat Commun. 9: 2794.
Expression of murine muscle-enriched A-type lamin-interacting protein (MLIP) is regulated by tissue-specific alternative transcription start sites. Cattin ME, Deeke SA, Dick SA, Verret-Borsos ZJA, Tennakoon G, Gupta R, Mak E, Roeske CL, Weldrick JJ, Megeney LA, Burgon PG. J Biol Chem. 293: 19761-19770.
Targeting the MTF2-MDM2 Axis Sensitizes Refractory Acute Myeloid Leukemia to Chemotherapy. Maganti HB, Jrade H, Cafariello C, Manias Rothberg JL, Porter CJ, Yockell-Lelièvre J, Battaion HL, Khan ST, Howard JP, Li Y, Grzybowski AT, Sabri E, Ruthenburg AJ, Dilworth FJ, Perkins TJ, Sabloff M, Ito CY, Stanford WL. Cancer Discov. 8:1376-1389.
The Dystrophin Glycoprotein Complex Regulates the Epigenetic Activation of Muscle Stem Cell Commitment. Chang NC, Sincennes MC, Chevalier FP, Brun CE, Lacaria M, Segalés J, Muñoz-Cánoves P, Ming H, Rudnicki MA. Cell Stem Cell. 22: 755-768.
Cdk1 phosphorylation of Esp1/Separase functions with PP2A and Slk19 to regulate pericentric Cohesin and anaphase onset. Lianga N, Doré C, Kennedy EK, Yeh E, Williams EC, Fortinez CM, Wang A, Bloom KS, Rudner AD. PLoS Genet. 14: e1007029.
The role of ISWI chromatin remodeling complexes in brain development and neurodevelopmental disorders. Goodwin LR, Picketts DJ. Mol Cell Neurosci. 87: 55-64.
Mtf2-PRC2 control of canonical Wnt signaling is required for definitive erythropoiesis. Rothberg JLM, Maganti HB, Jrade H, Porter CJ, Palidwor GA, Cafariello C, Battaion HL, Khan ST, Perkins TJ, Paulson RF, Ito CY, Stanford WL. Cell Discov. 4:21.
Ectopic expression of aPKC-mediated phosphorylation in p300 modulates hippocampal neurogenesis, CREB binding and fear memory differently with age. Syal C, Seegobin M, Sarma SN, Gouveia A, Hsu K, Niibori Y, He L, Wondisford FE, Frankland PW, Wang J. Sci Rep. 8: 13489.
2017
Molecular basis for the methylation specificity of ATXR5 for histone H3. Bergamin E, Sarvan S, Malette J, Eram MS, Yeung S, Mongeon V, Joshi M, Brunzelle JS, Michaels SD, Blais A, Vedadi M, Couture JF. Nucleic Acids Res. 45:6375-6387.
Epigenetic Activation of Pro-angiogenic Signaling Pathways in Human Endothelial Progenitors Increases Vasculogenesis. Fraineau S, Palii CG, McNeill B, Ritso M, Shelley WC, Prasain N, Chu A, Vion E, Rieck K, Nilufar S, Perkins TJ, Rudnicki MA, Allan DS, Yoder MC, Suuronen EJ, Brand M. Stem Cell Reports. 9:1573-1587.
Lysine acetyltransferase NuA4 and acetyl-CoA regulate glucose-deprived stress granule formation in Saccharomyces cerevisiae. Rollins M, Huard S, Morettin A, Takuski J, Pham TT, Fullerton MD, Côté J, Baetz K. PLoS Genet 13: e1006626.
Reprogramming progeria fibroblasts re-establishes a normal epigenetic landscape. Chen Z, Chang WY, Etheridge A, Strickfaden H, Jin Z, Palidwor G, Cho JH, Wang K, Kwon SY, Doré C, Raymond A, Hotta A, Ellis J, Kandel RA, Dilworth FJ, Perkins TJ, Hendzel MJ, Galas DJ, Stanford WL. Aging Cell. 16:870-887.
The aPKC-CBP Pathway Regulates Post-stroke Neurovascular Remodeling and Functional Recovery. Gouveia A, Seegobin M, Kannangara TS, He L, Wondisford F, Comin CH, Costa LDF, Béïque JC, Lagace DC, Lacoste B, Wang J. Stem Cell Reports. 9: 1735-1744.
NuA4 Lysine Acetyltransferase Complex Contributes to Phospholipid Homeostasis in Saccharomyces cerevisiae. Dacquay L, Flint A, Butcher J, Salem D, Kennedy M, Kaern M, Stintzi A, Baetz K. G3 (Bethesda). 7: 1799-1809.
Drosophila H2A and H2A.Z Nucleosome Sequences Reveal Different Nucleosome Positioning Sequence Patterns. Yang D, Ioshikhes I. J Comput Biol. 24: 289-298.
Whole-transcriptome sequencing in blood provides a diagnosis of spinal muscular atrophy with progressive myoclonic epilepsy. Kernohan KD, Frésard L, Zappala Z, Hartley T, Smith KS, Wagner J, Xu H, McBride A, Bourque PR, Consortium CRC, Bennett SAL, Dyment DA, Boycott KM, Montgomery SB, Warman Chardon J. Hum Mutat 38: 611-614.
Nucleic acid extraction from buccal tissue for prediction of red blood cell phenotype. Berardi P, Clarke G, Cote J, Ribeiro E, Scalia V, Liwski R, Goldman M. Transfusion. 57: 2547-2548.
Uncovering robust patterns of microRNA co-expression across cancers using Bayesian Relevance Networks. Ramachandran P, Sánchez-Taltavull D, Perkins TJ. PLoS One. 12:e0183103.
2016
H3K27-demethylase activity of UTX/KDM6A is essential for skeletal muscle regeneration. Faralli H, Wang C, Nakka K, Benyoucef A, Sebastian S, Zhuang L, Chu A, Palii CG, Liu C, Camellato B, Brand M, Ge K, Dilworth FJ. J Clin Invest 126: 1555-1565.
UTX inhibition as selective epigenetic therapy against TAL1-driven T cell acute lymphoblastic leukemia. Benyoucef A, Palii CG, Wang C, Porter CJ, Chu A, Dai F, Tremblay V, Rakopoulos P, Singh K, Huang S, Pflumio F, Hébert J, Couture JF, Perkins TJ, Ge K, Dilworth FJ, Brand M. Genes & Dev 30: 508-521.
Mitochondrial Dynamics Impacts Stem Cell Identity and Fate Decisions by Regulating a Nuclear Transcriptional Program. Khacho M, Clark A, Svoboda DS, Azzi J, MacLaurin JG, Meghaizel C, Sesaki H, Lagace DC, Germain M, Harper ME, Park DS, Slack RS. Cell Stem Cell. 19: 232-247.
The aPKC-CBP Pathway Regulates Adult Hippocampal Neurogenesis in an Age-Dependent Manner. Gouveia A, Hsu K, Niibori Y, Seegobin M, Cancino GI, He L, Wondisford FE, Bennett S, Lagace D, Frankland PW, Wang J. Stem Cell Reports. doi: 10.1016/j.stemcr.2016.08.007.
Folic Acid Supplementation in Pregnancy and the Risk of Pre-Eclampsia-A Cohort Study. Wen SW, Guo Y, Rodger M, White RR, Yang Q, Smith GN, Perkins SL, Walker MC. PLoS One e0149818.
Nicotinamide Suppresses the DNA Damage Sensitivity of Saccharomyces cerevisiae Independently of Sirtuin Deacetylases. Rössl A, Bentley-DeSousa A, Tseng YC, Nwosu C, Downey M. Genetics. pii: genetics.116.193524.
Temporal activation of XRCC1-mediated DNA repair is essential for muscle differentiation. Al-Khalaf MH, Blake LE, Larsen BD, Bell RA, Brunette S, Parks RJ, Rudnicki MA, McKinnon PJ, Jeffrey Dilworth F, Megeney LA. Cell Discov. doi: 10.1038/celldisc.2015.41.
NAD⁺ repletion improves mitochondrial and stem cell function and enhances life span in mice. Zhang H, Ryu D, Wu Y, Gariani K, Wang X, Luan P, D'Amico D, Ropelle ER, Lutolf MP, Aebersold R, Schoonjans K, Menzies KJ, Auwerx J. Science 352: 1436-1443.
Stalled replication forks within heterochromatin require ATRX for protection. Huh MS, Ivanochko D, Hashem LE, Curtin M, Delorme M, Goodall E, Yan K, Picketts DJ. Cell Death Dis. 7:e2220.
Nucleosome Presence at AML-1 Binding Sites Inversely Correlates with Ly49 Expression: Revelations from an Informatics Analysis of Nucleosomes and Immune Cell Transcription Factors. Wight A, Yang D, Ioshikhes I, Makrigiannis AP. PLoS Comput Biol. 12:e1004894.
New Perspective on Impact of Folic Acid Supplementation during Pregnancy on Neurodevelopment/Autism in the Offspring Children - A Systematic Review. Gao Y, Sheng C, Xie RH, Sun W, Asztalos E, Moddemann D, Zwaigenbaum L, Walker M, Wen SW. PLoS One. 11: e0165626.
2015
A phosphorylation switch on RbBP5 regulates histone H3 Lys4 methylation. Zhang P, Chaturvedi CP, Tremblay V, Cramet M, Brunzelle JS, Skiniotis G, Brand M, Shilatifard A, Couture JF. Genes Dev. 29: 123-128.
BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates. Ramachandran P, Palidwor GA, Perkins TJ. Epigenetics Chromatin. 8:33. doi: 10.1186/s13072-015-0028-2.
Genome-wide association between Six4, MyoD, and the histone demethylase Utx during myogenesis. Chakroun I, Yang D, Girgis J, Gunasekharan A, Phenix H, Kærn M, Blais A. FASEB J. 29: 4738-4755.
NAD+ repletion improves muscle function in muscular dystrophy and counters global PARylation. Ryu D, Zhang H, Ropelle ER, Sorrentino V, Mázala DA, Mouchiroud L, Marshall PL, Campbell MD, Ali AS, Knowels GM, Bellemin S, Iyer SR, Wang X, Gariani K, Sauve AA, Cantó C, Conley KE, Walter L, Lovering RM, Chin ER, Jasmin BJ, Marcinek DJ, Menzies KJ, Auwerx J. Sci Transl Med. 8: 361.
Discovery of substrates for a SET domain lysine methyltransferase predicted by multistate computational protein design. Lanouette S, Davey JA, Elisma F, Ning Z, Figeys D, Chica RA, Couture JF. Structure 23: 206-215.
A KAP1 phosphorylation switch controls MyoD function during skeletal muscle differentiation. Singh K, Cassano M, Planet E, Sebastian S, Jang SM, Sohi G, Faralli H, Choi J, Youn HD, Dilworth FJ, Trono D. Genes Dev. 29: 513-525.
Macrophage Mitochondrial Energy Status Regulates Cholesterol Efflux and Is Enhanced by Anti-miR33 in Atherosclerosis. Karunakaran D, Thrush AB, Nguyen MA, Richards L, Geoffrion M, Singaravelu R, Ramphos E, Shangari P, Ouimet M, Pezacki JP, Moore KJ, Perisic L, Maegdefessel L, Hedin U, Harper ME, Rayner KJ. Circ Res. 117: 266-278.
2014
Trichostatin A enhances vascular repair by injected human endothelial progenitors through increasing the expression of TAL1-dependent genes. Palii CG, Vulesevic B, Fraineau S, Pranckeviciene E, Griffith AJ, Chu A, Faralli H, Li Y, McNeill B, Sun J, Perkins TJ, Dilworth FJ, Perez-Iratxeta C, Suuronen EJ, Allan DS, Brand M. Cell Stem Cell. 14: 644-657.
Selective methylation of histone H3 variant H3.1 regulates heterochromatin replication. Jacob Y, Bergamin E, Donoghue MT, Mongeon V, LeBlanc C, Voigt P, Underwood CJ, Brunzelle JS, Michaels SD, Reinberg D, Couture JF, Martienssen RA. Science. 343: 1249-1253.
Snf2h-mediated chromatin organization and histone H1 dynamics govern cerebellar morphogenesis and neural maturation. Alvarez-Saavedra M, De Repentigny Y, Lagali PS, Raghu Ram EV, Yan K, Hashem E, Ivanochko D, Huh MS, Yang D, Mears AJ, Todd MA, Corcoran CP, Bassett EA, Tokarew NJ, Kokavec J, Majumder R, Ioshikhes I, Wallace VA, Kothary R, Meshorer E, Stopka T, Skoultchi AI, Picketts DJ. Nat Commun. 5: 4181.
2013
Identification of cis-regulatory modules in promoters of human genes exploiting mutual positioning of transcription factors. Nandi S, Blais A, Ioshikhes I. Nucleic Acids Res. 41: 8822-8841.
Chromatin tandem affinity purification sequencing.Soleimani VD, Palidwor GA, Ramachandran P, Perkins TJ, Rudnicki MA. Nat Protoc. 8: 1525-1534.
Tissue-specific splicing of a ubiquitously expressed transcription factor is essential for muscle differentiation. Sebastian S, Faralli H, Yao Z, Rakopoulos P, Palii C, Cao Y, Singh K, Liu QC, Chu A, Aziz A, Brand M, Tapscott SJ, Dilworth FJ. Genes Dev. 27: 1247-1259.
Six1 regulates MyoD expression in adult muscle progenitor cells. Liu Y, Chakroun I, Yang D, Horner E, Liang J, Aziz A, Chu A, De Repentigny Y, Dilworth FJ, Kothary R, Blais A. PLoS One 8: e67762.
mChIP-KAT-MS, a method to map protein interactions and acetylation sites for lysine acetyltransferases. Mitchell L, Huard S, Cotrut M, Pourhanifeh-Lemeri R, Steunou AL, Hamza A, Lambert JP, Zhou H, Ning Z, Basu A, Côté J, Figeys DA, Baetz K. Proc Natl Acad Sci U S A. 110: E1641-50.
MicroRNA-133 controls brown adipose determination in skeletal muscle satellite cells by targeting Prdm16. Yin H, Pasut A, Soleimani VD, Bentzinger CF, Antoun G, Thorn S, Seale P, Fernando P, van Ijcken W, Grosveld F, Dekemp RA, Boushel R, Harper ME, Rudnicki MA. Cell Metab. 17: 210-224.
Opposing regulation of Sox2 by cell-cycle effectors E2f3a and E2f3b in neural stem cells. Julian LM, Vandenbosch R, Pakenham CA, Andrusiak MG, Nguyen AP, McClellan KA, Svoboda DS, Lagace DC, Park DS, Leone G, Blais A, Slack RS. Cell Stem Cell. 12: 440-452.
