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Research

Publications: Dr Miguel Branco

De Borre M, Branco MR ( 2021 ) . Oxidative Bisulfite Sequencing: An Experimental and Computational Protocol . vol. 2198 , 333 - 348 .
Senner CE, Chrysanthou S, Burge S, Lin HY, Branco MR, Hemberger M ( 2020 ) . TET1 and 5-Hydroxymethylation Preserve the Stem Cell State of Mouse Trophoblast . Stem Cell Reports vol. 15 , ( 6 ) 1301 - 1316 .
Shendy NAM, Raghu D, Roy S, Perry CH, Safi A, Branco MR, Homayouni R, Abell AN ( 2020 ) . Coordinated regulation of Rel expression by MAP3K4, CBP, and HDAC6 controls phenotypic switching . Communications Biology vol. 3 , ( 1 )
Deniz Ö, Ahmed M, Todd CD, Rio-Machin A, Dawson MA, Branco MR ( 2020 ) . Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukaemia . Nature Communications vol. 11 , ( 1 )
Santiago M, Antunes C, Guedes M, Iacovino M, Kyba M, Reik W, Sousa N, Pinto L et al. ( 2020 ) . Correction to: Tet3 regulates cellular identity and DNA methylation in neural progenitor cells (Cellular and Molecular Life Sciences, (2020), 77, 14, (2871-2883), 10.1007/s00018-019-03335-7) . Cellular and Molecular Life Sciences vol. 77 , ( 14 )
Branco MR, Chuong EB ( 2020 ) . Crossroads between transposons and gene regulation . Philosophical Transactions of the Royal Society B: Biological Sciences vol. 375 , ( 1795 )
Schlesinger S, Branco MR, Mermoud JE ( 2020 ) . Chapter 7 Roles and regulation of endogenous retroviruses in pluripotency and early development . Stem Cell Epigenetics ,
Antunes C, Da Silva JD, Guerra-Gomes S, Alves ND, Ferreira F, Loureiro-Campos E, Branco MR, Sousa N et al. ( 2020 ) . Tet3 ablation in adult brain neurons increases anxiety-like behavior and regulates cognitive function in mice . Molecular Psychiatry
Carrillo-Jimenez A, Deniz Ö, Niklison-Chirou MV, Ruiz R, Bezerra-Salomão K, Stratoulias V, Amouroux R, Yip PK et al. ( 2019 ) . TET2 Regulates the Neuroinflammatory Response in Microglia . Cell Reports vol. 29 , ( 3 ) 697 - 713.e8 .
Todd CD, Deniz Ö, Taylor D, Branco MR ( 2019 ) . Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells . eLife vol. 8 ,
Deniz Ö, Frost JM, Branco MR ( 2019 ) . Author Correction: Regulation of transposable elements by DNA modifications . Nat Rev Genet
Deniz Ö, Frost JM, Branco MR ( 2019 ) . Regulation of transposable elements by DNA modifications . Nat Rev Genet
Olova N, Krueger F, Andrews S, Oxley D, Berrens RV, Branco MR, Reik W ( 2019 ) . Correction to: Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data (Genome Biology (2018) 19 (33) DOI: 10.1186/s13059-018-1408-2) . Genome Biology vol. 20 , ( 1 )
Santiago M, Antunes C, Guedes M, Iacovino M, Kyba M, Reik W, Sousa N, Pinto L et al. ( 2019 ) . Tet3 regulates cellular identity and DNA methylation in neural progenitor cells . Cellular and Molecular Life Sciences
Schoenfelder S, Mifsud B, Senner CE, Todd CD, Chrysanthou S, Darbo E, Hemberger M, Branco MR ( 2018 ) . Divergent wiring of repressive and active chromatin interactions between mouse embryonic and trophoblast lineages . Nature Communications vol. 9 , ( 1 )
Olova N, Krueger F, Andrews S, Oxley D, Berrens RV, Branco MR, Reik W ( 2018 ) . Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data . Genome Biology vol. 19 , ( 1 )
Deniz Ö, de la Rica L, Cheng KCL, Spensberger D, Branco MR ( 2018 ) . SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells . Genome Biology vol. 19 , ( 1 )
Garcia-Gomez A, Li T, Kerick M, Català-Moll F, Comet NR, Rodríguez-Ubreva J, De La Rica L, Branco MR et al. ( 2017 ) . TET2- and TDG-mediated changes are required for the acquisition of distinct histone modifications in divergent terminal differentiation of myeloid cells . Nucleic Acids Research vol. 45 , ( 17 ) 10002 - 10017 .
Barbieri M, Xie SQ, Torlai Triglia E, Chiariello AM, Bianco S, De Santiago I, Branco MR, Rueda D et al. ( 2017 ) . Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells . Nature Structural and Molecular Biology vol. 24 , ( 6 ) 515 - 524 .
Beagrie RA, Scialdone A, Schueler M, Kraemer DCA, Chotalia M, Xie SQ, Barbieri M, De Santiago I et al. ( 2017 ) . Complex multi-enhancer contacts captured by genome architecture mapping . Nature vol. 543 , ( 7646 ) 519 - 524 .
de la Rica L, Deniz Ö, Cheng KC, Todd CD, Cruz C, Houseley J, Branco MR ( 2016 ) . TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells . Genome Biol vol. 17 , ( 1 ) 234 - 234 .
Branco MR, King M, Perez-Garcia V, Bogutz AB, Caley M, Fineberg E, Lefebvre L, Cook SJ et al. ( 2016 ) . Maternal DNA Methylation Regulates Early Trophoblast Development . Developmental Cell vol. 36 , ( 2 ) 152 - 163 .
de la Rica L, Stanley JS, Branco MR ( 2016 ) . Profiling DNA methylation and hydroxymethylation at retrotransposable elements . vol. 1400 , 387 - 401 .
Booth MJ, Ost TWB, Beraldi D, Bell NM, Branco MR, Reik W, Balasubramanian S ( 2013 ) . Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine . Nat Protoc vol. 8 , ( 10 ) 1841 - 1851 .
Ficz G, Hore TA, Santos F, Lee HJ, Dean W, Arand J, Krueger F, Oxley D et al. ( 2013 ) . FGF signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency . Cell Stem Cell vol. 13 , ( 3 ) 351 - 359 .
Ficz G, Hore TA, Santos F, Lee HJ, Dean W, Arand J, Krueger F, Oxley D et al. ( 2013 ) . FGF signalling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency . Clinical Epigenetics vol. 5 , ( Suppl 1 )
Branco MR ( 2013 ) . Bridging genomics technology and biology . Genome Biol vol. 14 , ( 10 )
Hackett JA, Reddington JP, Nestor CE, Dunican DS, Branco MR, Reichmann J, Reik W, Surani MA et al. ( 2012 ) . Promoter DNA methylation couples genome-defence mechanisms to epigenetic reprogramming in the mouse germline . Development vol. 139 , ( 19 ) 3623 - 3632 .
Raiber E-A, Beraldi D, Ficz G, Burgess HE, Branco MR, Murat P, Oxley D, Booth MJ et al. ( 2012 ) . Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase . Genome Biol vol. 13 , ( 8 )
Arand J, Spieler D, Karius T, Branco MR, Meilinger D, Meissner A, Jenuwein T, Xu G et al. ( 2012 ) . In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases . PLoS Genet vol. 8 , ( 6 )
Booth MJ, Branco MR, Ficz G, Oxley D, Krueger F, Reik W, Balasubramanian S ( 2012 ) . Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution . Science vol. 336 , ( 6083 ) 934 - 937 .
Pombo A, Branco MR ( 2012 ) . Intermingling of chromosome territories, translocations and interchromosomal associations . MUTAGENESIS . vol. 27 , 118 - 118 .
Krueger C, King MR, Krueger F, Branco MR, Osborne CS, Niakan KK, Higgins MJ, Reik W ( 2012 ) . Pairing of homologous regions in the mouse genome is associated with transcription but not imprinting status . PLoS One vol. 7 , ( 7 )
Branco MR, Ficz G, Reik W ( 2011 ) . Uncovering the role of 5-hydroxymethylcytosine in the epigenome . Nat Rev Genet vol. 13 , ( 1 ) 7 - 13 .
Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F, Hore TA, Marques CJ, Andrews S et al. ( 2011 ) . Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation . Nature vol. 473 , ( 7347 ) 398 - 402 .
Ferrai C, Xie SQ, Luraghi P, Munari D, Ramirez F, Branco MR, Pombo A, Crippa MP ( 2010 ) . Poised transcription factories prime silent uPA gene prior to activation . PLoS Biol vol. 8 , ( 1 )
Redrup L, Branco MR, Perdeaux ER, Krueger C, Lewis A, Santos F, Nagano T, Cobb BS et al. ( 2009 ) . The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing . DEVELOPMENT vol. 136 , ( 4 ) 525 - 530 .
Branco MR, Oda M, Reik W ( 2008 ) . Safeguarding parental identity: Dnmt1 maintains imprints during epigenetic reprogramming in early embryogenesis . Genes Dev vol. 22 , ( 12 ) 1567 - 1571 .
Noordermeer D, Branco MR, Splinter E, Klous P, van Ijcken W, Swagemakers S, Koutsourakis M, van der Spek P et al. ( 2008 ) . Transcription and chromatin organization of a housekeeping gene cluster containing an integrated beta-globin locus control region . PLoS Genet vol. 4 , ( 3 )
Noordermeer D, Branco MR, Splinter E, Klous P, van IJcken W, Swagemakers S, Koutsourakis M, van der Spek P et al. ( 2008 ) . Correction: Transcription and Chromatin Organization of a Housekeeping Gene Cluster Containing an Integrated β-Globin Locus Control Region . PLOS Genetics vol. 4 , ( 3 )
Branco MR, Branco T, Ramirez F, Pombo A ( 2008 ) . Changes in chromosome organization during PHA-activation of resting human lymphocytes measured by cryo-FISH . Chromosome Res vol. 16 , ( 3 ) 413 - 426 .
Pombo A, Branco MR ( 2007 ) . Functional organisation of the genome during interphase . Curr Opin Genet Dev vol. 17 , ( 5 ) 451 - 455 .
Branco MR, Pombo A ( 2007 ) . Chromosome organization: new facts, new models . Trends Cell Biol vol. 17 , ( 3 ) 127 - 134 .
Branco MR, Pombo A ( 2006 ) . Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations . PLoS Biol vol. 4 , ( 5 )
Pombo A, Branco MR ( 2006 ) . Mapping chromosome interactions in the nucleus of mammalian cells . EUROPEAN JOURNAL OF CELL BIOLOGY . vol. 85 , 100 - 100 .
BRANCO M, Xie SQ, Martin S, Pombo A ( 2006 ) . Correlative microscopy using Tokuyasu cryosections: applications for immunolabeling and in situ hybridization . Cell Imaging , Editors: Stephens, D , Scion Publishing Ltd
Branco MR, Marinho HS, Cyrne L, Antunes F ( 2004 ) . Decrease of H2O2 plasma membrane permeability during adaptation to H2O2 in Saccharomyces cerevisiae . J Biol Chem vol. 279 , ( 8 ) 6501 - 6506 .
Branco MR, Pedros N, Sousa-Lopes A, Marinho HS, Cyrne L, Antunes F ( 2004 ) . Regulation of the permeability of biomembranes to H2O2: Implications for redox compartmentalization . FREE RADICAL BIOLOGY AND MEDICINE . vol. 37 , S60 - S60 .