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Publications:  Dr Miguel Branco

Senner CE, Chrysanthou S, Burge S, Lin H-Y, Branco MR, Hemberger M(2020). TET1 and 5-Hydroxymethylation Preserve the Stem Cell State of Mouse Trophoblast. Stem Cell Reports
10.1016/j.stemcr.2020.04.009
Branco MR, Chuong EB(2020). Crossroads between transposons and gene regulation. Philosophical Transactions of the Royal Society B: Biological Sciences vol. 375, (1795)
10.1098/rstb.2019.0330
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, (2019), 10.1007/s00018-019-03335-7). Cellular and Molecular Life Sciences
10.1007/s00018-019-03443-4
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
10.1038/s41380-020-0695-7
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.
10.1016/j.celrep.2019.09.013
https://qmro.qmul.ac.uk/xmlui/handle/123456789/61509
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,
10.7554/eLife.44344
https://qmro.qmul.ac.uk/xmlui/handle/123456789/57670
Deniz Ö, Frost JM, Branco MR(2019). Author Correction: Regulation of transposable elements by DNA modifications. Nat Rev Genet
10.1038/s41576-019-0117-3
Deniz Ö, Frost JM, Branco MR(2019). Regulation of transposable elements by DNA modifications. Nat Rev Genet
10.1038/s41576-019-0106-6
https://qmro.qmul.ac.uk/xmlui/handle/123456789/57725
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)
10.1186/s13059-019-1656-9
https://qmro.qmul.ac.uk/xmlui/handle/123456789/57095
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
10.1007/s00018-019-03335-7
https://qmro.qmul.ac.uk/xmlui/handle/123456789/62344
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)
10.1038/s41467-018-06666-4
https://qmro.qmul.ac.uk/xmlui/handle/123456789/49063
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)
10.1186/s13059-018-1408-2
https://qmro.qmul.ac.uk/xmlui/handle/123456789/36083
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)
10.1186/s13059-017-1376-y
https://qmro.qmul.ac.uk/xmlui/handle/123456789/31784
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.
10.1093/nar/gkx666
https://qmro.qmul.ac.uk/xmlui/handle/123456789/27424
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.
10.1038/nsmb.3402
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.
10.1038/nature21411
https://qmro.qmul.ac.uk/xmlui/handle/123456789/31874
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.
10.1186/s13059-016-1096-8
https://qmro.qmul.ac.uk/xmlui/handle/123456789/18153
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.
10.1016/j.devcel.2015.12.027
https://qmro.qmul.ac.uk/xmlui/handle/123456789/11274
de la Rica L, Stanley JS, Branco MR(2016). Profiling DNA methylation and hydroxymethylation at retrotransposable elements. vol. 1400, 387-401.
10.1007/978-1-4939-3372-3_24
https://qmro.qmul.ac.uk/xmlui/handle/123456789/12732
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.
10.1038/nprot.2013.115
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.
10.1016/j.stem.2013.06.004
Branco MR(2013). Bridging genomics technology and biology. Genome Biol vol. 14, (10)
10.1186/gb4135
https://qmro.qmul.ac.uk/xmlui/handle/123456789/17895
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.
10.1242/dev.081661
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)
10.1186/gb-2012-13-8-r69
https://qmro.qmul.ac.uk/xmlui/handle/123456789/17906
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)
10.1371/journal.pgen.1002750
https://qmro.qmul.ac.uk/xmlui/handle/123456789/17768
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.
10.1126/science.1220671
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)
10.1371/journal.pone.0038983
https://qmro.qmul.ac.uk/xmlui/handle/123456789/17905
Branco MR, Ficz G, Reik W(2011). Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nat Rev Genet vol. 13, (1) 7-13.
10.1038/nrg3080
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.
10.1038/nature10008
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)
10.1371/journal.pbio.1000270
https://qmro.qmul.ac.uk/xmlui/handle/123456789/17904
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.
10.1242/dev.031328
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.
10.1101/gad.1690508
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)
10.1371/journal.pgen.1000016
https://qmro.qmul.ac.uk/xmlui/handle/123456789/17903
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.
10.1007/s10577-008-1230-x
Pombo A, Branco MR(2007). Functional organisation of the genome during interphase. Curr Opin Genet Dev vol. 17, (5) 451-455.
10.1016/j.gde.2007.08.008
Branco MR, Pombo A(2007). Chromosome organization: new facts, new models. Trends Cell Biol vol. 17, (3) 127-134.
10.1016/j.tcb.2006.12.006
Branco MR, Pombo A(2006). Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol vol. 4, (5)
10.1371/journal.pbio.0040138
https://qmro.qmul.ac.uk/xmlui/handle/123456789/17902
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.
10.1074/jbc.M311818200
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.
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