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Publications:  Dr Miguel Branco

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
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
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 Biol vol. 20, (1)
10.1186/s13059-019-1656-9
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. Nat Commun vol. 9, (1)
10.1038/s41467-018-06666-4
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 Biol vol. 19, (1)
10.1186/s13059-018-1408-2
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 Biol vol. 19, (1)
10.1186/s13059-017-1376-y
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 Res vol. 45, (17) 10002-10017.
10.1093/nar/gkx666
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. Nat Struct Mol Biol 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
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
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. Dev Cell vol. 36, (2) 152-163.
10.1016/j.devcel.2015.12.027
de la Rica L, Stanley JS, Branco MR(2016). Profiling DNA Methylation and Hydroxymethylation at Retrotransposable Elements. Methods Mol Biol vol. 1400, 387-401.
10.1007/978-1-4939-3372-3_24
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
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
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
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
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
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
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
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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