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Identification

Personal identification

Full name
Miguel Ramos Alegre Zenner Branco

Citation names

  • Branco, Miguel

Author identifiers

Ciência ID
D914-AC5A-BD1B
ORCID iD
0000-0001-9447-1548
Education
Degree Classification
2007
Concluded
 PhD (Doutoramento)
MRC Clinical Sciences Centre, United Kingdom
2003
Concluded
 Bioquímica (Licenciatura)
Universidade de Lisboa Faculdade de Ciências, Portugal
Affiliation

Science

Category
Host institution 		Employer
2013 - Current Principal Investigator (Research) Queen Mary University of London, United Kingdom
2008 - 2013 Postdoc (Research) Babraham Institute, United Kingdom
2007 - 2008 Postdoc (Research) MRC Clinical Sciences Centre, United Kingdom
Projects

Grant

Designation Funders
2023/09/01 - 2027/08/31 Impact of pregnancy-specific glycoproteins on development and ageing
N/A
Supervisor
Biotechnology and Biological Sciences Research Council
Ongoing
2017/09/22 - 2022/06/21 Novel approaches for epigenomic profiling of repetitive elements
BB/R505997/1
Supervisor
Biotechnology and Biological Sciences Research Council
Concluded
2019/05/01 - 2021/04/30 Investigating the Activity of transposon Derived Regulatory Sequences in the placenta
841172
Supervisor
Concluded
2014/09/22 - 2018/09/21 Epigenetic influence of retrotransposons on the genome
N/a
Supervisor
Concluded
2015/07/01 - 2018/06/30 Functional epigenetics of LINE1 retrotransposition
PCOFUND-GA-2013-608765
Supervisor
2015/04/01 - 2018/03/31 Functional epigenetic regulation of retrotransposable elements in tumorigenesis
PCOFUND – GA – 2013 – 608765
Supervisor
Concluded

Contract

Designation Funders
2023/03/01 - 2026/02/28 Epigenetic regulation of cell-autonomous type I interferon responses in trophoblast
MR/X008487/1
Principal investigator
Medical Research Council
Ongoing
2022/09/01 - 2024/08/31 Does transposable element expression drive placental inflammation
N/A
Principal investigator
Ongoing
2023/04/01 - 2024/03/31 Modelling the impact of maternal infection and inflammation on placental trophoblast function
N/A
Co-Principal Investigator (Co-PI)
Barts Charity
Ongoing
2019/11/11 - 2023/03/31 Assessing the impact of endogenous retroviruses on trophoblast gene regulation
BB/T000031/1
Principal investigator
Ongoing
2020/12/15 - 2023/01/11 The role of endogenous retroviruses in the development of the primate placenta
N/A
Co-Principal Investigator (Co-PI)
Leakey Foundation
Concluded
2021/05/01 - 2022/12/31 Investigating genetic links between transposable elements and pregnancy complications
MRC0297
Principal investigator
Barts Charity
2013/10/01 - 2019/09/30 Epigenetic control of retrotransposable elements
101225/Z/13/Z
Principal investigator
Wellcome Foundation Ltd

The Royal Society
Concluded
Outputs

Publications

Journal article
  1. Debosree Pal; Manthan Patel; Fanny Boulet; Jayakumar Sundarraj; Olivia A. Grant; Miguel R. Branco; Srinjan Basu; et al. "H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function". Nature Structural & Molecular Biology (2023): https://doi.org/10.1038/s41594-023-01016-5.
    10.1038/s41594-023-01016-5
  2. Darren Taylor; Robert Lowe; Claude Philippe; Kevin C L Cheng; Olivia A Grant; Nicolae Radu Zabet; Gael Cristofari; Miguel R Branco. "Locus-specific chromatin profiling of evolutionarily young transposable elements". Nucleic Acids Research (2021): https://doi.org/10.1093/nar/gkab1232.
    10.1093/nar/gkab1232
  3. Noha Ahmed Mohammed Shendy; Deepthi Raghu; Sujoy Roy; Charles Hamilton Perry; Adiba Safi; Miguel Ramos Branco; Ramin Homayouni; Amy Noel Abell. "Coordinated regulation of Rel expression by MAP3K4, CBP, and HDAC6 controls phenotypic switching". Communications Biology 3 1 (2020): https://doi.org/10.1038/s42003-020-01200-z.
    10.1038/s42003-020-01200-z
  4. Özgen Deniz; Mamataz Ahmed; Christopher D. Todd; Ana Rio-Machin; Mark A. Dawson; Miguel R. Branco. "Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukaemia". Nature Communications (2020): https://doi.org/10.1038/s41467-020-17206-4.
    10.1038/s41467-020-17206-4
  5. Miguel R. Branco; Edward B. Chuong. "Crossroads between transposons and gene regulation". Philosophical Transactions of the Royal Society B: Biological Sciences 375 1795 (2020): 20190330-20190330. https://doi.org/10.1098/rstb.2019.0330.
    10.1098/rstb.2019.0330
  6. Cláudia Antunes; Jorge D. Da Silva; Sónia Guerra-Gomes; Nuno D. Alves; Fábio Ferreira; Eduardo Loureiro-Campos; Miguel R. Branco; et al. "Tet3 ablation in adult brain neurons increases anxiety-like behavior and regulates cognitive function in mice". Molecular Psychiatry (2020): https://doi.org/10.1038/s41380-020-0695-7.
    10.1038/s41380-020-0695-7
  7. Özgen Deniz; Jennifer M. Frost; Miguel R. Branco. "Author Correction: Regulation of transposable elements by DNA modifications". Nature Reviews Genetics 20 7 (2019): 432-432. https://doi.org/10.1038/s41576-019-0117-3.
    10.1038/s41576-019-0117-3
  8. Christopher D Todd; Özgen Deniz; Darren Taylor; Miguel R Branco. "Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells". eLife 8 (2019): https://doi.org/10.7554/eLife.44344.
    10.7554/eLife.44344
  9. Özgen Deniz; Jennifer M. Frost; Miguel R. Branco. "Regulation of transposable elements by DNA modifications". Nature Reviews Genetics 20 7 (2019): 417-431. https://doi.org/10.1038/s41576-019-0106-6.
    10.1038/s41576-019-0106-6
  10. Stefan Schoenfelder; Borbala Mifsud; Claire E. Senner; Christopher D. Todd; Stephanie Chrysanthou; Elodie Darbo; Myriam Hemberger; Miguel R. Branco. "Divergent wiring of repressive and active chromatin interactions between mouse embryonic and trophoblast lineages". Nature Communications 9 1 (2018): https://doi.org/10.1038/s41467-018-06666-4.
    10.1038/s41467-018-06666-4
  11. Deniz Ö; de la Rica L; Cheng KCL; Spensberger D; Branco MR. "SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells.". Genome biology (2018): http://europepmc.org/abstract/med/29351814.
    10.1186/s13059-017-1376-y
  12. Garcia-Gomez A; Li T; Kerick M; Català-Moll F; Comet NR; Rodríguez-Ubreva J; de la Rica L; et al. "TET2- and TDG-mediated changes are required for the acquisition of distinct histone modifications in divergent terminal differentiation of myeloid cells.". Nucleic acids research (2017): http://europepmc.org/abstract/med/28973458.
    10.1093/nar/gkx666
  13. Mariano Barbieri; Sheila Q Xie; Elena Torlai Triglia; Andrea M Chiariello; Simona Bianco; Inês de Santiago; Miguel R Branco; et al. "Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells". Nature Structural & Molecular Biology 24 6 (2017): 515-524. https://doi.org/10.1038/nsmb.3402.
    10.1038/nsmb.3402
  14. Beagrie RA; Scialdone A; Schueler M; Kraemer DC; Chotalia M; Xie SQ; Barbieri M; et al. "Complex multi-enhancer contacts captured by genome architecture mapping.". (2017): http://europepmc.org/abstract/med/28273065.
    10.1038/nature21411
  15. de la Rica L; Deniz Ö; Cheng KC; Todd CD; Cruz C; Houseley J; Branco MR. "TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells.". (2016): http://europepmc.org/abstract/med/27863519.
  16. Branco MR; King M; Perez-Garcia V; Bogutz AB; Caley M; Fineberg E; Lefebvre L; et al. "Maternal DNA Methylation Regulates Early Trophoblast Development.". (2016): http://europepmc.org/abstract/med/26812015.
    10.1016/j.devcel.2015.12.027
  17. de la Rica L; Stanley JS; Branco MR. "Profiling DNA Methylation and Hydroxymethylation at Retrotransposable Elements.". (2016): http://europepmc.org/abstract/med/26895066.
    10.1007/978-1-4939-3372-3_24
  18. Booth MJ; Ost TW; Beraldi D; Bell NM; Branco MR; Reik W; Balasubramanian S. "Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine.". (2013): http://europepmc.org/abstract/med/24008380.
    10.1038/nprot.2013.115
  19. Ficz G; Hore TA; Santos F; Lee HJ; Dean W; Arand J; Krueger F; et al. "FGF signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency.". (2013): http://europepmc.org/abstract/med/23850245.
    10.1016/j.stem.2013.06.004
  20. Branco MR. "Bridging genomics technology and biology.". (2013): http://europepmc.org/abstract/med/24176165.
    10.1186/gb4135
  21. Ficz G; Hore TA; Santos F; Lee HJ; Dean W; Arand J; Krueger F; et al. "FGF signalling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency.". (2013): http://europepmc.org/abstract/PMC/PMC3751494.
  22. Hackett JA; Reddington JP; Nestor CE; Dunican DS; Branco MR; Reichmann J; Reik W; et al. "Promoter DNA methylation couples genome-defence mechanisms to epigenetic reprogramming in the mouse germline.". (2012): http://europepmc.org/abstract/med/22949617.
    10.1242/dev.081661
  23. Raiber EA; Beraldi D; Ficz G; Burgess HE; Branco MR; Murat P; Oxley D; et al. "Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase.". (2012): http://europepmc.org/abstract/med/22902005.
    10.1186/gb-2012-13-8-r69
  24. Arand J; Spieler D; Karius T; Branco MR; Meilinger D; Meissner A; Jenuwein T; et al. "In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases.". (2012): http://europepmc.org/abstract/med/22761581.
    10.1371/journal.pgen.1002750
  25. Booth MJ; Branco MR; Ficz G; Oxley D; Krueger F; Reik W; Balasubramanian S. "Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution.". (2012): http://europepmc.org/abstract/med/22539555.
    10.1126/science.1220671
  26. Branco MR; Ficz G; Reik W. "Uncovering the role of 5-hydroxymethylcytosine in the epigenome.". (2012): http://europepmc.org/abstract/med/22083101.
    10.1038/nrg3080
  27. Krueger C; King MR; Krueger F; Branco MR; Osborne CS; Niakan KK; Higgins MJ; Reik W. "Pairing of homologous regions in the mouse genome is associated with transcription but not imprinting status.". (2012): http://europepmc.org/abstract/med/22802932.
    10.1371/journal.pone.0038983
  28. Ficz G; Branco MR; Seisenberger S; Santos F; Krueger F; Hore TA; Marques CJ; Andrews S; Reik W. "Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation.". (2011): http://europepmc.org/abstract/med/21460836.
    10.1038/nature10008
  29. Ferrai C; Xie SQ; Luraghi P; Munari D; Ramirez F; Branco MR; Pombo A; Crippa MP. "Poised transcription factories prime silent uPA gene prior to activation.". (2010): http://europepmc.org/abstract/med/20052287.
    10.1371/journal.pbio.1000270
  30. Redrup L; Branco MR; Perdeaux ER; Krueger C; Lewis A; Santos F; Nagano T; et al. "The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing.". (2009): http://europepmc.org/abstract/med/19144718.
    10.1242/dev.031328
  31. Branco MR; Oda M; Reik W. "Safeguarding parental identity: Dnmt1 maintains imprints during epigenetic reprogramming in early embryogenesis.". (2008): http://europepmc.org/abstract/med/18559472.
    10.1101/gad.1690508
  32. Noordermeer D; Branco MR; Splinter E; Klous P; van IJcken W; Swagemakers S; Koutsourakis M; et al. "Correction: Transcription and Chromatin Organization of a Housekeeping Gene Cluster Containing an Integrated ß-Globin Locus Control Region.". (2008): http://europepmc.org/abstract/PMC/PMC2637086.
  33. Noordermeer D; Branco MR; Splinter E; Klous P; van Ijcken W; Swagemakers S; Koutsourakis M; et al. "Transcription and chromatin organization of a housekeeping gene cluster containing an integrated beta-globin locus control region.". (2008): http://europepmc.org/abstract/med/18369441.
    10.1371/journal.pgen.1000016
  34. Branco MR; Branco T; Ramirez F; Pombo A. "Changes in chromosome organization during PHA-activation of resting human lymphocytes measured by cryo-FISH.". (2008): http://europepmc.org/abstract/med/18461481.
    10.1007/s10577-008-1230-x
  35. Pombo A; Branco MR. "Functional organisation of the genome during interphase.". (2007): http://europepmc.org/abstract/med/17920259.
    10.1016/j.gde.2007.08.008
  36. Branco MR; Pombo A. "Chromosome organization: new facts, new models.". (2007): http://europepmc.org/abstract/med/17197184.
    10.1016/j.tcb.2006.12.006
  37. Branco MR; Pombo A. "Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations.". (2006): http://europepmc.org/abstract/med/16623600.
    10.1371/journal.pbio.0040138
  38. Branco MR; Marinho HS; Cyrne L; Antunes F. "Decrease of H2O2 plasma membrane permeability during adaptation to H2O2 in Saccharomyces cerevisiae.". (2004): http://europepmc.org/abstract/med/14645222.
    10.1074/jbc.M311818200
Preprint
  1. Claire E. Senner; Ziqi Dong; Miguel R. Branco; Erica D. Watson. "One-carbon metabolism is required for epigenetic stability in the mouse placenta". 2023. https://doi.org/10.1101/2023.04.04.535221.
    10.1101/2023.04.04.535221
  2. Debosree Pal; Manthan Patel; Fanny Boulet; Jayakumar Sundarraj; Olivia A Grant; Miguel R. Branco; Srinjan Basu; et al. "H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function". 2022. https://doi.org/10.1101/2022.04.29.488986.
    10.1101/2022.04.29.488986
  3. Jennifer M. Frost; Samuele M. Amante; Hiroaki Okae; Eleri M. Jones; Brogan Ashley; Rohan M. Lewis; Jane K. Cleal; et al. "Regulation of human trophoblast gene expression by endogenous retroviruses". 2022. https://doi.org/10.1101/2022.04.26.489485.
    10.1101/2022.04.26.489485
  4. Miguel Branco; Jennifer Frost; Samuele Amante; Hiroaki Okae; Eleri Jones; Brogan Ashley; Rohan Lewis; et al. "Regulation of human trophoblast gene expression by endogenous retroviruses". 2022. https://doi.org/10.21203/rs.3.rs-1648736/v1.
    10.21203/rs.3.rs-1648736/v1

Other

Other output
  1. Locus-specific chromatin profiling of evolutionarily young transposable elements. 2021. Darren Taylor; Robert Lowe; Claude Philippe; Kevin C. L. Cheng; Olivia A. Grant; Nicolae Radu Zabet; Gael Cristofari; Miguel R. Branco. https://doi.org/10.1101/2021.08.25.457666.
    10.1101/2021.08.25.457666
  2. Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukaemia. 2019. Özgen Deniz; Mamataz Ahmed; Christopher D. Todd; Ana Rio-Machin; Mark A. Dawson; Miguel R. Branco. https://doi.org/10.1101/772954.
    10.1101/772954
  3. Functional evaluation of transposable elements as transcriptional enhancers in mouse embryonic and trophoblast stem cells. 2018. Christopher D. Todd; Özgen Deniz; Miguel R. Branco. https://doi.org/10.1101/500322.
    10.1101/500322
  4. SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells. 2017. Özgen Deniz; Lorenzo de la Rica; Kevin C. L. Cheng; Dominik Spensberger; Miguel R. Branco. https://doi.org/10.1101/193854.
    10.1101/193854
  5. Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data. 2017. Nelly Olova; Felix Krueger; Simon Andrews; David Oxley Oxley; Miguel R. Branco; Wolf Reik. https://doi.org/10.1101%2F165449.
    10.1101/165449
  6. Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells. 2017. Mariano Barbieri; Sheila Q. Xie; Elena Torlai Triglia; Inês de Santiago; Miguel R. Branco; David Rueda; Mario Nicodemi; Ana Pombo. https://doi.org/10.1101/111773.
    10.1101/111773