Santos Lab 7/16/25 Santos Lab 7/16/25

Alpha satellite RNA marks the perinucleolar compartment and represses ribosomal RNA expression in naïve human embryonic stem cells

Authors: Mittal K, Ataei L, Ramalho-Santos M.

Reference: bioRxiv, 2025.07.11.664446; doi: 10.1101/2025.07.11.664446

Santos Lab 3/12/25 Santos Lab 3/12/25

20 years of stemness: From stem cells to hypertranscription and back

Authors: Kim YK, Ramalho-Santos M.
Reference: Stem Cell Reports, 2025 Mar 11;20(3):102406. doi: /10.1016/j.stemcr.2025.102406
PMID: 39919752

Santos Lab 12/20/24 Santos Lab 12/20/24

LINE1 elements at distal junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells

Authors: Ataei L, Zhang J, Monis S, Giemza K, Mittal K, Yang J, Shimomura M, McStay B, Wilson MD, Ramalho-Santos M.
Reference: Genes Dev, 2025 Feb 3;39(3-4):280-298. doi: 10.1101/gad.351979.124
PMID: 39797762

Santos Lab 9/13/24 Santos Lab 9/13/24

Hypertranscription: the invisible hand in stem cell biology

Authors: Kim YK, Collignon E, Martin SB, Ramalho-Santos M.

Reference: Trends in Genetics, 2024, https://doi.org/10.1016/j.tig.2024.08.005

Santos Lab 9/7/23 Santos Lab 9/7/23

m6A RNA methylation orchestrates transcriptional dormancy during paused pluripotency

Authors: Collignon E, Cho B, Furlan G, Fothergill-Robinson J, Martin SB, McClymont SA, Ross RL, Limbach PA, Ramalho-Santos M.

Reference: Nature Cell Biology, 2023, https://doi.org/10.1038/s41556-023-01212-x

Santos Lab 1/12/23 Santos Lab 1/12/23

Absolute scaling of single-cell transcriptomes identifies pervasive hypertranscription in adult stem and progenitor cells

Authors: Kim YK, Cho B, Cook DP, Trcka D, Wrana JL, Ramalho-Santos M.

Reference: Cell Reports, 2023, https://www.cell.com/cell-reports/fulltext/S2211-1247(22)01882-4

Santos Lab 8/30/22 Santos Lab 8/30/22

Regulation, functions and transmission of bivalent chromatin during mammalian development

Authors: Macrae TA, Fothergill-Robinson J, Ramalho-Santos M.

Reference: Nat Rev Mol Cell Bio, https://doi.org/10.1038/s41580-022-00518-2

Santos Lab 8/11/21 Santos Lab 8/11/21

Chd1 regulates repair of promoter-proximal DNA breaks to sustain hypertranscription in embryonic stem cells

Authors: Bulut-Karslioglu A, Jin H, Kim YK, Cho B, Guzman-Ayala M, JK Williamson A, Hejna M, Stötzel M, Whetton AD, S. Song J, Ramalho-Santos M

Reference: Nature Communications, 2021 Aug 11;12(1):4859.

Santos Lab 3/25/21 Santos Lab 3/25/21

The deubiquitinase Usp9x regulates PRC2-mediated chromatin reprogramming during mouse development

Authors: Macrae TA, Ramalho-Santos M.

Reference: Nature Communications. 2021 Mar 25;12(1):1865.

PMID: 33767158

Santos Lab 3/1/18 Santos Lab 3/1/18

The Transcriptionally Permissive Chromatin State of Embryonic Stem Cells Is Acutely Tuned to Translational Output.

Authors: Bulut-Karslioglu A, Macrae TA, Oses-Prieto JA, Covarrubias S, Percharde M, Ku G, Diaz A, McManus MT, Burlingame AL, Ramalho-Santos M.
Reference: Cell Stem Cell. 2018 Mar 1;22(3):369-383.e8. doi: 10.1016/j.stem.2018.02.004.
PMID: 29499153

Santos Lab 6/6/17 Santos Lab 6/6/17

Global Hypertranscription in the Mouse Embryonic Germline

Authors: Percharde M, Wong P, Ramalho-Santos M.
Reference: Cell Rep. 2017 Jun 6;19(10):1987-1996. doi: 10.1016/j.celrep.2017.05.036.
PMID: 28591571

Santos Lab 1/9/17 Santos Lab 1/9/17

Hypertranscription in Development, Stem Cells, and Regeneration.

Authors: Percharde M, Bulut-Karslioglu A, Ramalho-Santos M.
Reference: Dev Cell. 2017 Jan 9;40(1):9-21. doi: 10.1016/j.devcel.2016.11.010. Epub 2016 Dec 15. Review.
PMID: 27989554

Santos Lab 4/7/15 Santos Lab 4/7/15

Emergence of hematopoietic stem and progenitor cells involves a Chd1-dependent increase in total nascent transcription.

Authors: Koh FM, Lizama CO, Wong P, Hawkins JS, Zovein AC, Ramalho-Santos M.
Reference: Proc Natl Acad Sci U S A. 2015 Apr 7;112(14):E1734-43. doi: 10.1073/pnas.1424850112. Epub 2015 Mar 23.
PMID: 25831528

Santos Lab 1/1/15 Santos Lab 1/1/15

Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast.

Authors: Guzman-Ayala M, Sachs M, Koh FM, Onodera C, Bulut-Karslioglu A, Lin CJ, Wong P, Nitta R, Song JS, Ramalho-Santos M.
Reference: Development. 2015 Jan 1;142(1):118-27. doi: 10.1242/dev.114843. Epub 2014 Dec 5.
PMID: 25480920

Santos Lab 8/11/14 Santos Lab 8/11/14

Hira-mediated H3.3 incorporation is required for DNA replication and ribosomal RNA transcription in the mouse zygote.

Authors: Lin CJ, Koh FM, Wong P, Conti M, Ramalho-Santos M.
Reference: Dev Cell. 2014 Aug 11;30(3):268-79. doi: 10.1016/j.devcel.2014.06.022. Epub 2014 Jul 31.
PMID: 25087892

Santos Lab 6/27/13 Santos Lab 6/27/13

Bivalent chromatin marks developmental regulatory genes in the mouse embryonic germline in vivo.

Authors: Sachs M, Onodera C, Blaschke K, Ebata KT, Song JS, Ramalho-Santos M.
Reference: Cell Rep. 2013 Jun 27;3(6):1777-84. doi: 10.1016/j.celrep.2013.04.032. Epub 2013 May 30.
PMID: 23727241

Santos Lab 1/11/11 Santos Lab 1/11/11

Open chromatin in pluripotency and reprogramming.

Authors: Gaspar-Maia A, Alajem A, Meshorer E, Ramalho-Santos M.
Reference: Nat Rev Mol Cell Biol. 2011 Jan;12(1):36-47. doi: 10.1038/nrm3036. Review. Erratum in: Nat Rev Mol Cell Biol. 2011 Apr;12(4):273.
PMID: 21179060

Santos Lab 7/2/10 Santos Lab 7/2/10

Parallel gateways to pluripotency: open chromatin in stem cells and development.

Authors: Koh FM, Sachs M, Guzman-Ayala M, Ramalho-Santos M.
Reference: Curr Opin Genet Dev. 2010 Oct;20(5):492-9. doi: 10.1016/j.gde.2010.06.002. Epub 2010 Jul 2. Review.
PMID: 20598875

Santos Lab 8/13/09 Santos Lab 8/13/09

Chd1 regulates open chromatin and pluripotency of embryonic stem cells.

Authors: Gaspar-Maia A, Alajem A, Polesso F, Sridharan R, Mason MJ, Heidersbach A, Ramalho-Santos J, McManus MT, Plath K, Meshorer E, Ramalho-Santos M.
Reference: Nature. 2009 Aug 13;460(7257):863-8. doi: 10.1038/nature08212. Epub 2009 Jul 8.
PMID: 19587682

Santos Lab 9/26/04 Santos Lab 9/26/04

Stem cells as probabilistic self-producing entities.

Authors: Ramalho-Santos M.
Reference: Bioessays. 2004 Sep;26(9):1013-6.
PMID: 15351971

Publications From The Santos Lab