Publications From The Santos Lab
20 years of stemness: From stem cells to hypertranscription and back
Authors: Kim YK, Ramalho-Santos M.
Reference: Stem Cell Reports, 2025. https://www.cell.com/stem-cell-reports/fulltext/S2213-6711(25)00010-4
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 and Development, 2024. http://www.genesdev.org/cgi/doi/10.1101/gad.351979.124
LINE1 and PRC2 control nucleolar organization and repression of the 8C state in human ESCs
Authors: Zhang J, Ataei L, Mittal K, Wu L, Caldwell L, Huynh L, Sarajideen S, Tse K, Simon MM, Mazid A, Cook DP, Trcka D, Kwan T, Hoffman MM, Wrana JL, Esteban MA, Ramalho-Santos M.
Reference: Developmental Cell, 2024. https://doi.org/10.1016/j.devcel.2024.09.024
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
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
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
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
Depletion of nuclear LINE1 RNA in mouse ESCs and embryos
Authors: Percharde M, Lin CJ, Ramalho-Santos M.
Reference: STAR Protocols, Volume 2, Issue 3, 2021, 100726, ISSN 2666-1667.
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.
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
Homotypic clustering of L1 and B1/Alu repeats compartmentalizes the 3D genome
Authors: Lu JY, Chang L, Li T, Wang T, Yin Y, Zhan G, Han X, Zhang K, Tao Y, Percharde M, Wang L, Peng Q, Yan P, Zhang H, Bi X, Shao W, Hong Y, Wu Z, Ma R, Wang P, Li W, Zhang J, Chang Z, Hou Y, Zhu B, Santos MR, Li P, Xie W, Na J, Sun Y, Shen X.
Reference : Cell Research. 2021 Jan 29, 10.1038/s41422-020-00466-6
PMID: 33514913
Colorectal Cancer Cells Enter a Diapause-like DTP State to Survive Chemotherapy
Authors: Rehman AK, Haynes J, Collignon E, Brown KR, Wang Y, Nixon AML, Bruce JP, Wintersinger JA, Mer AS, Lo EBL, Leung C, Lima-Fernandes E, Pedley NM, Soares F, McGibbon S, He HH, Pollet A, Pugh TJ, Haibe-Kains B, Morris Q, Ramalho-Santos M, Goyal S, Moffat J, O'Brien CA
Reference :Cell. 2021 Jan 7; 184(1):226-242.
PMID: 33417860
Sex-specific epigenetic profile of inner cell mass of mice conceived in vivo or by IVF
Authors: Ruggeri E, Lira-Albarrán S, Grow EJ, Liu X, Harner R, Maltepe E, Ramalho-Santos M, Donjacour A, Rinaudo P.
Reference: Mol Hum Reprod. 2020 Nov 1;26(11):866-878. doi: 10.1093/molehr/gaaa064.
PMID: 33010164
Genomic Repeats Categorize Genes with Distinct Functions for Orchestrated Regulation
Authors: Lu JY, Shao W, Chang L, Yin Y, Li T, Zhang H, Hong Y, Percharde M, Guo L, Wu Z, Liu L, Liu W, Yan P, Ramalho-Santos M, Sun Y, Shen X.
Reference: Cell Rep. 2020 Mar 10; 30 (10) :3296-3311
PMID: 32160538
What Doesn’t Kill You Makes You Stronger: Transposons as Dual Players in Chromatin Regulation and Genomic Variation
Authors: Percharde M, Sultana T, Ramalho-Santos M.
Reference: Bioessays. 2020 Feb 13. https://onlinelibrary.wiley.com/doi/full/10.1002/bies.201900232
PMID: 32053231
Maternal vitamin C regulates reprogramming of DNA methylation and germline development
Authors: DiTroia SP, Percharde M, Guerquin MJ, Wall E, Collignon E, Ebata KT, Mesh K, Mahesula S, Agathocleous M, Laird DJ, Livera G, Ramalho-Santos M.
Reference: Nature. 2019 Sep 04. https://doi.org/10.1038/s41586-019-1536-1
PMID: 31719689
A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity.
Authors: Percharde M, Lin CJ, Yin Y, Guan J, Peixoto GA, Bulut-Karslioglu A, Biechele S, Huang B, Shen X, Ramalho-Santos M.
Reference: Cell. 2018 Jun 19. pii: S0092-8674(18)30655-X. doi: 10.1016/j.cell.2018.05.043.
PMID: 29937225
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
Tet2 Rescues Age-Related Regenerative Decline and Enhances Cognitive Function in the Adult Mouse Brain.
Authors: Gontier G, Iyer M, Shea JM, Bieri G, Wheatley EG, Ramalho-Santos M, Villeda SA.
Reference: Cell Rep. 2018 Feb 20;22(8):1974-1981. doi: 10.1016/j.celrep.2018.02.001.
PMID: 29466726
Vitamin C induces specific demethylation of H3K9me2 in mouse embryonic stem cells via Kdm3a/b.
Authors: Ebata KT, Mesh K, Liu S, Bilenky M, Fekete A, Acker MG, Hirst M, Garcia BA, Ramalho-Santos M.
Reference: Epigenetics Chromatin. 2017 Jul 12;10:36. doi: 10.1186/s13072-017-0143-3. eCollection 2017.
PMID: 28706564