Publications From The Santos Lab

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. https://www.cell.com/stem-cell-reports/fulltext/S2213-6711(25)00010-4

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 and Development, 2024. http://www.genesdev.org/cgi/doi/10.1101/gad.351979.124

Santos Lab 10/15/24 Santos Lab 10/15/24

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

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 9/17/21 Santos Lab 9/17/21

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.

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 2/5/21 Santos Lab 2/5/21

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

Santos Lab 1/20/21 Santos Lab 1/20/21

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

Santos Lab 11/25/20 Santos Lab 11/25/20

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

Santos Lab 3/10/20 Santos Lab 3/10/20

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

Santos Lab 2/19/20 Santos Lab 2/19/20

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

Santos Lab 9/4/19 Santos Lab 9/4/19

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

Santos Lab 6/19/18 Santos Lab 6/19/18

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

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 2/20/18 Santos Lab 2/20/18

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

Santos Lab 7/12/17 Santos Lab 7/12/17

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