Publications_Index — Santos Lab

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 LabSeptember 7, 20232023

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 LabJanuary 12, 20232023

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 LabAugust 30, 20222022

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 LabSeptember 17, 20212021

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 LabAugust 11, 20212021

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 LabMarch 25, 20212021

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 LabFebruary 5, 20212021

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 LabJanuary 20, 20212021

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 LabNovember 25, 20202020

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 LabMarch 10, 20202020

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 LabFebruary 19, 20202020

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 LabSeptember 4, 20192019

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 LabJune 19, 20182-cell stage, Dux, ESCs, Kap1, LINE1, MERVL, Nucleolin, hypertranscription, rRNA, retrotransposons, 2018

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

Santos LabFebruary 20, 2018Tet2, adult neurogenesis, aging; cognition, hippocampus, hydroxymethylation, rejuvenation, 2018

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

CHD1 loss sensitizes prostate cancer to DNA damaging therapy by promoting error-prone double-strand break repair

Authors: Shenoy TR, Boysen G, Wang MY, Xu QZ, Guo W, Koh FM, Wang C, Zhang LZ, Wang Y, Gil V, Aziz S, Christova R, Rodrigues DN, Crespo M, Rescigno P, Tunariu N, Riisnaes R, Zafeiriou Z, Flohr P, Yuan W, Knight E, Swain A, Ramalho-Santos M, Xu DY, de Bono J, Wu H.
Reference: Ann Oncol. 2017 Jul 1;28(7):1495-1507. doi: 10.1093/annonc/mdx165.
PMID: 28383660

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 LabJune 6, 2017Myc, P-TEFb, cell competitionm, germline, hypertranscription, l-Myc, n-Myc, primordial germ, 2017

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

Inhibition of mTOR induces a paused pluripotent state.

Authors: Bulut-Karslioglu A, Biechele S, Jin H, Macrae TA, Hejna M, Gertsenstein M, Song JS, Ramalho-Santos M.
Reference: Nature. 2016 Dec 1;540(7631):119-123. doi: 10.1038/nature20578. Epub 2016 Nov 23.
PMID: 27880763

Santos LabDecember 1, 20162016

Publications From The Santos Lab