Miguel Ramalho-Santos

Research

Chromatin Transcription Epigenetics Embryonic Stem Cells Developmental Biology Breast Cancer Models Hypertranscription Heterochromatin

Latest papers

Nodal/Smad2 signaling sustains developmental pausing by repressing Pparg-mediated lipid metabolism.
Developmental cell · 2026 · senior author
α-Satellite RNA marks the perinucleolar compartment and represses ribosomal RNA expression in naive human embryonic stem cells.
Genes & development · 2026 · senior author
CHD1 is a synthetic lethal vulnerability in MYC-driven breast cancer.
Oncogene · 2026 · senior author

All 22 publications

Latest funding

Regulation and function of hypertranscription
CIHR · 2024 · Nominated PI
$1,132,200
Regulation of nuclear compartmentalization by LINE1 RNA
CIHR · 2023 · Nominated PI
$1,063,350
Molecular and behavioural consequences of maternal depression and antidepressant use during pregnancy
CIHR · 2022 · Supervisor
$135,000

All 6 grants and awards

22 publications.

01

Nodal/Smad2 signaling sustains developmental pausing by repressing Pparg-mediated lipid metabolism.

Furlan G, Martin SB, Cho B, Ng YY, McClymont SA, Rahman A, Robertson EJ, Collignon E, Ramalho-Santos M

Developmental cell2026Senior author

DOI: 10.1016/j.devcel.2026.07.006 PMID: 42551436

02

α-Satellite RNA marks the perinucleolar compartment and represses ribosomal RNA expression in naive human embryonic stem cells.

Mittal K, Ataei L, Ramalho-Santos M

Genes & development2026Senior author

DOI: 10.1101/gad.353162.125 PMID: 41730687

03

CHD1 is a synthetic lethal vulnerability in MYC-driven breast cancer.

Cho B, Furlan G, Lin P, Shen M, Mittal K, Mazzanti A, Penn LZ, Ramalho-Santos M

Oncogene2026Senior author

DOI: 10.1038/s41388-026-03709-9 PMID: 41795021

04

Publisher Correction: m6A RNA methylation orchestrates transcriptional dormancy during paused pluripotency.

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

Nature cell biology2025Senior author

DOI: 10.1038/s41556-025-01664-3 PMID: 40175667

05

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

Kim YK, Ramalho-Santos M

Stem cell reports2025Senior author

DOI: 10.1016/j.stemcr.2025.102406 PMID: 39919752

06

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

Ataei L, Zhang J, Monis S, Giemza K, Mittal K, Yang J, Shimomura M, McStay B, Wilson MD, Ramalho-Santos M

Genes & development2025Senior author

DOI: 10.1101/gad.351979.124 PMID: 39797762

07

LINE1 and PRC2 control nucleolar organization and repression of the 8C state in human ESCs.

Zhang J, Ataei L, Mittal K, Wu L, Caldwell L, Huynh L, Sarajideen S, Tse K, Simon MM, Mazid MA, Cook DP, Trcka D, Kwan T, Hoffman MM, Wrana JL, Esteban MA, Ramalho-Santos M

Developmental cell2025Senior author

DOI: 10.1016/j.devcel.2024.09.024 PMID: 39413784

08

Hypertranscription: the invisible hand in stem cell biology.

Kim YK, Collignon E, Martin SB, Ramalho-Santos M

Trends in genetics : TIG2024Senior author

DOI: 10.1016/j.tig.2024.08.005 PMID: 39271397

09

m6A RNA methylation orchestrates transcriptional dormancy during paused pluripotency.

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

Nature cell biology2023Senior author

DOI: 10.1038/s41556-023-01212-x PMID: 37696947

10

m 6 A RNA methylation orchestrates transcriptional dormancy during developmental pausing.

Collignon E, Cho B, Fothergill-Robinson J, Furlan G, Ross RL, Limbach PA, Ramalho-Santos M

bioRxiv : the preprint server for biology2023Senior author

DOI: 10.1101/2023.01.30.526234 PMID: 36778216

Regulation and function of hypertranscription

Nominated PICIHR2024Project Grant

Principal investigators: Ramalho-Santos, Miguel

Keywords: Breast Cancer Models; Chromatin; Embryonic Stem Cells; Epigenetics; Hypertranscription; Transcription

$1,132,200

Regulation of nuclear compartmentalization by LINE1 RNA

Nominated PICIHR2023Project Grant

Principal investigators: Ramalho-Santos, Miguel

Keywords: Heterochromatin; Human Embryonic Stem Cells; Line1; Nuclear Compartments; Nuclear Lamina; Nucleolus; Transposable Elements

$1,063,350

Molecular and behavioural consequences of maternal depression and antidepressant use during pregnancy

SupervisorCIHR2022CIHR Fellowship

Principal investigators: McClymont, Sarah Anne

Keywords: Antidepressants; Atac-Seq; Depression; Development; Epigenetics; Neural Development; Pre-Implantation; Primordial Germ Cells; Rna-Seq; Serotonin

$135,000

Transcriptional and post-transcriptional regulation of mammalian developmental pausing

Nominated PICIHR2021Project Grant

Principal investigators: Ramalho-Santos, Miguel

Keywords: Cellular Dormancy; Chromatin; Developmental Biology; Diapause; Embryonic Stem Cells; Histone Modifications; Pre-Implantation Development; Rna Modifications; Transcription

$948,600

Regulation and Function of Hypertranscription during Mammalian Development

Nominated PICIHR2019Project Grant

Principal investigators: Ramalho-Santos, Miguel

Keywords: Chromatin; Developmental Biology; Embryology; Epigenetics; Mouse; Stem Cells; Transcription

$1,074,826

Canada 150 Research Chair

Nominated PICIHR2017Canada 150 Research Chairs - CIHR Funded

Principal investigators: Ramalho-Santos, Miguel

Keywords: C150

$2,450,000

From CIHR, NSERC and SSHRC funding decisions: CIHR since 2008, NSERC since 1991 and SSHRC since 1998, including their latest published competition results.

Frequent collaborators

Lunenfeld-Tanenbaum Research Institute
Radiation Oncology/Medical Physics
Genetics and Genome Biology
Donnelly Centre

Co-authors at University of Toronto, colored by department. Thicker lines mean more shared papers; select anyone to open their profile and their own map.

Quaid Morris

Donnelly Centre

1 shared papers, latest 2021

Benjamin Haibe-Kains

Radiation Oncology/Medical Physics

1 shared papers, latest 2021

Jason Moffat

Genetics and Genome Biology

1 shared papers, latest 2021

Write to this professor

A short, specific email works best. This draft uses one of their recent papers; replace the parts in brackets with your own details before sending.

Applying for

Paper to mentionMention their CIHR grant from 2024

Subject: Prospective PhD student: Chromatin Dear Professor Ramalho-Santos, My name is [your name], and I am a [your current degree or role] at [your institution]. I am applying for a PhD position starting in [term and year]. I read your paper "Nodal/Smad2 signaling sustains developmental pausing by repressing Pparg-mediated lipid metabolism." (2026), and it connects closely to my own work on [your research topic]. [One or two sentences on what you did and what you learned.] I also saw your CIHR-funded project "Regulation and function of hypertranscription" (2024), and I would be glad to contribute to work in that direction. Are you accepting new PhD students for [term and year]? I have attached my CV and transcripts, and I would be glad to talk at a time that suits you. Thank you for your time. Kind regards, [your name]

Miguel Ramalho-Santos

Research

Latest papers

Latest funding

Nodal/Smad2 signaling sustains developmental pausing by repressing Pparg-mediated lipid metabolism.

&#x3b1;-Satellite RNA marks the perinucleolar compartment and represses ribosomal RNA expression in naive human embryonic stem cells.

CHD1 is a synthetic lethal vulnerability in MYC-driven breast cancer.

Publisher Correction: m6A RNA methylation orchestrates transcriptional dormancy during paused pluripotency.

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

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

LINE1 and PRC2 control nucleolar organization and repression of the 8C state in human ESCs.

Hypertranscription: the invisible hand in stem cell biology.

m6A RNA methylation orchestrates transcriptional dormancy during paused pluripotency.

m 6 A RNA methylation orchestrates transcriptional dormancy during developmental pausing.

Regulation and function of hypertranscription

Regulation of nuclear compartmentalization by LINE1 RNA

Molecular and behavioural consequences of maternal depression and antidepressant use during pregnancy

Transcriptional and post-transcriptional regulation of mammalian developmental pausing

Regulation and Function of Hypertranscription during Mammalian Development

Canada 150 Research Chair

Frequent collaborators

Quaid Morris

Benjamin Haibe-Kains

Jason Moffat

α-Satellite RNA marks the perinucleolar compartment and represses ribosomal RNA expression in naive human embryonic stem cells.