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Miguel Ramalho-Santos

@mrsantos.bsky.social
503 followers 162 following 77 posts

Scientist and Professor in Developmental Epigenetics. Lunenfeld-Tanenbaum Research Institute Dpt Molecular Genetics, University of Toronto, Canada Lab: mrsantoslab.org Coimbra, Portugal -> Cambridge, MA, USA -> S. Francisco, CA, USA -> Toronto, ON, Canada

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Miguel Ramalho-Santos @mrsantos.bsky.social · 28/09/2026
We are recruiting at the Lunenfeld-Tanenbaum Research Institute (LTRI) and the University of Toronto! In the areas of Reproduction, Pregnancy and Developmental Biology, at Assistant or Associate Professor level. Deadline: Nov 29, 2026 Find more and apply👇: 🔗 apply.interfolio.com/192324
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Miguel Ramalho-Santos @mrsantos.bsky.social · 25/09/2026
Our PhD student Bryn Martin received the Dr. Louis Siminovitch Catalyst Award from the Dep. of Molecular Genetics at U. Toronto! For excellence in research and mentoring. Note: Louis Siminovitch was a founder of both the Department and the LTRI. Congratulations, Bryn! @sinaihealth.bsky.social
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Miguel Ramalho-Santos @mrsantos.bsky.social · 08/09/2026
Discussed @mrsantos.bsky.social Lit Review: Molecular mediators of cold adaptation in mammalian cells. www.nature.com/articles/s42...
nature.com
Molecular mediators of cold adaptation in mammalian cells - Communications Biology
This review outlines how mammalian cells adapt to cold via ion channels, uncoupling proteins, epigenetic changes, and RNA-binding proteins, with insights from hibernators highlighting therapeutic pote...
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Miguel Ramalho-Santos @mrsantos.bsky.social · 31/08/2026
Discussed @mrsantos.bsky.social Lit Review: Human haematopoietic stem cells remember inflammatory stress. www.nature.com/articles/s41...
nature.com
Human haematopoietic stem cells remember inflammatory stress - Nature
Using xenograft inflammation–recovery models and single-cell multiomics, a haematopoietic stem cell population after inflammatory stress is identified.
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Miguel Ramalho-Santos @mrsantos.bsky.social · 17/08/2026
Congratulations Giacomo Furlan + Evelyne Collignon for the paper out now in Dec Cell! Mouse embryos don't go to sleep unless told to do so by Nodal/Smad2. Thank you, Liz Robertson! @cp-devcell.bsky.social @sinaihealth.bsky.social 2month full-text access here: www.sciencedirect.com/science/arti...
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Miguel Ramalho-Santos @mrsantos.bsky.social · 27/07/2026
Lab artists go the Art Gallery of Ontario! - Jul 2026
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Miguel Ramalho-Santos @mrsantos.bsky.social · 07/07/2026
Congratulations to our Lab PhD student on successfully passing the PhD defense on June 22, 2026! Your dedication, perseverance, and commitment have culminated in this remarkable achievement. Wishing you continued success in the next chapter of your career. Congratulations, Dr.Andrew!
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Miguel Ramalho-Santos @mrsantos.bsky.social · 17/06/2026
Discussed @mrsantos.bsky.social lit review: Germline epigenome editing identifies H3K9me3 as a mediator of intergenerational DNA methylation recovery in mice. www.nature.com/articles/s41...
nature.com
Germline epigenome editing identifies H3K9me3 as a mediator of intergenerational DNA methylation recovery in mice - Nature Communications
The authors develop a system to erase DNA methylation at H19-DMR in mouse sperm. Despite loss, methylation partly recovers via H3K9me3 after fertilization, revealing partial intergenerational epigenet...
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Miguel Ramalho-Santos @mrsantos.bsky.social · 15/06/2026
Love the smell of "accepted in principle" in the (Monday) morning...
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Miguel Ramalho-Santos @mrsantos.bsky.social · 10/06/2026
Discussed @mrsantos.bsky.social lit review: Nascent transcriptome of embryonic genome activation reveals a regulatory axis linking transcriptional priming to early lineage specification in mouse embryos. academic.oup.com/nar/article/...
academic.oup.com
Nascent transcriptome of embryonic genome activation reveals a regulatory axis linking transcriptional priming to early lineage specification in mouse embryos
Abstract. Embryonic genome activation (EGA) marks a critical developmental transition, yet its regulatory architecture remains incompletely defined. Here,
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Miguel Ramalho-Santos @mrsantos.bsky.social · 08/05/2026
In our latest anti-bias lab meeting, we discussed the global impacts for societies and scientific research of the blockade of the Strait of Hormuz arising from the war of US and Israel with Iran.
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Miguel Ramalho-Santos @mrsantos.bsky.social · 02/04/2026
Discussed @mrsantos.bsky.social lit review: Live-Cell RNA Imaging via Clickable TriPPPro Nucleotide Reporters. onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com
Live‐Cell RNA Imaging via Clickable TriPPPro Nucleotide Reporters
The intracellular delivery of trans-cyclooctene and bicyclo[6.1.0]nonyne as sterically demanding groups for the inverse electron-demand Diels–Alder was achieved by the triphosphate prodrug (TriPPPro)...
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Miguel Ramalho-Santos @mrsantos.bsky.social · 25/03/2026
Discussed @mrsantos.bsky.social lit review: Heritable changes in chromatin contacts associated with transgenerational susceptibility to diet induced insulin dysregulation and obesity. rdcu.be/e910l
rdcu.be
Heritable changes in chromatin contacts associated with transgenerational susceptibility to diet-induced insulin dysregulation and obesity
Nature Communications - Gestational exposure of mice to the obesogen tributyltin alters 3-D chromatin interactions in primordial germ cells leading to stable reduction of hepatic Ide expression and...
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Miguel Ramalho-Santos @mrsantos.bsky.social · 24/03/2026
Great work by Brandon Cho, our fantastic student-turned-postdoc, out now in Oncogene. Great collaboration w Linda Penn (Toronto). We put the chromatin remodeller CHD1 in an "epistasis battle" with overexpression of THE oncogene MYC in a breast cancer model. 1/2 www.nature.com/articles/s41...
nature.com
CHD1 is a synthetic lethal vulnerability in MYC-driven breast cancer - Oncogene
Oncogene - CHD1 is a synthetic lethal vulnerability in MYC-driven breast cancer
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Miguel Ramalho-Santos @mrsantos.bsky.social · 12/03/2026
Really proud of our stellar lab manager, Kirti Mittal! 1st author in a paper out in @genesdev.bsky.social. From chromatin-bound RNA to functional studies in human ESCs, she discovered a new role for alpha-satellite repeats in nuclear compartmentalization. Congrats! pubmed.ncbi.nlm.nih.gov/41730687/
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Miguel Ramalho-Santos @mrsantos.bsky.social · 25/02/2026
Discussed @mrsantosny.bsky.social lit review: Stress controls heterochromatin inheritance via histone H3 ubiquitylation. www.nature.com/articles/s41...
nature.com
Stress controls heterochromatin inheritance via histone H3 ubiquitylation - Nature
A histone ubiquitin-dependent regulatory hub governs stimulus-dependent heterochromatin propagation, with important implications for understanding mechanisms governing rapid changes in the epigen...
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Miguel Ramalho-Santos @mrsantos.bsky.social · 18/02/2026
Discussed @mrsantos.bsky.social lit review: Cell-type-specific RNA polymerase II activity maps in intact tissues provide a gateway to mammalian gene regulatory mechanisms in vivo. www.cell.com/developmenta...
cell.com
Cell-type-specific RNA polymerase II activity maps in intact tissues provide a gateway to mammalian gene regulatory mechanisms in vivo
Chovatiya et al. developed PReCIS-seq, an in vivo approach that maps transcriptionally engaged RNA polymerase II in Cre-targeted cells within intact mouse tissues, without cell isolation. They report ...
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Miguel Ramalho-Santos @mrsantos.bsky.social · 02/12/2025
Discussed @mrsantos.bsky.social lit review: Stabilizing a mammalian RNA thermometer confers neuroprotection in subarachnoid hemorrhage. www.nature.com/articles/s41...
nature.com
Stabilizing a mammalian RNA thermometer confers neuroprotection in subarachnoid hemorrhage - Nature Communications
Here the authors identify RNA G-quadruplexes as temperature-sensitive regulators of alternative splicing and gene expression, opening potential therapeutic avenues such as neuroprotection with potassi...
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Miguel Ramalho-Santos @mrsantos.bsky.social · 26/11/2025
Discussed @mrsantos.bsky.social lit review: Analog epigenetic memory revealed by targeted chromatin editing. www.sciencedirect.com/science/arti...
sciencedirect.com
Analog epigenetic memory revealed by targeted chromatin editing
Cells store information by means of chromatin modifications that persist through cell divisions and can hold gene expression silenced over generations…
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Miguel Ramalho-Santos @mrsantos.bsky.social · 10/11/2025
Trick or Treat! 👻🎃
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Miguel Ramalho-Santos @mrsantos.bsky.social · 22/10/2025
Discussed @mrsantos.bsky.social lit review: Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells. www.biorxiv.org/content/10.1...
biorxiv.org
Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells
Acquisition of specific cell shapes and morphologies is a central component of cell fate transitions. Although signaling circuits and gene regulatory networks that regulate pluripotent stem cell diffe...
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Miguel Ramalho-Santos @mrsantos.bsky.social · 21/10/2025
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Miguel Ramalho-Santos @mrsantos.bsky.social · 15/10/2025
Discussed @mrsantos.bsky.social lit review: Preventing CpG hypermethylation in oocytes safeguards mouse development. www.cell.com/developmenta...
cell.com
Preventing CpG hypermethylation in oocytes safeguards mouse development
Kawamura et al. show that H3K36me2 removal by the KDM2A and KDM2B histone demethylases restricts DNMT3A in establishing global DNA methylation in oocytes. Maternal Kdm2a/Kdm2b knockout embryos die dur...
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Miguel Ramalho-Santos @mrsantos.bsky.social · 09/10/2025
(1/4) New Pre-print! 🌟 Embryonic development is usually seen as a continuous process, yet some embryos can pause their development to survive harsh conditions, a phenomenon known as diapause. How this pausing is actively maintained has remained a mystery.
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Reposted by Miguel Ramalho-Santos
ISSCR @isscr.org · 08/10/2025
The ISSCR is seeking nominations for Vice President and three Director positions. This is an opportunity to help shape the future of stem cell research and contribute to a global scientific community. Nominations are due 22 October 2025. Learn more 👉 www.isscr.org/nominations
isscr.org
2026 Election Nominations — International Society for Stem Cell Research
Elections and nominations for the International Society for Stem Cell Research board of directors and officers.
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Miguel Ramalho-Santos @mrsantos.bsky.social · 07/10/2025
John Gurdon was a true giant: - founder of cell reprogramming; - founder of molecular embryology; - unabashed advocate for basic research; - advisor to numerous successful trainees/PIs; - gentle human that touched so many. In dark times with science under attack, let his vision be a guiding light.
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Miguel Ramalho-Santos @mrsantos.bsky.social · 24/09/2025
🚨 JOB ALERT 🚨 We are hiring TWO principal investigators in systems, cellular, chemical or molecular biology in Toronto, Canada at @sinaihealth.bsky.social. We provide a generous startup, fully funded salary and academic appointment at U of Toronto. Apply now or repost!
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Miguel Ramalho-Santos @mrsantos.bsky.social · 09/09/2025
Thank you for this honor and the continued trust in our group's research! We hope that our work will honor the memory and legacy of Anne and Max Tanenbaum. It is truly a privilege to be part of the amazing communities of @uoftmedicine.bsky.social and @sinaihealth.bsky.social.
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Miguel Ramalho-Santos @mrsantos.bsky.social · 04/09/2025
(1/4) New preprint from the lab! The MYC transcription factor is a potent cancer driver when its expression is dysregulated, but efforts to target MYC directly have not been fruitful. We identify CHD1 as a synthetic lethal vulnerability in MYC-driven breast cancer. www.biorxiv.org/content/10.1...
biorxiv.org
CHD1 is a synthetic lethal vulnerability in MYC-driven breast cancer
The MYC transcription factor is a key regulator of growth during development and a potent cancer driver when its expression is dysregulated. Strategies to inhibit MYC oncogenic activity would mark a s...
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Miguel Ramalho-Santos @mrsantos.bsky.social · 12/08/2025
‪Discussed @mrsantos.bsky.social lit review: A single-cell time-lapse of mouse prenatal development from gastrula to birth. www.nature.com/articles/s41...
nature.com
A single-cell time-lapse of mouse prenatal development from gastrula to birth - Nature
Single-cell transcriptome profiling of mouse embryos and newborn pups is combined with previously published data to construct a tree of cell-type relationships tracing development from zygote to birth...
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Miguel Ramalho-Santos @mrsantos.bsky.social · 25/07/2025
🌞 Let's enjoy the summer time in Toronto! 🏖️
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Miguel Ramalho-Santos @mrsantos.bsky.social · 22/07/2025
Discussed @mrsantos.bsky.social lit review: Recovering undersampled single-cell transcriptomes with HyperCell. www.researchsquare.com/article/rs-6...
researchsquare.com
Recovering undersampled single-cell transcriptomes with HyperCell
Single-cell transcriptomic technology has now matured, allowing quantification of mRNA transcripts corresponding to tens of thousands of genes within a cell. However, still only a small fraction of th...
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Miguel Ramalho-Santos @mrsantos.bsky.social · 21/07/2025
(1/3) Latest preprint from the lab! 📝 This work points towards regulatory roles of alpha satellite RNA in nuclear compartmentalization and tuning ribosomal RNA expression in naïve human embryonic stem cells. doi.org/10.1101/2025...
doi.org
Alpha satellite RNA marks the perinucleolar compartment and represses ribosomal RNA expression in naïve human embryonic stem cells
While most newly synthesized RNA is exported to the cytoplasm, a portion of non-coding RNA is retained in the nucleus and remains highly associated with chromatin. The strong binding of this RNA fract...
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Reposted by Miguel Ramalho-Santos
Maria Alcolea @mariapalcolea.bsky.social · 04/07/2025
⏳Only 1 week left to submit your talk for the Fusion Stem Cells & Cancer Conference! 🧪Share your exciting discoveries with us!! 📍Malta 🗓️Talk Deadline: July 10 🔗http://bit.ly/49sCfJp @joneslabucsf.bsky.social, Kathrin Plath, @katemiro.bsky.social at @fusionconf.bsky.social
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Miguel Ramalho-Santos @mrsantos.bsky.social · 17/06/2025
‪Discussed @mrsantos.bsky.social lit review: Maternal iron deficiency causes male-to-female sex reversal in mouse embryos www.nature.com/articles/s41...
nature.com
Maternal iron deficiency causes male-to-female sex reversal in mouse embryos - Nature
Iron-deficient conditions in pregnant mice can cause XY mouse embryos to develop female rather than male genitalia, revealing that iron metabolism has a role in determining male sex in mice.
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Miguel Ramalho-Santos @mrsantos.bsky.social · 12/06/2025
Congrats to Dr. Cho on the successful PhD defense!
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Miguel Ramalho-Santos @mrsantos.bsky.social · 11/06/2025
Discussed @mrsantos.bsky.social lit review: Stem-loop binding protein is a multifaceted cellular regulator of HIV-1 replication. pubmed.ncbi.nlm.nih.gov/27454292/
pubmed.ncbi.nlm.nih.gov
Stem-loop binding protein is a multifaceted cellular regulator of HIV-1 replication - PubMed
A rare subset of HIV-1-infected individuals is able to maintain plasma viral load (VL) at low levels without antiretroviral treatment. Identifying the mechanisms underlying this atypical response to i...
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Miguel Ramalho-Santos @mrsantos.bsky.social · 06/05/2025
Discussed @mrsantos.bsky.social lit review: Identification of genes supporting cold resistance of mammalian cells: lessons from a hibernator. www.nature.com/articles/s41...
nature.com
Identification of genes supporting cold resistance of mammalian cells: lessons from a hibernator - Cell Death & Disease
Cell Death & Disease - Identification of genes supporting cold resistance of mammalian cells: lessons from a hibernator
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Miguel Ramalho-Santos @mrsantos.bsky.social · 30/04/2025
Discussed @mrsantos.bsky.social lit review: Genome-coverage single-cell histone modifications for embryo lineage tracing. www.nature.com/articles/s41...
nature.com
Genome-coverage single-cell histone modifications for embryo lineage tracing - Nature
Two new methods, target chromatin indexing and tagmentation (TACIT) and combined TACIT (CoTACIT), enabled single-cell profiling of the epigenome and lineage tracing from mouse zygotes to blastocy...
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Miguel Ramalho-Santos @mrsantos.bsky.social · 23/04/2025
Discussed @mrsantos.bsky.social lit review: How epigenetic inheritance fails to explain the Black-White health gap. www.sciencedirect.com/science/arti...
sciencedirect.com
How epigenetic inheritance fails to explain the Black-White health gap
Slavery, legal segregation, and ongoing discrimination have exacted an unfathomable toll on the black population in the United States, particularly wi…
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Miguel Ramalho-Santos @mrsantos.bsky.social · 02/04/2025
Discussed @mrsantos.bsky.social lit review: RNA polymerase II at histone genes predicts outcome in human cancer. www.science.org/doi/10.1126/...
science.org
RNA polymerase II at histone genes predicts outcome in human cancer
Genome-wide hypertranscription is common in human cancer and predicts poor prognosis. To understand how hypertranscription might drive cancer, we applied our formalin-fixed paraffin-embedded (FFPE)–cl...
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Miguel Ramalho-Santos @mrsantos.bsky.social · 13/03/2025
Thank you @isscr.org Stem Cell Reports for selecting our work for the March cover! Caption: (1/3) In this issue, Kim and Ramalho-Santos provide a perspective on the history of stem cell transcriptomics. They show that a stemness signature from the early 2000’s foreshadowed hypertranscription.
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Reposted by Miguel Ramalho-Santos
Research at Sinai Health @sinaihealth.bsky.social · 13/02/2025
Read the recent review by @mrsantos.bsky.social that marks two decades of stem cell breakthroughs 🔬 🙌 🎉 Discover how a serendipitous discovery of a stem cell gene signature has led to understanding hypertranscription, with implications for health and disease. www.cell.com/stem-cell-re...
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Reposted by Miguel Ramalho-Santos
Romain Koszul @rkoszul.bsky.social · 13/02/2025
Two more weeks to apply to join us in Paris ! research.pasteur.fr/en/call/call...
research.pasteur.fr
Call for applications 2025 - Creation of new research groups at the Institut Pasteur - Research
The Institut Pasteur launches an international call to recruit new junior research group leaders in the application of cutting-edge transdisciplinary approaches to the exploration of host-microbe, tis...
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Miguel Ramalho-Santos @mrsantos.bsky.social · 07/02/2025
Out now at Stem Cell Reports @isscr.org: a Perspective on the history of stem cell transcriptomics. We show that a stemness signature from the early 2000’s (Miguel's PhD work) foreshadowed stem cell hypertranscription. Thanks @pairedbox.bsky.social for this adventure! www.cell.com/stem-cell-re...
cell.com
20 years of stemness: From stem cells to hypertranscription and back
Kim and Ramalho-Santos provide a historical perspective starting from the first studies in stem cell transcriptomics in the early 2000s to our present day understanding of hypertranscription in stem c...
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Miguel Ramalho-Santos @mrsantos.bsky.social · 29/01/2025
🗞️Breaking News: our team was just awarded a new, 5-year CIHR Project Grant for our studies of the regulation of hypertranscription! We are very grateful to the Canadian Institutes of Health Research for their continued support of our research in developmental epigenetics. @sinaihealth.bsky.social
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Miguel Ramalho-Santos @mrsantos.bsky.social · 02/01/2025
We found that copies of the LINE1 transposon are key “architects” of the nucleolar genome in human embryonic stem cells. This work brings together two facets of Barbara McClintock’s pioneering research: nucleolar organizer regions and transposable elements. www.genesdev.org/cgi/doi/10.1...
genesdev.org
LINE1 elements at distal junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells
A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields
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