Miguel Branco
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brancolab.bsky.social
Miguel Branco
@brancolab.bsky.social
1.8K followers 1.1K following 130 posts
Transposons and epigenetics.
https://brancolaboratory.com/
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Reposted by Miguel Branco
smllmp.bsky.social
Molecular effects of transposable element sequences in mammalian cells #TESky

(Wen, MC.C., Welch, J.D. Genome Biol 26, 403 (2025)).

Interesting review of new-found functions of TEs in mammalian genomes, especially over the last three years.
doi.org/10.1186/s130... #TEWorldwide
Molecular effects of transposable element sequences in mammalian cells - Genome Biology
Transposable elements (TEs) are often epigenetically repressed in eukaryotic cells, but still affect the molecular state of the cell in certain contexts. A flurry of recent studies have elucidated new...
doi.org
November 28, 2025 at 8:05 AM
brancolab.bsky.social
Despite having been scooped big time by this paper from William Pastor's lab, really quite enjoyed reading it. Congrats to the authors.
Divergent roles of DNA methylation, TRIM28, and p53 surveillance in human embryonic and trophoblast stem cells
Transcriptional regulation of transposons and genes by TRIM28 and 5mC is critical for proper mammalian embryonic development, but the specific roles for these mediators in human embryonic and placenta...
www.biorxiv.org
November 28, 2025 at 10:56 AM
brancolab.bsky.social
😩
pedrobeltrao.bsky.social Pedro Beltrao @pedrobeltrao.bsky.social · 9d
Finally the scary example. The image of a western blot with a time course experiment, staining a protein of interest, showing the increase of protein over time and a second staining with a control antibody that does not change over time
November 21, 2025 at 1:58 PM
Reposted by Miguel Branco
alexdemendoza.bsky.social
Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9
Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes - Nature Genetics
Long-read sequencing in 18 unicellular eukaryotes reveals that 6mA is widespread across eukaryotes and is enriched at transcriptionally permissive regions, which are also marked by H3K4me3.
www.nature.com
November 18, 2025 at 12:00 PM
Reposted by Miguel Branco
hansonmark.bsky.social
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision. A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
November 11, 2025 at 11:52 AM
Reposted by Miguel Branco
bedform.org
ooof this feels like most every university rn
bunch of executives on the deck of a ship with only one guy rowing and a quote "I don't understand, after so many budget cuts why dont we move faster?"
November 12, 2025 at 3:28 AM
Reposted by Miguel Branco
erc.europa.eu
📣 Meet the new ERC Synergy Grant awardees!

Sixty-six research teams have been selected for funding, bringing together 239 scientists. Congratulations to all!

➡️ buff.ly/PSn3bi9

#EUfunded #HorizonEurope #ERCSyG
November 6, 2025 at 11:12 AM
brancolab.bsky.social
Transposable elements drive species-specific and tissue-specific transcriptomes in human development - PubMed
Our results characterize the global profile of TE-initiated transcription and enhance our understanding of TE contribution to the primate-specific gene regulatory networks in human development.
pubmed.ncbi.nlm.nih.gov
November 5, 2025 at 12:39 PM
brancolab.bsky.social
ERV3-MLT1 provides cis-regulatory elements for human placental functioning and are commonly dysregulated in human-specific preeclampsia - PubMed
We conclude that ERV3-MLT1functions as a trophoblast-specific CRE for several human genes and may be dysregulated in preeclampsia. As EPS8L1 has a form in maternal circulation, it may have utility in diagnostics.
pubmed.ncbi.nlm.nih.gov
November 5, 2025 at 12:39 PM
brancolab.bsky.social
Transposon invasion of primate genomes shaped human inflammatory enhancers and susceptibility to inflammatory diseases - PubMed
Human inflammatory response reflects adaptive alteration of immune-cell regulatory elements during human evolution. Yet the impact of the deeper evolutionary history of these elements, within primate genomes reshaped by transposon expansions, remains unclear. Tracing sequence changes in human immune …
pubmed.ncbi.nlm.nih.gov
November 4, 2025 at 1:46 PM
brancolab.bsky.social
Comparative analysis of rhesus macaque and human placental organoids highlights evolutionary differences in placentation - PubMed
Throughout evolution, the placenta has diversified in structure and composition while maintaining its essential role in supporting fetal development. Trophoblasts, cells responsible for nutrient exchange and immune modulation, are a conserved feature of all placentas. Although primate placentas shar …
pubmed.ncbi.nlm.nih.gov
November 3, 2025 at 8:22 AM
brancolab.bsky.social
The Chromosome 19 miRNA cluster guards trophoblasts against overacting innate immunity - PubMed
To maintain pregnancy health, the human placenta delicately balances protection of the developing fetus from invading pathogens with suppression of excessive inflammation that could lead to fetal and neonatal autoimmune disorders. Previous research, including our own, has shown that small RNA produc …
pubmed.ncbi.nlm.nih.gov
October 31, 2025 at 11:15 AM
brancolab.bsky.social
N6-methyladenosine on L1PA governs the trans-silencing of LTRs and restrains totipotency in naive human embryonic stem cells - PubMed
Transposable elements (TEs) occupy nearly half of the genome and drive developmental innovation, yet the mechanisms of silencing long terminal repeats (LTRs) remain incompletely understood. We demonstrate that methyltransferase-like 3 deficiency reverts naive human embryonic stem cells (hESCs) to a …
pubmed.ncbi.nlm.nih.gov
October 31, 2025 at 11:01 AM
brancolab.bsky.social
Young KRAB-zinc finger gene clusters are highly dynamic incubators of ERV-driven genetic heterogeneity in mice - PubMed
KRAB-zinc finger proteins (KZFPs) comprise the largest family of mammalian transcription factors, rapidly evolving within and between species. Most KZFPs in human and mice have been found to repress endogenous retroviruses (ERVs) and other retrotransposons, with KZFP gene numbers correlating with th …
pubmed.ncbi.nlm.nih.gov
October 31, 2025 at 10:54 AM
Reposted by Miguel Branco
labrowe.bsky.social
How do pluripotent stem cells resist harmful interferon responses to safeguard development? Through total epigenetic lockdown of ligands, sensors and effectors of IFN-I. In our preprint, James Holt shares his PhD discoveries on the ground state of immune evasion 😊: www.biorxiv.org/cgi/content/...
Epigenetic lockdown of type I interferon sensing and signalling in human pluripotent cells.
The Human Silencing Hub (HUSH) complex safeguards genome integrity in human somatic cells by repressing transposable elements and regulating type I interferon (IFN-I) induction. In early development, ...
www.biorxiv.org
October 29, 2025 at 6:03 PM
Reposted by Miguel Branco
maxvcg.bsky.social
Spread the word! There is a professor position opening at our University @upcite.bsky.social. There are several possible (great) labs to join, but if you are interested in DNA methylation and epigenetics in mammals, don't hesitate to contact me directly!
ijmonod.bsky.social Institut Jacques Monod @ijmonod.bsky.social · Oct 28
#JobOffer

💼 Un poste susceptible d’être vacant de Professeur en stabilité des génomes devrait s’ouvrir pour la rentrée 2026 au sein de l’Institut Jacques Monod

➡️ Informations concernant ce poste et la procédure de candidature 🔗 www.ijm.fr/poste-de-pro...
October 28, 2025 at 1:51 PM
Reposted by Miguel Branco
jakobssonasap.bsky.social
📣 New preprint from the Jakobsson lab!

We describe a detailed protocol to inhibit the expression of transposable elements in human pluripotent stem cells, developed thanks to @asapresearch.parkinsonsroadmap.org funding.
Special shoutout to @anitaada.bsky.social!

www.biorxiv.org/content/10.1...
A framework for efficient CRISPRi-mediated silencing of retrotransposons in human pluripotent stem cells
This protocol describes the workflow for transcriptional silencing of transposable elements (TEs) in human induced pluripotent stem cells (hiPSCs). The protocol illustrates how to design gRNAs to targ...
www.biorxiv.org
October 29, 2025 at 8:24 AM
Reposted by Miguel Branco
monteirolab.bsky.social
For those interested in GRN evolution, please join us!
October 28, 2025 at 12:31 AM
Reposted by Miguel Branco
robertseaborne.bsky.social
🚨Hiring a 2yr postdoc in the lab work on muscle biology, genomics & ALS. Expertise in the above advantageous, but work ethic, desire to learn/develop and being a good scientist/person more important

Good collab with @droch.bsky.social so travel to CPH involved as well

www.kcl.ac.uk/jobs/126245-...
Postdoctoral Research Associate in Muscle Biology and Genomics | King's College London
www.kcl.ac.uk
September 25, 2025 at 5:01 PM
brancolab.bsky.social
Activity of the SWI/SNF complex is indispensable for syncytiotrophoblast formation - PubMed
Developmental transitions are characterized by coordinated changes in lineage-specific gene expression programs and chromatin states. Yet, how these shifts in cell fate occur during placental development remains largely unknown. Here, we used human trophoblast stem cells (hTSCs), genetic depletion, …
pubmed.ncbi.nlm.nih.gov
October 24, 2025 at 2:17 PM
Reposted by Miguel Branco
loke-ctr.bsky.social
Looking to pursue cutting-edge research in early development, maternal-fetal interaction, or placental biology? See 👇

- Funded PhD www.trophoblast.cam.ac.uk/phd-students...
- Next Generation Fellowship www.trophoblast.cam.ac.uk/next-generat...
- MPhil www.mphil.bio.cam.ac.uk/mphil-pathwa...
October 2, 2025 at 8:15 AM
Reposted by Miguel Branco
robklose.bsky.social
Come join us in Geneva for everything epigenetics and gene regulation. It will be a great meeting! Please repost!
www.keystonesymposia.org/conferences/...
Epigenetics and Gene Regulation in Health and Disease: Linking Basic Mechanisms with Therapeutic Opportunities | Keystone Symposia
Join us at the Keystone Symposia on Epigenetics and Gene Regulation in Health and Disease: Linking Basic Mechanisms with Therapeutic Opportunities, March 2026, in Geneva, with field leaders!
www.keystonesymposia.org
October 17, 2025 at 2:36 PM
Reposted by Miguel Branco
robklose.bsky.social
We are recuiting two new Associate Professors here in Oxford Biochemistry. Come join us! Reach out to me if you have any questions. Please repost! tinyurl.com/mr3m7bd3
October 17, 2025 at 2:56 PM
brancolab.bsky.social
A TE insertion controls throat colour in wheatears. The gene involved (ASIP) is the same one that is epigenetically affected by an IAP insertion the famous Avy mice.

As if we needed more reasons to love TEs.
A mosaic of modular variation at a single gene underpins convergent plumage coloration
The reshuffling of genomic variation from multiple origins is an important contributor to phenotypic diversification, yet insights into the evolutionary trajectories of this combinatorial process and ...
www.science.org
October 17, 2025 at 11:43 AM
brancolab.bsky.social
A histone methyltransferase-independent function of PRC2 controls small RNA dynamics during programmed DNA elimination in Paramecium - PubMed
To limit transposable element (TE) mobilization, most eukaryotes have evolved small RNAs to silence TE activity via homology-dependent mechanisms. Small RNAs, 20-30 nucleotides in length, bind to PIWI...
pubmed.ncbi.nlm.nih.gov
October 17, 2025 at 11:24 AM