Manthan

Hominoid-specific retrotransposons fuel regulatory novelty in early brain development , by @retrogenomics.bsky.social.

➡️ www.cell.com/cell-genomic...

Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotency In primed human pluripotent stem cells (hPSCs) resembling post-implantation epiblast, numerous lineage-specific enhancers assume the poised chromatin state, co-marked by H3K4me1 and Polycomb-associate...

Many enhancers that drive tissue-specific gene expression are already connected to gene promoters in human pluripotent cells.

In a new preprint, we share some clues about when, how, and why this happens!

www.biorxiv.org/content/10.1...

A human-specific regulatory mechanism revealed in a pre-implantation model Nature - Genetic manipulation of blastoids reveals the role of recently emerged transposable elements and genes in human development.

Today in @nature.com, we present our work leveraging functional genomics and human blastoids to uncover a human-specific mechanism in preimplantation development driven by the endogenous retrovirus HERVK.
Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD

Histone acetylation - not always about transcriptional activation: H4K16ac safeguards the genome replication program by repressing premature replication of heterochromatin. Well done Marta Milan! tinyurl.com/yuy9m8t3

Emergence of activation or repression in transcriptional control under a fixed molecular context | PNAS Transcription factors (TFs) can be both activators and repressors of gene transcription. This can manifest as “duality,” where the transcriptional ...

Emergence of activation or repression in transcriptional control under a fixed molecular context www.pnas.org/doi/10.1073/...

Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication.
www.biorxiv.org/content/10.1...
A🧵👇

Hepatic acetyl-CoA metabolism modulates neuroinflammation and depression susceptibility via acetate @cp-cellmetabolism.bsky.social
www.cell.com/cell-metabol...

Our study on the role of LTR5HS and SVAs in regulation of human neural crest migration is now published as peer-reviewed paper on @molsystbiol.org!
Congrats to first author brilliant postdoc Laura Deelen, and all the authors involved! @imperialsci.bsky.social
www.embopress.org/doi/full/10....

L1 insertion intermediates recombine with one another or with DNA breaks to form genome rearrangements LINE-1 retrotransposition is common in human cancers and rearrangements at insertion sites can contribute to cancer-driving oncogene amplifications and promote genome instability. However, the mechani...

Check out our pre-print: We show that L1 insertion intermediates can recombine with one another or with DNA breaks to form genome rearrangements, highlighting the risk of L1 retrotransposition generating substrates for aberrant recombination and genome instability.

www.biorxiv.org/content/10.1...

Functional maps of a genomic locus reveal confinement of an enhancer by its target gene Genes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alt...

✨Exciting news: the main story of my PhD is out in Science!

Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.

📖 Read the full story here: www.science.org/doi/10.1126/...

WDR5 and Myc Cooperate to Regulate Formation of Neural Crest Stem Cells https://www.biorxiv.org/content/10.1101/2025.09.19.677424v1

Have you ever wondered how the exact location of a gene affects it's activity?

The main story of my PhD deals with exactly that question, and is now published in Science! ✨
www.science.org/doi/10.1126/...

My amazing co-author and friend @mathiaseder.bsky.social summarized the highlights for you

Transposable elements are vectors of recurrent transgenerational epigenetic inheritance @science.org @pierrebaduel.bsky.social
www.science.org/doi/10.1126/...

Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome:

The E2G Portal! e2g.stanford.edu

This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.

Uses cases 👇

1/

A subset of transposable elements as mechano-response enhancer elements in controlling human embryonic stem cell fate - Nature Cell Biology Sun et al. identify a subset of transposable elements that serve as mechano-response enhancer elements that control gene expression and human stem cell fate.

Transposons turning into enhancers again! #TEsky

ASOG: AntiSense Oligonucleotide Generator. #Oligonucleotides #ComputationalStructuralBiotechnology 🧬 🖥️
www.sciencedirect.com/science/arti...

Thrilled to share our story in its final form! nature.com/articles/s41... 💥 After ~10 years, we show that BMAL1 represses transposons via chromatin regulation in embryonic stem cells—rather than circadian rhythms as in adult tissues.

Very proud of our paper on "scrambling-by-hopping" LADs, which was just published: www.nature.com/articles/s41.... Congrats to Lise Dauban and the rest of the team – this was a real tour-de-force!

Multiple overlapping binding sites determine transcription factor occupancy - Nature A new method enables comprehensive screening and identification of low-affinity DNA binding sites for transcription factors, and reveals that nucleotides flanking high-affinity binding sites create ov...

"We propose a model in which TF binding is not determined by individual binding sites, but rather by the sum of multiple, overlapping binding sites."

www.nature.com/articles/s41...

ADAR1 as a Placental Innate Immune Rheostat Sustaining the Homeostatic Balance of Intrinsic Interferon Response at the Maternal‐Fetal Interface This study reveals that ADAR1, an RNA-editing enzyme, fine-tunes immune responses in the placenta by preventing the accumulation of immunogenic double-stranded RNAs (dsRNAs) from interferon-stimulate...

New paper from Bin Cao, showing that placenta-specific KO of ADAR1 is embryonic lethal.

LINE-1 retrotransposons mediate cis-acting transcriptional control in human pluripotent stem cells and regulate early brain development Adami et al. demonstrate that evolutionarily young L1s are expressed in human pluripotent stem cells and are dynamically regulated throughout neural differentiation. The study examines the role of L1s...

New paper from our lab! We found that LINE-1 transposons contribute to early human brain development.

Funded by @asapresearch.parkinsonsroadmap.org

www.cell.com/cell-genomic...

Distinct specificity and functions of PRC2 subcomplexes in human stem cells and cardiac differentiation Much et al. reveal that the PRC2 subcomplexes PRC2.1 and PRC2.2 play distinct roles in the epigenetic repression of developmental genes in human stem cells. Interactions between the PRC2 core and its ...

Excited to share our work on the specificity of PRC2 subcomplexes in stem cell and differentiation. We show that PRC2.1 and PRC2.2 exhibit distinct H3K27 methylation specificity in human pluripotent stem cells and opposing role in differentiation. Now online at Mol Cell: www.cell.com/molecular-ce...

Widespread 3′ UTR splicing regulates expression of oncogene transcripts through multiple mechanisms. #3UTRsplicing #TranscriptRegulation #Genomics @narjournal.bsky.social
academic.oup.com/nar/article/...

Epigenetic dysregulation of transposable elements in cognitive impairment and Alzheimer’s disease - GeroScience Aging and cognitive impairment increase the risk for Alzheimer’s disease (AD), and growing evidence suggests that transposable elements (TEs) in the genome play a role in aging and AD. The mechanisms ...

🚨New paper just dropped!🚨

We found that transposable element transcripts that are elevated in the blood of older adults and those with dementia are also epigenetically dysregulated, and may predict peripheral markers of inflammation & neurodegeneration
link.springer.com/article/10.1...

DNA methylation at retrotransposons protects the germline by preventing NRF1-mediated activation | EMBO reports imageimageIn spermatogenesis, loss of promoter DNA methylation reactivates retrotransposons in patterns shaped by chromatin modifications and the binding of DNA methylation-sensitive transcription fac...

Really beautiful work led by Jessica Leismann in Joan Barau’s lab @imbmainz.bsky.social . If you like elegant mouse genetics, the transposon arms race, and a healthy dose of epigenetics, this one’s for you. www.embopress.org/doi/full/10.... @emboreports.org

Gene-Set Enrichment Analysis and visualization on the web using EnrichmentMap: RNASeq. #GSEA #WebTool #RNAseq #Bioinformatics @bioinfoadv.bsky.social 🧬 🖥️
academic.oup.com/bioinformati...

My first first author manuscript has posted! I’m very excited to share SWIF-TE with yall. It is a fast, memory efficient tool to identify novel TE insertions from short-read data. 🧬 #TEworldwide #transposons

U-rich elements drive pervasive cryptic splicing in 3’ UTR massively parallel reporter assays - Nature Communications Massively parallel reporter assays (MPRAs) are powerful technologies for measuring the impact of non-coding sequences on gene expression. Here, the authors demonstrate that MPRA reporters often underg...

Our collaboration with Tony Mustoe's lab us out today. MPRA libraries and possible cryptic splicing in MPRA reporters, or reporters in general. The additional novelty here is that such events are controlled or influenced by AU-rich sequences.

www.nature.com/articles/s41...

A single-cell transposable element atlas of human cell identity Reyes-Gopar et al. introduce Stellarscope, a computational approach for quantifying locus-specific transposable element expression in single-cell RNA sequencing data. The authors profile human PBMCs a...

🧵1/ Introducing Stellarscope: an EM-based tool for quantifying locus-specific transposable element expression in single cells.

A single-cell transposable element atlas of human cell identity: Cell Reports Methods www.cell.com/cell-reports...

@hamarillo.bsky.social #TEHub #singlecell #genomics

Happy to share our recent publication on benchmarking peak calling methods for CUT&RUN.
academic.oup.com/bioinformati...
Published in @oxunipress.bsky.social Bioinformatics | led by aminnoorani.bsky.social

#Epigenomics #Genomics #Bioinformatics #MachineLearning #CUTandRUN #CompBio #4DNucleome