Transposable element-host genome evolutionary arms race revealed by multi-modal epigenomic profiling in a telomere-to-telomere human genome reference www.biorxiv.org/content/10.64898/2026.03...

MBE | The evolutionary genomics of meiotic drive Meiotic drivers gain transmission advantages by distorting equal, Mendelian segregation. This review discusses the evolutionary genomics of meiotic drive. The figure highlights the interactions of meiotic drive elements with other classes of selfish genetic elements including: direct interactions between drivers and transposable elements (TEs) (A) or satellites (C) that can facilitate the spread of drivers; other drive systems that cause the mutual destruction of all gametes (B; e.g. the presence of multiple toxin-antidote systems); indirect interactions where the host machinery responsible for silencing TEs are recruited to silence drivers (D); dosage-sensitive interactions involving sex-linked drivers that result in gene amplifications (E); and tradeoffs between suppressing drive and TEs (F).

For a new MBE Review, Presgraves et al. argue that many features of genome evolution, content, and organization seemingly inexplicable by adaptation or nearly neutral processes are instead best accounted for by meiotic drive.

🔗 academic.oup.com/mbe/article/...

#evobio #molbio

Concurrent L1 retrotransposition events promote reciprocal translocations in human tumorigenesis LINE-1 (L1) retrotransposition generates somatic genomic variation in human cancer, but short-read sequencing has limited our understanding of its structural consequences and dynamics. Using long-read...

Today in
@science.org:
We are pleased to present our last work entitled:
"Concurrent L1 retrotransposition events promote reciprocal translocations in human tumorigenesis"
by Zumalave et al.
www.science.org/doi/10.1126/...

Transposable elements in the dark genome - Nature Biotechnology Transposable elements (TEs), such as retrotransposons and endogenous retroviruses, are increasingly recognized for their important roles in genome function and impact on disease development. Residing ...

Transposable elements in the dark genome go.nature.com/4tQ1zTn

Global reorganization of genome architecture at the transition to gametogenesis - Nature Structural & Molecular Biology Huang, Rigau and colleagues observe major changes in how DNA is organized in early germ cells before they start developing into sperm or eggs. These results show that germline removes structural ‘memo...

Happy to share our latest paper.

Our findings uncover a unique chromatin architecture and spatial chromosome arrangement in gonadal germ cells and document that alongside global DNA demethylation, the germline epigenetic reprogramming involves reorganisation of the 3D genome.

Ancient co-option of LTR retrotransposons as yeast centromeres - Nature Evolutionarily related ‘proto-point’ centromeres providing resolution to the evolutionary origins of point centromeres are identified in yeast, and comparison shows they evolved in an ancestor with re...

Our paper is now out in Nature:

“Ancient co-option of LTR retrotransposons as yeast centromeres”

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

A short thread on how retrotransposons helped give rise to yeast point centromeres.

1/14

Lesson learned: Repetitive regions of the genome, like the short arms of the acrocentrics, are prone to recombination and duplication. This makes them a pain to sequence, but also very dynamic. Natural selection can take advantage of that instability to effect rapid change [19/21]

Loss of SETDB1-mediated H3K9me3 in human neural progenitor cells leads to transcriptional activation of L1 retrotransposons Abstract. Heterochromatin is characterized by an inaccessibility to the transcriptional machinery and is associated with the histone mark H3K9me3. However,

New paper from my lab out in NAR. We found that young L1 elements are controlled by SETDB1 and H3K9me3 in human neural progenitor cells via a mechanism independent of HUSH and TRIM28/KZNFs.

academic.oup.com/nar/article/...

M18BP1 valency and a distributed interaction footprint determine epigenetic centromere specification in humans - The EMBO Journal The histone H3 variant CENP-A is considered an epigenetic landmark of centromeres. Its deposition reflects cell-cycle-regulated assembly of M18BP1, HJURP, and PLK1 on a divalent MIS18α/β scaffold. The...

It’s out! 🥳 Excited to share our new paper (with Kai Walstein, @andrea-musacchio.bsky.social and all others) on the role of M18BP1 in CENP-A loading!

“M18BP1 valency and a distributed interaction footprint determine epigenetic centromere specification in humans”
link.springer.com/article/10.1...

Dissecting the contribution of transposable elements to interphase chromosome structure - Genome Biology Background Transposable elements (TEs) occupy nearly half of the human genome and play diverse biological roles. Despite their abundance, the extent to which TEs contribute to three-dimensional (3D) g...

Transposable elements determine 3D genome organization—beyond CTCF binding
#TEsky
link.springer.com/article/10.1...

New tool from @alexsweeten.bsky.social to find and classify all your satellites: "AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates"
📄 www.biorxiv.org/content/10.6...
📦 github.com/marbl/anianns

Our findings identify centromeric cohesion protection as a modifiable determinant of egg quality.
This is, to our knowledge, the first molecular intervention shown to improve chromosome cohesion in human eggs.
(9/10)

Fresh news on de novo genes! Happy to present our latest work published in Nature communications: www.nature.com/articles/s41...

Keywords not in specific order: intergenic ORFs, de novo genes, GC content, foldability, genetic code, ancestral sequence reconstruction and more :)

Human eggs must segregate their chromosomes with exquisite precision — yet errors rise with maternal age, causing miscarriage & infertility.
Our new article on @biorxivpreprint.bsky.social shows why chromosome cohesion fails in aging eggs & how to improve it.
www.biorxiv.org/content/10.6... (1/10)

Somatic and germline mutational processes across the tree of life www.biorxiv.org/content/10.64898/2025.12...

Haplotype-Resolved Genomics Reveals Conserved Chromatin Architecture and Epigenetic Constraints of Human Neocentromeres www.biorxiv.org/content/10.64898/2025.12...

Origin and evolution of acrocentric chromosomes in human and great apes www.biorxiv.org/content/10.64898/2025.12...

The discovery of the first kinetochore proteins (CENP-A, CENP-B, CENP-C) was reported by Bill Earnshaw and Naomi Rothfield in 1985 in Chromosoma. Forty years later, Chromosoma/Chromosome Research has published a special issue (most articles are open access)
link.springer.com/collections/...

What sets the mutation rate of a cell type in an animal species? Germline mutation rates per generation are strikingly similar across animals, despite vast differences in life histories. Analogously, in at least one somatic cell type, mutation rates at the end of l...

Happy to highlight an essay I wrote together with @marcdemanuel.bsky.social,
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n

Human acrocentric chromosome short arm de novo mutation and recombination www.biorxiv.org/content/10.64898/2025.12...

Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance www.biorxiv.org/content/10.64898/2025.12...

Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...

Very happy that this part of my postdoc work is now out as a preprint!! Our findings reveal a new mechanism by which retroviral pandemics may have shaped primate brain evolution 🧬🐒🧠 This was a true team effort! w/ @ofeliakarlsson.bsky.social @raquelgarza.bsky.social @jakobssonlab.bsky.social #TEsky

If you ever need to fuzzy search some DNA, sassy is your tool.

Please spread the word; I think many people just outside my own circle could benefit from this :)

cc @rickbitloo.bsky.social

github.com/RagnarGrootK...

Boundary issues: SWI/SNF shapes chromatin patterns in and around centromeres Abstract. The SWI/SNF family of chromatin remodelling complexes, comprising BAF, PBAF and ncBAF, is known for their critical roles in regulating chromatin

Some Friday reading...new review in Open Biology where we discuss how SWI/SNF maintains the chromatin environment around centromeres, building on recent work from ourselves and others. Lots of fun putting this together with @alison-harrod.bsky.social and @thedownslab.bsky.social!

GitHub - lh3/human-asm: A collection of high-quality human genomes A collection of high-quality human genomes. Contribute to lh3/human-asm development by creating an account on GitHub.

579 high-quality human genomes from @humanpangenome.bsky.social, Arab Pangenome and individual papers (CHM13, CN1, KSA001, I002C, YAO and KOREF1). Sequences available in the AGC format (3.7GB) and FM-index in the ropebwt3 format (20.3GB). For details, see github.com/lh3/human-asm

Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀

Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function

now revised and journal accepted at www.science.org/doi/10.1126/...

🧵👇

How do new centromeres evolve while staying compatible with the division machinery?

Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.

👉 doi.org/10.1038/s41586-025-09779-1

differential contribution of H3K9 methyltransferases to boundaries at satellites

A new and fascinating story from @bencarty.bsky.social and the group, with crucial help from the teams of @naltemose.bsky.social, Simona Giunta, and @dfachinetti.bsky.social. Many thanks to all for a fantastic collaboration.
www.nature.com/articles/s41...

Happy to share the “International Symposium on Chromosome Dynamics: from Structure to Cellular Function” that will be held in Japan 31st of May 2026 www.fbs.osaka-u.ac.jp/labs/fukagaw.... Registrations will open on December 1st! Plenty of opportunities to present your work! Hope to seeing you