your starter pack for Single Molecule Genomics! Why you should do it (or not) - How you should do it. Collective effort with @vram142.bsky.social @stirlingchurchman.bsky.social @naltemose.bsky.social A Stergachis M Stadler W Greenleaf @embl.org rdcu.be/PmzSEV529GRa

Long-read sequencing reveals pre-meiotic gene conversion in sperm www.nature.com/articles/s41...

Long-read sequencing reveals pre-meiotic gene conversion in sperm - Nature

Single-molecule long-read sequencing of human sperm reveals variation in recombination across donors and that a substantial fraction of non-crossover gene conversions arises before meio...

nature.com

Very happy to see this story finally out in @natbiotech.nature.com: www.nature.com/articles/s41... Fantastic collaboration with @lancasterlab.bsky.social on how to identify and ‘fix’ differentiation-compromised human pluripotent stem cells. @babrahaminst.bsky.social @mrclmb.ac.uk 🧵 below

Reversible epiblast regionalization determines differentiation potential of human pluripotent stem cells - Nature Biotechnology

The differentiation variability of human pluripotent stem cell lines is diagnosed and corrected.

nature.com

New issue alert👉https://cell.com/cell/current On the cover: The Telomere-to-Telomere Consortium has finished the complete, diploid genome of a person. The cover is inspired by a karyotype of the chromosomes in metaphase, representing the two haplotypes as different colors.

That’s a beautiful story that shows again how powerful long reads are for studying transposable elements. Exciting times! For accessing the Perspective piece without a paywall: www.science.org/eprint/NIKHD...

Why the X chromosome is rich in L1 mobile elements

Preferential insertion into the late-replicating inactive X explains L1 accumulation in this chromosome

science.org

The human genome's most variable and clinically important regions (centromeres, telomeres, and acrocentric short arms) have been hardest to study at scale. Thrilled to share KaryoScope, our new preprint that brings them within reach. 🧵 www.biorxiv.org/content/10.6...

👀"These results establish that naturally occurring copy-number variation within repetitive pericentromeric DNA is not merely noise, but a functional source of variation in chromosome segregation and gene regulation."

bioRxiv Genetics@biorxiv-genetic.bsky.social · 4mo ago

Pericentromeric repeat copy number tunes heterochromatin dosage to control chromosome segregation and gene expression in fission yeast https://www.biorxiv.org/content/10.64898/2026.05.08.723760v1

Loss is maintenance DNA methylation during cell proliferation/aging etc is not random. Intriguing new findings from the Rao lab show a strong correlation with dinucleotides flanking CpG sites. Seems likely to be important. www.biorxiv.org/content/10.6...

Transposable element-host genome evolutionary arms race revealed by multi-modal epigenomic profiling in a telomere-to-telomere human genome reference https://www.biorxiv.org/content/10.64898/2026.03.19.712972v1

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

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/...

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...

science.org

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

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 ...

go.nature.com

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.

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...

nature.com

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

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...

nature.com

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]

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...

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...

link.springer.com

Transposable elements determine 3D genome organization—beyond CTCF binding #TEsky 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...

link.springer.com

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 https://www.biorxiv.org/content/10.64898/2025.12.28.691837v1

Haplotype-Resolved Genomics Reveals Conserved Chromatin Architecture and Epigenetic Constraints of Human Neocentromeres https://www.biorxiv.org/content/10.64898/2025.12.23.696241v1

Origin and evolution of acrocentric chromosomes in human and great apes https://www.biorxiv.org/content/10.64898/2025.12.22.696095v1

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/...

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

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...

biorxiv.org

Human acrocentric chromosome short arm de novo mutation and recombination https://www.biorxiv.org/content/10.64898/2025.12.16.694519v1

Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance https://www.biorxiv.org/content/10.64898/2025.12.14.693655v1

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...