Jeffrey Vedanayagam

De novo genes arise from previously non-coding sequences. This evolutionary path — when randomly expressed sequences become folded and active proteins — challenges our understanding of genetic innovation. New Review by @bornberglab.bsky.social and @lacholt.bsky.social out now!

Header image with the paper title: "Improved in vivo gene knockout with high specificity using multiplexed Cas12a sgRNAs"

Make your gene knockouts more efficient with multiplexed Cas12a sgRNAs. Our new paper is out now, with tools available from @addgene.bsky.social , www.plasmids.eu and @vdrc-flies.bsky.social.

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

#CRISPR #geneediting #Drosophila 🧪🧬✂️🔬🪰

Summary 🧵 below.

Long non-coding RNAs as orchestrators of dosage compensation Nature Reviews Genetics, Published online: 27 January 2026; doi:10.1038/s41576-026-00934-6In this Journal Club, Hodkinson and Larschan recall a 2002 paper by Meller and Rattner that used the power of Drosophila genetics to demonstrate the integral role of long non-coding RNAs in dosage compensation.

New online! Long non-coding RNAs as orchestrators of dosage compensation

Summary of germ cell development in various model organisms

Germ cell development across model organisms

From our #Review: How germ granules promote germ cell fate
by Melissa C. Pamula & Ruth Lehmann @remlehmann.bsky.social @whiteheadinstitute.bsky.social
Free to read here: rdcu.be/e05TK

This is an important paper, hopefully it will set the tone for similar efforts for rigor and reproducibility in other systems/fields.

In @eLife.bsky.social: Reproducibility of Scientific Claims in Drosophila Immunity: A Retrospective Analysis of 400 Publications doi.org/10.7554/eLif...

Restorative epistasis can occur between 2 complementary loss-of-function mutations (in yeast) if they happen to cooccur in just the right way (2 wrongs making a right).

"Predicting epistasis across proteins by structural logic"
by Tang et al. (2026, PNAS)
www.pnas.org/doi/10.1073/...

Review: DNA methylation in mammalian development and disease www.nature.com/articles/s41... (free: rdcu.be/dUbb8)

Check out our new paper in early access at Nature Communications!

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

Epimutations: raw material for evolution? - The EMBO Journal Epigenetics is fundamental to cell differentiation as it enables cells with identical genomes to adopt distinct fates. Some epigenetic information can also be transmitted between generations, in a pro...

Need a bit of escapism? Not exactly Lord of the Rings, but in similar vein:
doi.org/10.1038/s443...

Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity using CHANGE-seq-BE - Nature Biotechnology Base editor off-target effects are profiled with high precision in a tailored approach.

Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity using CHANGE-seq-BE - @stjuderesearch.bsky.social go.nature.com/4qB6qp8

The genetics, evolution, and maintenance of a biological rock-paper-scissors game Side-blotched lizards (Uta stansburiana) play a biological rock-paper-scissors game in which three differently colored male morphs utilize alternative mating strategies. We identified the genetic basi...

The genetics, evolution, and maintenance of a biological rock-paper-scissors game | Science www.science.org/doi/10.1126/...

I'm really excited to break up the holiday relaxation time with a new preprint that benchmarks AlphaFold3 (AF3)/“co-folding” methods with 2 new stringent performance tests.

Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...

Preprint:
www.biorxiv.org/content/10.6...

The Company of Biologists 100 logo to the left and QR code to the right. Portrait of Christiane Nüsslein-Volhard , to the left, text to the right 100 extraordinary biologists Christiane Nüsslein-Volhard Christiane Nüsslein-Volhard is a Nobel Prize winner and Emeritus Director of the Max Planck Institute for Developmental Biology in Tübingen, Germany. She led efforts to establish zebrafish as a genetic model for vertebrate development, contributing many papers to the famous 1996 zebrafish issue of Development. #100biologists #biologists100

Our next extraordinary biologist is Christiane Nüsslein-Volhard, a Nobel Prize winner and Emeritus Director of the Max Planck Institute for Developmental Biology in Tübingen, Germany. #100biologists

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

PNAS – Special Feature. Genetics of Canine Domestication, Migration, and Behavior.

How did dogs evolve from wolves—and what does their DNA reveal about behavior? 🐕 A new PNAS Special Feature explores canine domestication, migration, and genetic links to behavior and human traits. Read now: https://ow.ly/y4aS50XMxef

Hey all, I reached out to the PO of my NIGMS MIRA to ask if the gov't shut down, and rescheduling of study sections, might allow for some accommodation to the standard rule that PIs cannot resubmit a MIRA while their MIRA (or other RPG) is under review (waiting in scores or summary statements) 🧪

Recent discoveries on the acquisition of the highest levels of human performance Scientists have long debated the origins of exceptional human achievements. This literature review summarizes recent evidence from multiple domains on the acquisition of world-class performance. We re...

What does it take to achieve the highest level of human performance? Across athletics, science, chess, and music
@science.org

science.org/doi/10.1126/...

Transcriptomics in the era of long-read sequencing Nature Reviews Genetics - Advances in long-read sequencing are driving the implementation of these technologies for transcriptome profiling. The authors provide a comprehensive guide to long-read...

Transcriptomics in the era of long-read sequencing
#Review by @carolinamonzo.bsky.social, Tianyuan Liu & @anaconesa.bsky.social @conesalab.bsky.social @csic.es
Free to read here: rdcu.be/efBjP

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...

Escape from X inactivation is directly modulated by Xist noncoding RNA Nature Cell Biology - The authors show that increased Xist RNA levels can induce de novo silencing of genes that normally escape X inactivation. SPEN depletion prevents the silencing of escape...

Very happy to share our paper rdcu.be/eUImj out today in @natcellbio.nature.com 🎉🎉🎉
We uncover an unexpected role for endogenous Xist RNA in regulating X-linked genes that escape X-inactivation.

Dynamic evolution of EZHIP, an inhibitor of the Polycomb Repressive Complex 2 in mammals The Polycomb Repressive Complex 2 (PRC2) is an ancient, conserved chromatin-interacting complex that controls gene expression, facilitating differentiation and cellular identity during development. It...

@pravrutharaman.bsky.social got super intrigued about EZHIP/CATACOMB, previously identified as a histone H3K27M mimic of PRC2. You can read about her efforts here: www.biorxiv.org/content/10.6... We hope these analyses will help spur more analyses in this very cool gene! 1/

Can one map the genome-wide binding (1) and its protein partners (2) simultaneously from the same sample?

Yes, one can. with CUT&ID ✂️🪪

Spearheaded — singlehandedly — by @annanordin.bsky.social

No need of transgenesis, cloning and overexpression.

Check it out, it's fast and its works.

An RNA splicing system that excises DNA transposons from animal mRNAs - Nature A new type of mRNA splicing mechanism discovered in Caenorhabditis elegans that detects and removes inverted repeats also occurs in human cells, thereby providing another strategy to protect against t...

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

Confused by all the histones that are cropping up in organisms that are decidedly NOT eukaryotes? check out our review - fantastic work by team NucEvo in the #Lugerlab
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...

Targeted sequencing and iterative assembly of near-complete genomes - Nature Communications Long-read sequencing enables high-quality genome assemblies, but challenges remain. Here, the authors introduce Cornetto, a method that improves assembly quality, enables genome sequencing from saliva...

Our cornetto work is now published at www.nature.com/articles/s41...

It can do near-T2T assembly using @nanoporetech.com adaptive sampling
- with less 💸
- reference agnostic, so works for non-humans
- not just blood, even saliva

Just presented at #abacbs2025 yesterday.

Systematic analysis of noncanonical ribosomal protein paralogs does not provide evidence for specialized functions in Drosophila

So excited to finally be able to share my first paper and the culmination of my PhD work with @felipekteixeira.bsky.social 🪰🔬

www.pnas.org/doi/10.1073/...

a life changing opportunity made possible by the Nobel Prize funds awarded to John Sulston -- the @sangerinstitute.bsky.social runs the Sanger Prize scheme, open to an undergrad from any LMIC to spend 3 months here learning all about genomics. more details here www.sanger.ac.uk/about/study/...

🪱 Selfish genes are everywhere and drive some of biology’s biggest innovations (CRISPR, antibody recombination, epigenetics). Yet almost no one asks the obvious question: how does a selfish gene begin? Our new manuscript uncovers how selfishness can emerge directly from the host genome.

Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model - Nature Methods By leveraging both deep learning and hidden Markov models, Helixer achieves broad taxonomic coverage for ab initio gene annotation of eukaryotic genomes from fungi, plants, vertebrates and invertebrat...

We all wish peer review to be rapid and professional: doesn’t always go like that. But I am relieved to finally see Helixer by @alisandra-denton.bsky.social and team published in Nature Method. Congratulations! www.nature.com/articles/s41...

Today in @nature.com, in work led by @adititm.bsky.social, we report the ability to prompt Evo to generate functional de novo genes.

You shall know a gene by the company it keeps!