Neuro David

Gene regulatory networks: from correlative models to causal explanations Nature Reviews Genetics - In this Perspective, Maizels and Briscoe discuss the limitations of current models of gene regulatory networks and outline solutions to harness data abundance without...

New Perspective form Rory Maizels & me: "Gene regulatory networks: from correlative models to causal explanations"

Gene regulatory networks are supposed to give us mechanistic explanations of development, so why are we drowning in 'hairballs' of statistical correlations?

rdcu.be/e7zx7

RNA-specific local translation is patterned by condensates for multinucleate cell growth - Nature Cell Biology Geisterfer, Jalihal et al. show spatially distinct effects of Whi3 condensates on target translation in Ashbya syncytia. In vitro, translation is enriched at condensate–solute interfaces but repressed...

Condensates are powerful ways to break symmetry and cells do remarkable things with them. Here we show that in a multinucleate fungus, a condensate regulates translation of a cyclin and a formin in distinct locations.
www.nature.com/articles/s41...

Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.

The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...

Figure 1 shows they key result

Imaging spotlight: the axonal membrane-associated periodic skeleton - FocalPlane Imaging spotlight: the axonal membrane-associated periodic skeleton - News

🔬🔦In our latest Imaging spotlight, Nicholas Boyer takes us through the key results, & offers some top technical tips, from their research on the axonal membrane-associated periodic skeleton with Rohan Sharma, Christophe Leterrier @christlet.bsky.social, Subhojit Roy @roylab-ucsd.bsky.social & team.

Keeping cells fit Fragments of aberrant cytoplasmic mRNA pair with nuclear RNAs to augment transcription

In a new Science study, researchers report on transcriptional adaptation, a dual feedback and feedforward mechanism that uses genetic redundancy to compensate for mutations in protein-coding genes.

Learn more in a new #SciencePerspective: https://scim.ag/4ryeXtN

'Making of BDNF: role of promoters, enhancers, and untranslated regions'

by Eli-Eelika Esvald, Annela Avarlaid, Indrek Koppel, Jürgen Tuvikene & Tõnis Timmusk

www.cell.com/trends/neuro...

Good representation from teleosts 👍

Stress controls heterochromatin inheritance via histone H3 ubiquitylation - Nature A histone ubiquitin-dependent regulatory hub governs stimulus-dependent heterochromatin propagation, with important implications for understanding mechanisms governing rapid changes in the epigen...

Discussed @mrsantosny.bsky.social lit review: Stress controls heterochromatin inheritance via histone H3 ubiquitylation. www.nature.com/articles/s41...

From our new paper out now in @currentbiology.bsky.social: www.cell.com/current-biol... w/ @neurofishh.bsky.social @gkafetzis.bsky.social @denilsson.bsky.social

Looking across animals, the vertebrate eye is an obvious outlier. Why is it so different that other highly visual animals?

LINE-L1, HIV, Ty3 retrotransposons in insects.
several of these genomes are > 40% adenosine!

What is the molecular origin & evolutionary pressure resulting in A-rich genomes of retrotransposons & some retroviruses?

it must be so hardwired that hosts exploit this bias for genome defense

any ideas?

Ribosomal RNA expansion segments mediate the oligomerization of inactive animal ribosomes Cells down-regulate protein synthesis when stressed to conserve energy and shift resources toward repair. We found that in some mammalian cells, including neurons, stress also resulted in the formatio...

Out now in @science.org
Ribosomal RNA expansion segments mediate the oligomerization of inactive animal ribosomes | Science www.science.org/doi/10.1126/...

Single-cell and isoform-specific translational profiling of the mouse brain - Nature Post-transcriptional regulation of mRNA translation was explored using Ribo-STAMP and single-cell RNA sequencing to reveal cell-type-specific and isoform-specific translation patterns across hippocampal neuronal and non-neuronal cell types, highlighting functional differences between CA1 and CA3.

Nature research paper: Single-cell and isoform-specific translational profiling of the mouse brain

go.nature.com/4aYPQu7

Accurate predictions of disordered protein ensembles with STARLING - Nature The deep learning model STARLING can generate accurate ensembles of intrinsically disordered regions of proteins using only protein sequence as input.

Nature research paper: Accurate predictions of disordered protein ensembles with STARLING

go.nature.com/4cyskFw

Giant DNA viruses encode a hallmark translation initiation complex of eukaryotic life In contrast to living organisms, viruses were long thought to lack protein synthesis machinery and instead depend on host factors to translate viral t…

New work from @harvardcellbio.bsky.social faculty Amy Lee uncovered fundamental aspects of protein translation initiation by a giant DNA virus. www.sciencedirect.com/science/arti...

Advances in CLIP-derived methods have enabled high-resolution mapping of individual RNA binding protein-RNA interactions as well as RNA binding protein-associated RNA–RNA interactions #RNA #CLIP @evannostrandlab.bsky.social bit.ly/4bYjAsg

Emergence and evolution of protein-coding de novo genes Nature Reviews Genetics, Published online: 28 January 2026; doi:10.1038/s41576-025-00929-9De novo gene evolution entails the birth of new genes from previously non-coding DNA. In this Review, Bornberg-Bauer and Eicholt overview how protein-coding de novo genes are identified, the mechanistic and evolutionary processes underlying their emergence and evolution, and the patterns in their encoded protein structures.

FYI: New online! Emergence and evolution of protein-coding de novo genes

Annotating genomes at increased scale and resolution Nature Reviews Genetics, Published online: 17 February 2026; doi:10.1038/s41576-026-00937-3In this Review, Ji et al. overview how rapidly advancing experimental and computational methods are enabling improved and automated annotation of gene structure and function, providing researchers with genome annotation resources of unprecedented scale and resolution.

New online! Annotating genomes at increased scale and resolution

Cell-type-specific RNA polymerase II activity maps in intact tissues provide a gateway to mammalian gene regulatory mechanisms in vivo Chovatiya et al. developed PReCIS-seq, an in vivo approach that maps transcriptionally engaged RNA polymerase II in Cre-targeted cells within intact mouse tissues, without cell isolation. They report ...

Discussed @mrsantos.bsky.social lit review: Cell-type-specific RNA polymerase II activity maps in intact tissues provide a gateway to mammalian gene regulatory mechanisms in vivo.
www.cell.com/developmenta...

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

Evolutionary causes and consequences of gene duplication Nature Reviews Genetics, Published online: 16 February 2026; doi:10.1038/s41576-026-00935-5Gene duplication is a key evolutionary mechanism, as initially redundant paralogues diverge over time. The authors review how adaptive and non-adaptive forces influence the evolutionary fates of gene duplicates, highlighting the importance of function–fitness relationships and gene expression dynamics.

New online! Evolutionary causes and consequences of gene duplication

Bridging technical innovation and computational advances in studies of RNA–protein assemblies Nature Reviews Genetics, Published online: 16 February 2026; doi:10.1038/s41576-026-00931-9Empirical and artificial intelligence-based approaches are redefining how RNA-dependent protein assemblies are mapped, modelled and targeted, revealing their dynamic roles in health and disease and outlining closed-loop strategies for predictive functional RNA and ribonucleoprotein design.

New online! Bridging technical innovation and computational advances in studies of RNA–protein assemblies

Dynamical Aβ-Tau-Neurodegeneration Model Predicts Alzheimer's Disease Mechanisms and Biomarker Progression https://www.biorxiv.org/content/10.64898/2026.01.27.701320v1

#AlternativeSplicing analysis pipeline

MAJIQ v2 - VOILA v2 modulizer

👉Build gene splicegraph including unannotated, complex elements (e.g. de novo intron retention)
👉Quantify AS events & modules
👉Comparative analysis of GTEx v8 all 53 tissues

#NatComm 2023
www.nature.com/articles/s41...

Dissecting gene regulatory networks governing human cortical cell fate - Nature Systematic screening of transcription factors reveals conserved mechanisms governing cortical radial glia lineage progression across primates and provides a framework for functional dissecti...

1/ Our new study, led by Jingwen Ding, examines the role of transcription factors during human neurogenesis to identify gene regulatory networks influencing cell fate, maturation, and subtype specification
www.nature.com/articles/s41...

new paper from the Lai lab! Renfu Shang performs careful mechanistic dissection of miRNA cluster assistance and reveals many insights and surprises to this enigmatic regulatory strategy that gives suboptimal miRNAs a boost. if you love Northerns, you'll ♥️ this! 🧬

genesdev.cshlp.org/content/earl...

Antisense transcription can induce expression memory via stable promoter repression - Genome Biology Background The capacity of cells to retain a memory of previous signals enables acquisition of unique fates and adaptation to their environment. The underlying gene expression memory can arise from mu...

⚠️ The final work of two former PhD students Till @tschwammle.bsky.social and Verena @verenamutzel.bsky.social is out!
➡️⬅️ They dissect how memory can arise from antisense transcription using mathematical modelling 💻, genomics 🧬 and synthetic biology ⚒️! link.springer.com/article/10.1...

Subcellular depletion of importin β1 impairs presynaptic local translation and spatial memory Axonal localization of importin β1 is required for presynaptic functions that support spatial memory tasks.

Very happy to share our new paper in #ScienceSignaling revealing that importin β1 isn’t just important for nuclear transport or neuronal growth.

We now show it is key for presynaptic plasticity in the hippocampus, local translation, and memory!

www.science.org/doi/10.1126/...

Illustrated night sky with planets (cells), a shooting star, and star constellations against a blue grid background reminiscent of architectural drawings.

📢 Our February issue is live! go.nature.com/4jTt2z5
Reviewed topics include: how spatial omics has reshaped our understanding of human development and disease; multiplexed assays of variant effect (MAVEs); haplotype phasing and genotype imputation; forensic genetics in the omics era

Learn about #axon regulation in the EMBO | The Company of Biologists Workshop "Axonal degeneration and regeneration" in Onna-son, JP, 18–22 Oct.

Abstract submission/Registration by 31 May/15 Jun

https://meetings.embo.org/event/26-axonal-degeneration
#EMBOAxonalRegeneration #EMBOevents #meeting 🧪

Uncovering the role of LINE-1 in the evolution of lung adenocarcinoma - Nature Lung adenocarcinomas bearing the ID2 mutational signature display increased LINE-1 retrotransposon activity, which contributes to their fast evolutionary dynamics and aggressive phenotype.

Nature research paper: Uncovering the role of LINE-1 in the evolution of lung adenocarcinoma

go.nature.com/4oUHIPb