Jack Bateman

Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation Transcriptional adaptation (TA) is a genetic robustness mechanism through which mutant messenger RNA (mRNA) decay induces sequence-dependent up-regulation of so-called adapting genes. How cytoplasmica...

This is a fascinating paper that reveals defined and clear mechanism for a phenomenon that for some seemed unbelievable- the up regulation of genes paralogous to those with specific types of inactivating mutations. This is called transcriptional adaptation 1/ www.science.org/doi/10.1126/...

How does the piRNA pathway solve the self vs. non-self problem? 🧬

Since piRNAs come from single-stranded RNA, how does the cell choose the right ones? For years, "piRNA clusters" were seen as THE privileged source. But are they really special and earmarked for biogenesis? (1/19)

Direct visualization and tracing of chromatin folding in the Drosophila embryo - The EMBO Journal Chromatin organization, through the assembly of DNA with histones and the folding of nucleosome chains, regulates DNA accessibility for transcription, DNA replication and repair. Although models deriv...

We are in EMBO J. See DNA and non-octameric nucleosome-like particles in situ

link.springer.com/article/10.1...

Unique territorial and compartmental organization of chromosomes in the holocentric silkworm - The EMBO Journal Hallmarks of multicellular eukaryotic genome organization are chromosome territories, compartments, and loop-extrusion-mediated structures, including TADs. However, these have mainly been observed in ...

How do compartmentalization & loop extrusion organize eukaryotic genomes beyond classical model organisms?
Hi-C analysis of silkworm chromosomes by Drinnenberg, Muller, Mirny et al reveals new combination of these mechanisms, and a new, secluded “S” compartment
link.springer.com/article/10.1...

New preprint from the lab! We identify the ZnF protein Mulberry as a condensation-dependent structural regulator of genome topology that organizes “multi-way regulatory hubs” in early Drosophila embryos.
www.biorxiv.org/content/10.6...

EZHIP restricts noncanonical PRC2 binding and regulates H3K27me3 intergenerational inheritance and reprogramming Zeng et al. identify EZHIP as a critical epigenetic reprogramming factor in mouse early embryos, which promotes global erasure, intergenerational inheritance, and re-establishment of H3K27me3. They de...

EZHIP restricts noncanonical PRC2 binding and regulates H3K27me3 intergenerational inheritance and reprogramming www.cell.com/cell-stem-ce...

Right like is it happening irl but there’s no cameras

😭😭😭

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.

A new extreme of meiotic evolution:

✔️ 𝗻𝗼 crossovers
✔️ 𝗻𝗼 gene conversion
✔️ 𝗻𝗼𝗿𝗺𝗮𝗹 meiosis & fertility

Sex mimics clonality without becoming asexual, in the holocentric multicellular eukaryote 𝘙𝘩𝘺𝘯𝘤𝘩𝘰𝘴𝘱𝘰𝘳𝘢 𝘵𝘦𝘯𝘶𝘪𝘴.

more about it:
www.biorxiv.org/content/10.6...

Protein buffering of aneuploidy is driven by coordinated factors identified through machine learning - Molecular Systems Biology Aneuploidy, a hallmark of cancer, alters chromosome copy numbers and with that the abundance of hundreds of proteins. Evidence suggests that levels of proteins encoded on affected chromosomes are ofte...

Protein buffering of aneuploidy is driven by coordinated factors identified through machine learning link.springer.com/article/10.1...

The missing pants gag was so dumb but somehow cracked me up

lol I have not made it to extended data yet

Romcom! I’ll see if I can interest the lady

Construction of complex and diverse DNA sequences using DNA three-way junctions - Nature Sidewinder enables high-fidelity DNA assembly by separating the information that guides assembly from the final assembled sequence.

Construction of complex and diverse DNA sequences using DNA three-way junctions www.nature.com/articles/s41...

Insights into DNA repeat expansions among 900,000 biobank participants www.nature.com/articles/s41...

Directed evolution on compact landing pads yields highly efficient recombinases for large DNA integration academic.oup.com/nar/article/...

AI learns from chromatin data to uncover gene interactions Machine-learning tool for predicting gene expression.

AI learns from chromatin data to uncover gene interactions www.nature.com/articles/d41...

Medical breakthroughs in 2025 ... and a happy new year.

Medical breakthroughs in 2025 www.scientificdiscovery.dev/p/medical-br...

Models in biology: ‘accurate descriptions of our pathetic thinking’ - BMC Biology In this essay I will sketch some ideas for how to think about models in biology. I will begin by trying to dispel the myth that quantitative modeling is somehow foreign to biology. I will then point o...

"A mathematical model is a logical machine for converting assumptions into conclusions. If the model is correct and we believe its assumptions then we must, as a matter of logic, believe its conclusions. "

link.springer.com/article/10.1...

Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm - Nature Cell Biology Schooley et al. find that mitotically bookmarked loci drive a transient chromosome folding state during G1 entry that is subsequently modulated by factors inherited through the cytoplasm.

Exciting new paper out! @allanaschooley.bsky.social and Sergey Venev led this project that let to the discovery of two chromosome folding programs: one inherited via mitotic chromosomes and one mitotic inherited through the cytoplasm!

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

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.

An integrated view of the structure and function of the human 4D nucleome - Nature The 4D Nucleome Project demonstrates the use of genomic assays and computational methods to measure genome folding and then predict genomic structure from DNA sequence, facilitatin...

An integrated view of the structure and function of the human 4D nucleome www.nature.com/articles/s41...

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...

Functional maps of a genomic locus reveal confinement of an enhancer by its target gene | Science www.science.org/doi/10.1126/...

Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions Li et al. apply base-pair resolution Micro Capture-C ultra to map chromatin contacts between individual motifs within cis-regulatory elements and reveal a unified model of biophysically mediated enhan...

Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions www.cell.com/cell/fulltex...

The evolving landscape of RAS-targeted therapies www.nature.com/articles/s43...

High-fidelity human chromosome transfer and elimination The synthesis of human genomes and other gigabase-scale genomes will require new strategies. Here, we realized key steps in our pipeline for building synthetic human chromosomes. We established: (i) t...

High-fidelity human chromosome transfer and elimination www.science.org/doi/abs/10.1...

Multiscale structure of chromatin condensates explains phase separation and material properties The structure and interaction networks of molecules within biomolecular condensates are poorly understood. Using cryo–electron tomography and molecular dynamics simulations, we elucidated the structur...

Multiscale structure of chromatin condensates explains phase separation and material properties www.science.org/doi/10.1126/...

Cohesin drives chromatin scanning during the RAD51-mediated homology search Cohesin folds genomes into chromatin loops, the roles of which are under debate. We found that double-strand breaks (DSBs) induce de novo formation of chromatin loops in human cells, with the loop bas...

Cohesin drives chromatin scanning during the RAD51-mediated homology search www.science.org/doi/10.1126/...

Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences - PubMed The idea that liquid-liquid phase separation (LLPS) may be a general mechanism by which molecules in the complex cellular milieu may self-organize has generated much excitement and fervor in the cell biology community. While this concept is not new, its rise to preeminence has resulted in renewed in …

"We find that the evidence for in vivo LLPS is often phenomenological and inadequate to discriminate between phase separation and other possible mechanisms. Moreover, the causal relationship and functional consequences of LLPS in vivo are even more elusive"
(2019)

pubmed.ncbi.nlm.nih.gov/31594803/