An interesting paper analyzing the research trends of Wolbachia-Aedes aegypti studies over the last 2 decades www.mdpi.com/1660-4601/23...

Woolfe et al, 2026. Decoding the mystery of ultra-conservation in developmental enhancers: a role for nucleosome positioning, DNA structure and transcription factor binding www.biorxiv.org/content/10.6... ▶️conserved non-coding elements ... favor nucleosome occupancy at their borders

Per American Cancer Society: "...for the first time, the five-year relative survival rate for all cancers combined reached 70% for people diagnosed during 2015-2021 in the United States." pressroom.cancer.org/cancer-stati...

Chad Loder@chadloder.dev · last mo.

"We declared a War On Cancer in the 1970s and we have not made significant progress on treating cancer despite ever-increasing funding. It's a welfare program for academic labs" Bro what the FUCK are you talking about. The survival statistics do not bear this out even at first glance

(1/n) Very excited to share tri-lab collab (Mirny & Zechner) led by Harvey, Henrik & Jack: Q: How do enhancers & promoters interact in space (contact vs. action-at-a-distance) and time (stable vs. transient)? A: Transient E-P contact (~25-42 nm lasting ~10-20 sec): www.biorxiv.org/content/10.6...

Live-cell imaging of enhancer-promoter dynamics reveals transient contact-driven gene activation https://www.biorxiv.org/content/10.64898/2026.06.21.733446v1

Is distal gene activation by enhancers inherently different from promoter-proximal activation? We propose not. But both cohesin and cooperativity are important aspects of how transcription is affected. Happy to share our recent preprint (thread below) 1/ www.biorxiv.org/content/10.6...

This is really amazing- analysis of ~5000 year old DNA identifies a father and son that were buried 140 miles apart. I cannot think of the odds of observing this www.science.org/doi/10.1126/...

Long-distance genetic relatedness in megalithic central Europe

Megalithic monuments in Late Neolithic Europe are often viewed as symbols of shared ancestry. In this study, we analyzed genome-wide data of 203 individuals buried in six megalithic grave complexes as...

science.org

Non-Mendelian inheritance of DNA methylation patterns in mice www.nature.com/articles/s41...

Non-Mendelian inheritance of DNA methylation patterns in mice - Nature Genetics

Davidovich et al. investigate allele-specific DNA methylation inheritance patterns in mouse liver and muscle. Most patterns are Mendelian, but ~7% are non-Mendelian, including new imprinted genes and ...

nature.com

Loop extrusion creates rare, long-lived encounters underlying enhancer-promoter communication www.biorxiv.org/content/10.1...

Why can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬 Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪 🧵👇

How do pairs of DNA loci - such as enhancers and promoters - find each other inside the nucleus? 🤔 Most models assume the random forces driving locus motion are independent in space New preprint by @janniharju.bsky.social: this assumption fails in living cells 🧵 www.biorxiv.org/content/10.6...

Diving into evolutionary biology! What is the origin of the most abundant class of insect transcription factors, ZAD-ZnFs? We suggest that they evolved from ancestral insulator-binding proteins that control 3D genome topology. www.science.org/doi/10.1126/...

Decoding the molecular logic of rapidly evolving ZAD zinc finger proteins in Drosophila

Identification of ZAD-ZnF genes as key regulators of genome organization during Drosophila embryogenesis.

science.org

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/...

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...

science.org

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)

bioRxiv Molecular Biology@biorxiv-molbio.bsky.social · 6mo ago

A Naïve RNA Sampling Core Enables Adaptive piRNA Specificity Against Transposable Elements https://www.biorxiv.org/content/10.64898/2026.02.07.704324v1

We are in EMBO J. See DNA and non-octameric nucleosome-like particles in situ link.springer.com/article/10.1...

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...

link.springer.com

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...

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 ...

link.springer.com

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 www.cell.com/cell-stem-ce...

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...

cell.com

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

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...

link.springer.com

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

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.

nature.com

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 www.nature.com/articles/d41...

AI learns from chromatin data to uncover gene interactions

Machine-learning tool for predicting gene expression.

nature.com

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

Medical breakthroughs in 2025

... and a happy new year.

scientificdiscovery.dev

"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...

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...

link.springer.com

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...

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.

nature.com

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.

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...

rdcu.be

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

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...

nature.com