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Jack Bateman

@jbateman01.bsky.social
1.3K followers 1K following 117 posts

Biology professor at Bowdoin College. Genetics, flies, chromosomes, weird science 🥰

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Reposted by Jack Bateman
Lennart Hilbert @lennarthilbert.bsky.social · 03/10/2026
Just gonna leave this here while it’s still hot off the press 🤩 On the Structure and Function of Transcription Bodies Maciej A. Kerlin Shivali Dongre @shivalidongre.bsky.social Eleonora Perego Martino Ugolini Nadine Vastenhouw @nvastenhouw.bsky.social www.annualreviews.org/content/jour...
annualreviews.org
On the Structure and Function of Transcription Bodies
Transcription is a key process in the life of cells. In the 1990s, cell biologists observed that transcription often takes place in discrete transcription bodies in eukaryotic nuclei, which has sparke...
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Reposted by Jack Bateman
Anders Sejr Hansen @andersshansen.bsky.social · 28/09/2026
Very nice new paper from Paggi, Long, Zhang using physical modeling of RCMC data to reconstruct physical structures of euchromatin at the nucleosome scale: Euchromatin forms condensed domains and E-P interactions largely occur on the surface! www.nature.com/articles/s41...
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Jack Bateman @jbateman01.bsky.social · 23/09/2026
lol failed touching grass attempt
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Jack Bateman @jbateman01.bsky.social · 22/09/2026
😂
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Aurele Piazza @aurelepiazza.bsky.social · 18/09/2026
What molecular mechanisms underlie the needle-in-a-haystack search for homology required to fix a DNA break? In this preprint, we reveal multiple controls of homology search in cells: onset, coordination, reach and inactivation. www.biorxiv.org/content/10.6...
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Jack Bateman @jbateman01.bsky.social · 22/09/2026
👀
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Arjuna Rajakumar PhD @arjunarajakumar.bsky.social · 19/09/2026
So proud of my lab mate @sagrill.bsky.social (whose on the job market 👀) for this magnum opus from @remlehmann.bsky.social lab @whiteheadinstitute.bsky.social ScRNA-seq of 🪰 germ cells reveals new biology, answers age old questions, and proposes new paradigms! 1/8 www.biorxiv.org/content/10.6...
Drosophila stage 10b embryo w/HCR staining marking two germ cell clusters. One will successfully colonize the gonad and the other, like tears in the rain, will be lost forever
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Jack Bateman @jbateman01.bsky.social · 15/09/2026
Folding a broken genome: the versatile roles of cohesin in genome maintenance www.nature.com/articles/s41...
nature.com
Folding a broken genome: the versatile roles of cohesin in genome maintenance - Nature Reviews Genetics
The protein complex cohesin shapes 3D genome organization through both cohesion and loop extrusion. The authors review the roles of these two mechanistic functions in the cellular response to DNA doub...
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Reposted by Jack Bateman
The Interactive Fly @interactivefly.bsky.social · 11/09/2026
Xu, Y., Chao, A., Rinaldin, M., Kickuth, A., Brugues, J., Di Talia, S. (2025). The cell cycle oscillator and spindle length set the speed of chromosome separation in Drosophila embryos. Current biology : CB, 35(3):655-664.e653 www.cell.com/current-biol...
cell.com
The cell cycle oscillator and spindle length set the speed of chromosome separation in Drosophila embryos
Xu et al. investigate how the speed of chromosome separation is regulated during the cleavage divisions of the Drosophila blastoderm. They find that spindle length and the cell cycle oscillator jointl...
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Reposted by Jack Bateman
Philippe Batut @philippebatut.bsky.social · 10/09/2026
🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social A few highlights below... 🧵👇
science.org
Noncoding transcription controls the developmental dynamics of long-range gene regulation
The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...
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Arnaud Krebs @arnaudkr.bsky.social · 07/09/2026
Is activation of multiple enhancers and promoters coordinated? Short answer is yes. Check full story from @mathias-boulanger.bsky.social @kasitc.bsky.social leveraging long read single molecule sequencing to address this. @embl.org www.cell.com/molecular-ce...
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Alessandro Dulja @alessandrodulja.bsky.social · 07/09/2026
🚨Happy to share that the first part of my PhD is out on @cp-devcell.bsky.social! This has been an exciting project in the lab of @eileen-furlong.bsky.social @embl.org, studying the regulation of Pol II pausing across embryogenesis and its impact on gene expression dynamics. tinyurl.com/5n88ykk7
tinyurl.com
Chromatin context shapes SPT5 regulation of promoter-proximal Pol II, fine-tuning gene expression changes during Drosophila embryogenesis
Using rapid SPT5 depletion, Dulja et al. uncover different molecular phenotypes at different embryonic stages. In early embryos, SPT5 depletion shifts Pol II from the pausing site to the +1 nucleosome...
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Wendy Bickmore @wbickmor.bsky.social · 08/09/2026
It was great working with students Kun and Ryan and @hannahlong.bsky.social, combing the literature to try and find examples of bona fide disease-causing variants in non-coding elements - promoters, enhancers and silencers. www.nature.com/articles/s41...
nature.com
Mechanisms underlying disease-causing variants in promoters and enhancers - Nature Genetics
This Review discusses how rare-disease-causing variants in the noncoding genome impact gene regulation, why these examples are so few and how new approaches could accelerate discovery of noncoding var...
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Anders Sejr Hansen @andersshansen.bsky.social · 07/09/2026
Enhancer–promoter proximity predicts transcriptional competence but not transcriptional output in the Drosophila brain arxiv.org/pdf/2609.03058
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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 06/09/2026
Big review by Xizi Chen & Yanhui Xu in @natrevmcb.nature.com The molecular basis of transcription initiation by RNA polymerase II www.nature.com/articles/s41...
nature.com
The molecular basis of transcription initiation by RNA polymerase II - Nature Reviews Molecular Cell Biology
Recent technological breakthroughs have transformed our understanding of how transcription initiation in eukaryotes is regulated. This Review discusses the dynamics and roles of initiation-relevant pr...
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Reposted by Jack Bateman
Anton Goloborodko @golobor.bsky.social · 03/09/2026
1/ out in @science.org! We found a new asymmetry in large-scale chromosome structure: sister chromatids are shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! A close collaboration w/ @gerlichlab.bsky.social , led by @flaviacorsi.bsky.social www.science.org/doi/10.1126/...
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MwahahahahahadScientist @mads100tist.bsky.social · 29/08/2026
Do you work with microscopy images and segment to quantify or track? Do you study cell biology? development? Gather round! Let me tell you about FOCUS-3D, a segmentation algorithm that is fast, accurate and can be used on any model. We used it here to study zebrafish development. 🧪 (thread)
biorxiv.org
FOCUS‑3D: Robust, generalizable volumetric cell segmentation for three‑dimensional fluorescence microscopy
Understanding how cells establish spatial organization within tissues is a fundamental question in life sciences. While modern three-dimensional fluorescence microscopy captures large-volume tissue ar...
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Jack Bateman @jbateman01.bsky.social · 26/08/2026
Integrative spatial profiling of 3D genome organization and gene expression in tissue www.cell.com/cell/fulltex...?
cell.com
Integrative spatial profiling of 3D genome organization and gene expression in tissue
Spatial Hi-C-RNA simultaneously maps genome architecture and gene expression from the same tissue, revealing how spatial genome organization shapes cellular identity, development, and tumor evolution ...
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Shenzhi Chen @shenzhichen1999.bsky.social · 25/08/2026
Excited to share our paper in @natgenet.nature.com on the de novo design of tissue-specific mammalian enhancers that function in vivo in mouse embryos. 🧬🐭 www.nature.com/articles/s41...
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Job Dekker @jobdekker.bsky.social · 24/08/2026
How do nuclear compartments form inside cell nuclei? We show RNA glues certain loci together to form a nuclear compartment. This involves special GC-rich regions of highly expressed genes that also associate with nuclear speckles, but interactions between these loci are independent of speckles!
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Noam Ross @noamross.net · 21/08/2026
Three more days to comment on NSF's attempt to smuggle in OMB's already-rejected policies of terminating any grant without cause, gutting civil rights obligations and restricting international collaborations. Submit your comment today! Then call your representatives. 🧪
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Bas van Steensel lab (NKI) @basvansteensellab.bsky.social · 18/08/2026
Inferring transcription factor activity: use ATAC-seq, reporter assays, or both? link.springer.com/article/10.1...
link.springer.com
Systematic comparison of estimates of transcription factor activity by ATAC-seq and multiplexed reporter assays - Molecular Systems Biology
Transcription factors (TFs) are central to gene regulation and play critical roles in development, cellular homeostasis and disease. The ability to accurately measure TF activity is essential to under...
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Jack Bateman @jbateman01.bsky.social · 19/08/2026
Single-cell 3D genome imaging shows super-enhancer hubs are rare, nonspecific, and neither necessary nor sufficient for transcriptional bursting www.cell.com/cell-genomic...?
cell.com
Single-cell 3D genome imaging shows super-enhancer hubs are rare, nonspecific, and neither necessary nor sufficient for transcriptional bursting
Super-enhancers have been proposed to cluster in the nucleus when compared to other genomic elements. Le et al. found that super-enhancer clustering was rare and driven by non-specific interactions. P...
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Reposted by Jack Bateman
The Interactive Fly @interactivefly.bsky.social · 11/08/2026
Chmykhalo, V. K., Amendola, D., Shidlovskii, Y. V., Lebedeva, L. A., Schedl, P., Giordano, E. (2025). Functional Role of Bap170 Domains in Enhancer-Dependent Gene Activity in Drosophila melanogaster. Doklady Biochemistry and biophysics, 520(1):152-155 link.springer.com/article/10.1...
link.springer.com
Functional Role of Bap170 Domains in Enhancer-Dependent Gene Activity in Drosophila melanogaster - Doklady Biochemistry and Biophysics
Abstract The Bap170 subunit of the SWI/SNF chromatin remodeler exhibits activator functions when artificially recruited to the LacZ reporter promoter in enhancer-dependent transcription. In this study...
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Jack Bateman @jbateman01.bsky.social · 08/08/2026
Enhancer control of promoter activity and variability via frequency modulation of clustered transcriptional bursts www.nature.com/articles/s41...
nature.com
Enhancer control of promoter activity and variability via frequency modulation of clustered transcriptional bursts - Nature Genetics
Tünnermann et al. use live-cell imaging to study promoter activity under the control of an enhancer inserted at different genomic distances. RNA production from the promoter occurs in clusters of tran...
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Jack Bateman @jbateman01.bsky.social · 08/08/2026
Promoter strength and position govern promoter competition through transcript-dependent insulation www.nature.com/articles/s41...
nature.com
Promoter strength and position govern promoter competition through transcript-dependent insulation - Nature Genetics
By inserting diverse promoters at the mouse Sox2 locus, Koska et al. show that promoter strength, position and transcript length tune promoter competition through transcription-dependent insulation, i...
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bioRxivpreprint @biorxivpreprint.bsky.social · 06/08/2026
Cohesin loading at regulatory elements shapes 3D genome folding during erythropoiesis www.biorxiv.org/content/10.64898/20…
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Jason Rasgon @vectorgen.bsky.social · 29/07/2026
An interesting paper analyzing the research trends of Wolbachia-Aedes aegypti studies over the last 2 decades www.mdpi.com/1660-4601/23...
mdpi.com
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Teif lab @teiflab.bsky.social · 26/07/2026
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
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Arrianna Marie Planey, PhD MA @arrianna-planey.bsky.social · 25/06/2026
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...
pressroom.cancer.org
ACS Annual Statistics Report: Milestone 70 Percent 5-Year Survival Rate for all Cancers Combined; Largest Gains for Advanced and Fatal Cancers
ATLANTA, January 13, 2026 — The American Cancer Society (ACS) today released Cancer Statistics, 2026, the organization’s annual report on cancer facts and trends. The new findings show, for...
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Anders Sejr Hansen @andersshansen.bsky.social · 22/06/2026
(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...
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 22/06/2026
Live-cell imaging of enhancer-promoter dynamics reveals transient contact-driven gene activation www.biorxiv.org/content/10.64898/20…
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Elias Friman @eliasfriman.bsky.social · 11/05/2026
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...
biorxiv.org
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Craig Kaplan @triggerloop.bsky.social · 21/05/2026
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/...
science.org
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...
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Jack Bateman @jbateman01.bsky.social · 20/05/2026
Non-Mendelian inheritance of DNA methylation patterns in mice www.nature.com/articles/s41...
nature.com
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 ...
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Jack Bateman @jbateman01.bsky.social · 13/05/2026
Loop extrusion creates rare, long-lived encounters underlying enhancer-promoter communication www.biorxiv.org/content/10.1...
biorxiv.org
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Elphege Nora Lab at UCSF @elphegenoralab.bsky.social · 13/05/2026
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 🧪 🧵👇
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Jack Bateman @jbateman01.bsky.social · 12/05/2026
Ps #TCMbangee is a great typo, like if the movie is the banger than I’m the bangee
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Jack Bateman @jbateman01.bsky.social · 12/05/2026
Oh wowzers I didn’t know Wise did noir, going on my list
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Jack Bateman @jbateman01.bsky.social · 29/04/2026
Nice! Feeling sufficiently emotionally stable for American bleak. Just finished Best Years, that was great - sent me on a Harold Russell deep dive, that guy is amazing!
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Jack Bateman @jbateman01.bsky.social · 10/04/2026
Will look for this one
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Jack Bateman @jbateman01.bsky.social · 10/04/2026
I’ve seen this one! A remake I think? Did not expect that from Lucille Ball
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David Brückner @davidbrueckner.bsky.social · 14/03/2026
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...
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Jack Bateman @jbateman01.bsky.social · 08/03/2026
lol zero chance of 3 hour attention span is there a TikTok version
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Takashi Fukaya @fukayalab.bsky.social · 27/02/2026
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/...
science.org
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.
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Craig Kaplan @triggerloop.bsky.social · 16/02/2026
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/...
science.org
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...
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Dominik Handler @86dominik.bsky.social · 13/02/2026
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)
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eltsovmikhail.bsky.social @eltsovmikhail.bsky.social · 10/02/2026
We are in EMBO J. See DNA and non-octameric nucleosome-like particles in situ link.springer.com/article/10.1...
link.springer.com
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...
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The EMBO Journal @embojournal.org · 03/02/2026
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...
link.springer.com
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 ...
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Takashi Fukaya @fukayalab.bsky.social · 05/02/2026
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...
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