Ksenia Skvortsova
@kseskv.bsky.social
π€ 110
π₯ 99
π 0
Developmental and Disease Epigenomics Laboratory Head at the Garvan Institute, Australia.
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Ksenia Skvortsova
Allegra Angeloni
about 2 months ago
1/ Iβm very excited to share my postdoc work with
@kseskv.bsky.social
, in collaboration with
@oligriffith.bsky.social
. We explore embryonic DNA methylation reprogramming in the fat-tailed dunnart, an Australian marsupial π¦π
www.biorxiv.org/content/10.1...
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https://www.biorxiv.org/content/10.1101/2025.11.09.686659v1
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Ksenia Skvortsova
Lorne Genome Conference, Australia
about 2 months ago
The Abstract submission and Earlybird registration deadlines have been extended! You now have until π π«π’πππ² ππ ππ¨π―ππ¦πππ« to submit and save! Do not forget to apply for awards if eligible!
https://www.lornegenome.org/registrations
Looking forward to seeing you at Lorne!
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Registrations β Lorne Genome
Registrations are now open! Secure your ticket to attend Lorne Genome 2022!
https://www.lornegenome.org/registrations
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Aurora Ruiz-Herrera
3 months ago
π₯ Another fruitful collaboration! Along with
@obog.bsky.social
& Juan Tenaβs teams we provide a multiomics study of zebrafish spermatogenesis π#meiosis π
www.embopress.org/doi/full/10....
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Ksenia Skvortsova
Kaessmann Lab
3 months ago
Did transposable elements shape brain evolution β and if so, which ones, and in which cell states and lineages? Led by
@tyamadat.bsky.social
, we explored this question in cerebellum development using sequence-based deep learning models!
www.biorxiv.org/content/10.1...
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Ksenia Skvortsova
Lorne Genome Conference, Australia
3 months ago
Please join us for several days of fantastic science at Lorne Genome 2026! We're thrilled to welcome Prof Amander Clark, a renowned stem cell biologist whose work focuses on in vitro gametogenesis and ovarian reserve formation:
https://www.lornegenome.org/amander-clark
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Ksenia Skvortsova
Lorne Genome Conference, Australia
3 months ago
Secure your early bird rate for Lorne Genome 2026 before Nov 7th!
lornegenome.org
We are excited to welcome Prof Duncan Odom as a speaker - a leading researcher in regulatory genomics and cancer genome evolution https://www.
lornegenome.org
/duncan-odum
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Ksenia Skvortsova
Lorne Genome Conference, Australia
3 months ago
Don't forget to
register and submit an abstract
for the ππ¨π«π§π πππ§π¨π¦π ππππ! ππ‘π’π¬ π°πππ€'π¬ π¬π©πππ€ππ« π¬π©π¨ππ₯π’π π‘π:
ππ«π¨π ππ«ππ§ππ ππ§ππ«ππ°π¬
, a leading systems biologist whose research focuses on mapping genetic interaction networks and protein localisation patterns in yeast and human cells.
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Registrations β Lorne Genome
Registrations are now open! Secure your ticket to attend Lorne Genome 2022!
https://www.lornegenome.org/registrations
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Ksenia Skvortsova
Duncan Sproul
3 months ago
Just been reading this nice review. Taught someone who has never really done developmental biology a lot! Thanks and congrats to all involved.
#epigenetics
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Charlotte Wright
4 months ago
How many chromosomes can an animal have? In our paper out now in
@currentbiology.bsky.social
we show that the Atlas blue butterfly has 229 chromosome pairs- the highest in diploid Metazoa! These arose by rapid autosome fragmentation while sex chromosomes stayed intact.
www.cell.com/current-biol...
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Constraints on chromosome evolution revealed by the 229 chromosome pairs of the Atlas blue butterfly
The genome of the Atlas blue butterfly contains ten times more chromosomes than most butterflies, and more than any other known diploid animal. Wright et al. show that this extraordinary karyotype is ...
https://tinyurl.com/atlasbluebutterfly
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Ksenia Skvortsova
Lorne Genome Conference, Australia
4 months ago
Earlybird registration & abstract submissions now open for the ππππ‘ ππ¨π«π§π πππ§π¨π¦π ππ¨π§πππ«ππ§ππ, ππ-ππππ‘ π ππ ππππ:
https://www.lornegenome.org/registrations
(deadline 7th Nov 2025) Speakers:
https://www.lornegenome.org/speakers
We look forward to seeing you there!
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Speakers β Lorne Genome
No description found
https://www.lornegenome.org/speakers
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ANZSCDB
4 months ago
ANZSCDB is pleased to launch our Zoom seminar series! Our first seminar kicks off on Thursday August 28th, 2025 at 12pm AEST with Professor Jose Polo and Dr Melanie White. Please register and attend to ensure the success and long-term sustainability of this initiative.
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Arnaud Krebs
4 months ago
This is not a HiC map! Ever wondered if multiple enhancers get activated simultaneously? We measured chromatin accessibility on thousands of molecules by nanopore to create genome-wide co-accessibility maps. Proud of
@mathias-boulanger.bsky.social
@kasitc.bsky.social
Biology in the threadπ
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Lennart Hilbert
5 months ago
How do enhancer-gene contacts relate to transcription activation? In mouse embryonic stem cells, a combo of STED, oligoFISH & RNA FISH shows that 3% of Dppa3 alleles transcribe. For these, enhancers and promoters come closer (panel E). Stumberger ... Leonhardt & Harz
www.biorxiv.org/content/10.1...
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Abby Buchwalter
5 months ago
Another paper bluetorial! Today: how does the spatial location of genes influence their function? (1/n)
www.nature.com/articles/s41...
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The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate - Nature Cell Biology
Marin et al. report the role of lamin proteins and the lamin B receptor (LBR) in chromatin positioning at the nuclear periphery. Knockout of all lamins and LBR in mouse embryonic stem cells leads to h...
https://www.nature.com/articles/s41556-025-01703-z
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David Lowry
5 months ago
academic.oup.com/evolut/advan...
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The evolution of suppressed recombination between sex chromosomes and the lengths of evolutionary strata
Abstract. The idea that sex-differences in selection drive the evolution of suppressed recombination between sex chromosomes is well-developed in populatio
https://academic.oup.com/evolut/advance-article/doi/10.1093/evolut/qpaf045/8124961
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Ksenia Skvortsova
Kaessmann Lab
6 months ago
Our study on a male-essential microRNA and the evolution of other dosage compensation mechanisms in birds is now out in Nature!
www.nature.com/articles/s41...
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A male-essential miRNA is key for avian sex chromosome dosage compensation - Nature
Birds have evolved a unique sex chromosome dosage compensation mechanism involving the male-biased microRNA (miR-2954), which is essential for male survival by regulating the expression of dosage-sens...
https://www.nature.com/articles/s41586-025-09256-9
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Axel Visel
6 months ago
No new genes needed to fly - just rewire what you have! π¦π§¬ Great new paper from the labs of
@fany-real.bsky.social
@stemundi.bsky.social
@dariloops.bsky.social
doi.org/10.1038/s415...
#EvoDevo
#SingleCell
#BatWings
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Laurie Belcher
6 months ago
OrthoFinder just dropped a major update Itβs faster, more accurate, and ready for thousands of genomes Letβs break it down (1/10)
github.com/OrthoFinder/...
www.biorxiv.org/content/10.1...
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Jop Kind
6 months ago
I am very excited to share our latest work where we describe a new method to profile genome-wide chromatin transitions over time in single cells. Great collaborative effort with the van Oudenaarden group
@hubrechtinstitute.bsky.social
@oncodeinstitute.bsky.social
www.nature.com/articles/s41...
.
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Retrospective and multifactorial single-cell profiling reveals sequential chromatin reorganization during X inactivation - Nature Cell Biology
Kefalopoulou, Rullens et al. develop Dam&ChIC to assay chromatin state at two different time points in the same cell. The method was used to study the reorganization of LADs during cell division a...
https://www.nature.com/articles/s41556-025-01687-w
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Guillaume Andrey
6 months ago
Our work bridging enhancer-promoter proximity to phenotypic outcomes in vivo is out! Shout out to
@olimpiabompadre.bsky.social
, to Marie Kmita's lab, and to all the co-authors.
www.nature.com/articles/s41...
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Liebenberg syndrome severity arises from variations in Pitx1 locus topology and proportion of ectopically transcribing cells - Nature Communications
Here the authors show that reducing enhancer-promoter distance at the Pitx1 locus increases proportion of Pitx1 forelimb expressing cells, worsening skeletal defects in Liebenberg syndrome. They also ...
https://www.nature.com/articles/s41467-025-61615-2
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Juliane Glaser
6 months ago
Finally out! π₯³ Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published
@natgenet.nature.com
π§¬π¦ π Below is a brief description of the major findings. Check the full version of the paper for more details:
www.nature.com/articles/s41588-025-02248-5
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Enhancer adoption by an LTR retrotransposon generates viral-like particles, causing developmental limb phenotypes - Nature Genetics
Activation of an LTR retrotransposon inserted upstream of the Fgf8 gene produces viral-like particles in the mouse developing limb, triggering apoptosis and causing limb malformation. This phenotype c...
https://www.nature.com/articles/s41588-025-02248-5
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Evgeny Kvon
6 months ago
Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at
@nature.com
. Congrats to
@gracebower.bsky.social
who led the study. Below is a brief summary of the main findings
www.nature.com/articles/s41...
1/
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Range extender mediates long-distance enhancer activity - Nature
The REX element is associated with long-range enhancerβpromoter interactions.
https://www.nature.com/articles/s41586-025-09221-6
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Evgeny Kvon
6 months ago
How do non-coding variants in enhancers lead to disease? Happy to share our recent work, led by
@ewholling.bsky.social
, in which we discovered that poised chromatin sensitizes enhancers to aberrant activation by non-coding mutations, contributing to disease.
www.biorxiv.org/content/10.1...
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Aydan Bulut-Karslioglu
6 months ago
β οΈ I am really excited to share the work of Anastasios Balaskas, an excellent PhD candidate in the lab, with the wider world. Tasos made a significant advance: generating a stem cell-based embryo model that contains both posterior and anterior neural tissues of the late-stage gastrulating embryo.
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Kaessmann Lab
6 months ago
We are delighted to share our new preprint βThe evolution of gene regulatory programs controlling gonadal development in primatesβ
www.biorxiv.org/content/10.1...
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Bardin Lab
7 months ago
Students (Master's/PhD), do not miss this fantastic Developmental Biology course of
@sorbonne-universite.fr
and
@institutcurie.bsky.social
- It is FREE and open to international students, however, room and board + travel are not included.
training.institut-curie.org/courses/deve...
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Maxim Greenberg
7 months ago
This is 1) great news and 2) I think Iβm gonna sit on the multiome superenhancer story we were gonna submit nowβ¦ π
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Gonzalo Borrego-Yaniz
7 months ago
One thing still missing in many GWAS pipelines: chrX analysis... In this study from
@ajhgnews.bsky.social
, Mefford et al. explore X-GWAS across 48 UKBB traits and as expected, ~3% of trait heritability comes from chrX. Looks like itβs time we start doing this!
www.cell.com/ajhg/fulltex...
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Role of X chromosome and dosage-compensation mechanisms in complex trait genetics
We show that the X chromosome, understudied in genome-wide association studies, contributes to complex traits in a manner shaped by dosage-compensation mechanisms. We find near-full X inactivation bal...
https://www.cell.com/ajhg/fulltext/S0002-9297(25)00145-4?dgcid=raven_jbs_etoc_email#mmc1
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Graham Coop
7 months ago
Neat thread. Following these ideas, Yaniv Brandvain & I spent some time thinking about the consequences of the fact that sperm alleles could alter the outcomes of female meiosis:
pmc.ncbi.nlm.nih.gov/articles/PMC...
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Sperm should evolve to make female meiosis fair
Genomic conflicts arise when an allele gains an evolutionary advantage at a cost to organismal fitness. OΓΆgenesis is inherently susceptible to such conflicts because alleles compete for inclusion into...
https://pmc.ncbi.nlm.nih.gov/articles/PMC5539998/
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Alex de Mendoza
7 months ago
It was a pleasure to write a N&Vs on
@danielibrahim.bsky.social
's latest paper in
@natgenet.nature.com
. Enhancers tend to stay put even if their sequence changes beyond recognition. Quoting Il Gattopardo, everything must change so that everything can stay the same:
www.nature.com/articles/s41...
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Genome synteny reveals hidden enhancer conservation - Nature Genetics
Enhancer sequences evolve rapidly, which has led to the prevailing view that most are not functionally conserved across species. A study now challenges this assumption by leveraging interspecies point...
https://www.nature.com/articles/s41588-025-02194-2
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Daniel Ibrahim
7 months ago
How to find Evolutionary Conserved Enhancers in 2025? π£-π Check out our paper - fresh off the press!!! We find widespread functional conservation of enhancers in absence of sequence homology Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
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Conservation of regulatory elements with highly diverged sequences across large evolutionary distances
Nature Genetics - Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence...
https://rdcu.be/enVDN
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bioRxiv Cell Biology
7 months ago
Transcriptional activity generates chromatin motion that drives nuclear blebbing
https://www.biorxiv.org/content/10.1101/2025.05.20.655131v1
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Neil Shubin
7 months ago
New paper from the lab: Our teeth arose as sensory organs on the outside of the body of ancient jawless fish.!! Congrats to Yara Haridy and the team! Background and video:
phys.org/news/2025-05...
Open Access Paper:
www.nature.com/articles/s41...
News and Views:
www.nature.com/articles/d41...
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Teeth first evolved as sensory tissue in the armored exoskeletons of ancient fish, fossil scans find
Anyone who has ever squirmed through a dental cleaning can tell you how sensitive teeth can be. This sensitivity gives important feedback about temperature, pressureβand yes, painβas we bite and chew ...
https://phys.org/news/2025-05-teeth-evolved-sensory-tissue-armored.amp
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Turner Lab
8 months ago
We're excited to publish our latest study led by Bryony Leeke
@bryonyleeke.bsky.social
and Wazeer Varsally, now out in
@nature.com
πΎThis study focusses on the epigenome of marsupial embryos π¦ mapping DNA methylation in embryo development to specific embryo events
www.nature.com/articles/s41...
π§΅
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Divergent DNA methylation dynamics in marsupial and eutherian embryos - Nature
A study reports on the DNA methylation dynamics during embryogenesis in marsupials, showing that these differ from those occurring during embryogenesis in eutherian mammals.
https://www.nature.com/articles/s41586-025-08992-2
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Maxim Greenberg
8 months ago
Massive findings for anyone interested in DNA methylation, development, and evolution! Can't wait to dig in, congrats to all the authors!
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Evgeny Kvon
9 months ago
A tour de force study from Taipale&Yin labs. It expands the vocabulary of the Regulatory Code by adding 1131 TF:TF composite motifs that are different from the individual TF motifs. The new composite motifs are enriched in cell-type specific elements and active in vivo
www.nature.com/articles/s41...
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DNA-guided transcription factor interactions extend human gene regulatory code - Nature
A large-scale analysis of DNA-bound transcription factors (TFs) shows how the presence of DNA markedly affects the landscape of TF interactions, and identifies composite motifs that are recognized by ...
https://www.nature.com/articles/s41586-025-08844-z
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Ben Sabari
8 months ago
I am excited to share the latest paper from my lab where we leverage the selection bias of condensate-promoting oncofusions to uncover molecular rules governing condensate specificity and function.
www.cell.com/cell/fulltex...
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Cedric Boeckx
8 months ago
What did the two amino acid substitutions in
#FOXP2
that occurred uniquely in the human lineage do? π§ͺ𧬠π§ Fascinating new
@cp-cell.bsky.social
study by
@shadys11.bsky.social
D. Jarosz & J. Wysocka, uncovering a molecular function for these 2 substitutions in promoting the solubility of FOXP2. (1/n)
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DNA binding and mitotic phosphorylation protect polyglutamine proteins from assembly formation
DNA binding and phosphorylation protect FOXP2, a transcription factor with the longest polyQ track in the proteome, from aggregation during interphase and mitosis. Harnessing these native solubility-p...
https://www.cell.com/cell/fulltext/S0092-8674(25)00349-6
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Shady Saad
8 months ago
I am incredibly proud to share that my work has officially been published in Cell!
@cp-cell.bsky.social
This work was a product of years of dedication and countless hours of research in the labs of Joanna Wysocka and Dan Jarosz labs
@stanfordmedicine.bsky.social
www.cell.com/cell/fulltex...
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DNA binding and mitotic phosphorylation protect polyglutamine proteins from assembly formation
DNA binding and phosphorylation protect FOXP2, a transcription factor with the longest polyQ track in the proteome, from aggregation during interphase and mitosis. Harnessing these native solubility-p...
https://www.cell.com/cell/fulltext/S0092-8674(25)00349-6
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ME Torres-Padilla
9 months ago
we've put a Review together π Just came out at
www.nature.com/articles/s41...
hoping it is useful for those in the field but also for those not in the field who would like an overview on chromatin/epigenetics/replication/nuclear organisation in early embryos Enjoy :) - feedback welcome
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Kaia Mattioli
9 months ago
our work on the molecular differences between transcription factor isoforms is out now in Molecular Cell! key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
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Manuel Irimia
10 months ago
"The main fates after gene duplication are gene loss, redundancy, subfunctionalization and neofunctionalization". In our new review,
@fedemantica.bsky.social
and I argue we are missing the most prevalent one: specialization. And the same applies to alternative splicing! 1/7
tinyurl.com/45k7kbmp
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ARC Tracker
10 months ago
Hereβs a report by John Ross in
@timeshighered.bsky.social
on ARC Boardβs proposal to change grant schemes βΆοΈ
www.timeshighereducation.com/news/arc-gra...
[Free login required] Both
@scienceau.bsky.social
's & I am worried about opportunities & unintended consequences for early-career researchersπ
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Mark Dawson
12 months ago
Why can a human tolerate a drug that globally inhibits transcription? Why do transcription inhibitors not cure cancer? Our first paper of 2025 may help explain (some) of this! So incredibly proud of
@tobiaswilliams.bsky.social
& Ewa Michalak who led the work!
www.cell.com/molecular-ce...
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mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription
Transcription inhibitors also disrupt nuclear export. Here, Williams etΒ al. reveal that mRNA export factors sense transcription inhibition and adapt by storing mature export-competent mRNA in nuclear speckles. This enables rapid release when transcription resumes and ensures retention of cellular identity and viability during a transient global transcription insult.
https://www.cell.com/molecular-cell/abstract/S1097-2765(24)01004-9
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Emily Madden
about 1 year ago
Quote from farther down the thread, "Fun fact: mSCD-B5 was discovered in an uncharacterized phage from a sewage microbiome" You never know where you're going to find the next tool to advance biomedical research and I love that.
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Mitch Guttman
about 1 year ago
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
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ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics
ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for proteinβDNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...
https://www.nature.com/articles/s41588-024-02000-5
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Jess Kelley
about 1 year ago
Very excited that our paper describing a critical role for the PNUTS-PP1 phosphatase complex in transcription pause release is up online! This was a massive team effort with
@edimitrova.bsky.social
and the rest of the
@robklose.bsky.social
lab
www.cell.com/molecular-ce...
A short thread: (1/8)
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The PNUTS phosphatase complex controls transcription pause release
Kelley etΒ al. discover that the PNUTS phosphatase complex plays an essential role in gene transcription by controlling RNA polymerase II pause release. PNUTS achieves this through its TND, which recog...
https://www.cell.com/molecular-cell/fulltext/S1097-2765(24)00886-4
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The Lewis Lab
about 1 year ago
"Dark TFs": new manuscript mapped 166 uncharacterized human transcription factors, finding half bind genomic "dark matter," often closed chromatin rich in transposable elements.
www.biorxiv.org/content/10.1...
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