Ruifeng Hu
@ruifenghu.bsky.social
Reposted by Ruifeng Hu
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.
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
December 15, 2025 at 4:22 PM
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.
We uncover an unexpected role for endogenous Xist RNA in regulating X-linked genes that escape X-inactivation.
Reposted by Ruifeng Hu
A major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists!
www.nature.com/articles/s41...
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...
www.nature.com
December 17, 2025 at 8:59 PM
A major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ruifeng Hu
@science.org🧬Cohesin guides homology search during DNA repair using loops and sister chromatid linkages | Science www.science.org/doi/10.1126/... @fedeteloni.bsky.social @danielgerlich.bsky.social et al.
Cohesin guides homology search during DNA repair using loops and sister chromatid linkages
Accurate repair of DNA double-strand breaks (DSBs) is essential for genome stability, and defective repair underlies diseases such as cancer. Homologous recombination uses an intact homologous sequenc...
www.science.org
December 5, 2025 at 8:50 PM
@science.org🧬Cohesin guides homology search during DNA repair using loops and sister chromatid linkages | Science www.science.org/doi/10.1126/... @fedeteloni.bsky.social @danielgerlich.bsky.social et al.
Reposted by Ruifeng Hu
Our Science paper is out!
Huge congratulations to @huabin-zhou.bsky.social, Mike Rosen, and the brilliant @janhuemar.bsky.social @juliamaristany.bsky.social and @kieran-russell.bsky.social from our group
News: bit.ly/4avnkAr and bit.ly/3XBGVHS
Great perspective by @vram142.bsky.social +K Zhang
Huge congratulations to @huabin-zhou.bsky.social, Mike Rosen, and the brilliant @janhuemar.bsky.social @juliamaristany.bsky.social and @kieran-russell.bsky.social from our group
News: bit.ly/4avnkAr and bit.ly/3XBGVHS
Great perspective by @vram142.bsky.social +K Zhang
December 5, 2025 at 9:47 AM
Our Science paper is out!
Huge congratulations to @huabin-zhou.bsky.social, Mike Rosen, and the brilliant @janhuemar.bsky.social @juliamaristany.bsky.social and @kieran-russell.bsky.social from our group
News: bit.ly/4avnkAr and bit.ly/3XBGVHS
Great perspective by @vram142.bsky.social +K Zhang
Huge congratulations to @huabin-zhou.bsky.social, Mike Rosen, and the brilliant @janhuemar.bsky.social @juliamaristany.bsky.social and @kieran-russell.bsky.social from our group
News: bit.ly/4avnkAr and bit.ly/3XBGVHS
Great perspective by @vram142.bsky.social +K Zhang
Reposted by Ruifeng Hu
Thanks @pasquelab.bsky.social and his team for this collaboration.
𝐍𝐞𝐰 𝐩𝐫𝐞𝐩𝐫𝐢𝐧𝐭 𝐚𝐥𝐞𝐫𝐭! 🎉
“𝐗𝐈𝐒𝐓 𝐃𝐫𝐢𝐯𝐞𝐬 𝐗-𝐂𝐡𝐫𝐨𝐦𝐨𝐬𝐨𝐦𝐞 𝐈𝐧𝐚𝐜𝐭𝐢𝐯𝐚𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐒𝐚𝐟𝐞𝐠𝐮𝐚𝐫𝐝𝐬 𝐅𝐞𝐦𝐚𝐥𝐞 𝐄𝐱𝐭𝐫𝐚𝐞𝐦𝐛𝐫𝐲𝐨𝐧𝐢𝐜 𝐂𝐞𝐥𝐥𝐬 𝐢𝐧 𝐇𝐮𝐦𝐚𝐧𝐬” 𝐢𝐬 𝐧𝐨𝐰 𝐨𝐧 𝐛𝐢𝐨𝐑𝐱𝐢𝐯!
www.biorxiv.org/content/10.1...
“𝐗𝐈𝐒𝐓 𝐃𝐫𝐢𝐯𝐞𝐬 𝐗-𝐂𝐡𝐫𝐨𝐦𝐨𝐬𝐨𝐦𝐞 𝐈𝐧𝐚𝐜𝐭𝐢𝐯𝐚𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐒𝐚𝐟𝐞𝐠𝐮𝐚𝐫𝐝𝐬 𝐅𝐞𝐦𝐚𝐥𝐞 𝐄𝐱𝐭𝐫𝐚𝐞𝐦𝐛𝐫𝐲𝐨𝐧𝐢𝐜 𝐂𝐞𝐥𝐥𝐬 𝐢𝐧 𝐇𝐮𝐦𝐚𝐧𝐬” 𝐢𝐬 𝐧𝐨𝐰 𝐨𝐧 𝐛𝐢𝐨𝐑𝐱𝐢𝐯!
www.biorxiv.org/content/10.1...
XIST Drives X-Chromosome Inactivation and Safeguards Female Extraembryonic Cells in Humans
Dosage compensation of sex chromosomes through X-chromosome inactivation (XCI) is required for mice extra-embryonic tissue growth and embryo development. The species specificity in mechanisms and timi...
www.biorxiv.org
November 26, 2025 at 10:29 AM
Thanks @pasquelab.bsky.social and his team for this collaboration.
Reposted by Ruifeng Hu
A new and fascinating story from @bencarty.bsky.social and the group, with crucial help from the teams of @naltemose.bsky.social, Simona Giunta, and @dfachinetti.bsky.social. Many thanks to all for a fantastic collaboration.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
November 25, 2025 at 12:16 PM
A new and fascinating story from @bencarty.bsky.social and the group, with crucial help from the teams of @naltemose.bsky.social, Simona Giunta, and @dfachinetti.bsky.social. Many thanks to all for a fantastic collaboration.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ruifeng Hu
Last week @science.org mRNA initiation and termination are spatially coordinated | Science www.science.org/doi/10.1126/... from @anafiszbein.bsky.social @athmapai.bsky.social et al.
October 13, 2025 at 2:03 AM
Last week @science.org mRNA initiation and termination are spatially coordinated | Science www.science.org/doi/10.1126/... from @anafiszbein.bsky.social @athmapai.bsky.social et al.
Reposted by Ruifeng Hu
@science.org ATP-dependent remodeling of #chromatin #condensates reveals distinct #mesoscale outcomes | Science www.science.org/doi/10.1126/...
October 13, 2025 at 1:50 AM
@science.org ATP-dependent remodeling of #chromatin #condensates reveals distinct #mesoscale outcomes | Science www.science.org/doi/10.1126/...
Reposted by Ruifeng Hu
⚠️ Paper alert: Using a novel CRISPR screening approach, we mapped the entire regulatory network controlling Xist—key for X-chromosome inactivation.
👉 We discover how sex and development signals are decoded at a single gene locus.
www.nature.com/articles/s41...
👇 Bluetorial
👉 We discover how sex and development signals are decoded at a single gene locus.
www.nature.com/articles/s41...
👇 Bluetorial
Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus - Nature Structural & Molecular Biology
Here Schwämmle et al. develop CRISPR reporter screens to map transcription-factor-regulatory element interactions at the Xist locus, revealing a two-step mechanism integrating developmental and X-dosage signals to initiate X-chromosome inactivation.
www.nature.com
October 6, 2025 at 1:02 PM
⚠️ Paper alert: Using a novel CRISPR screening approach, we mapped the entire regulatory network controlling Xist—key for X-chromosome inactivation.
👉 We discover how sex and development signals are decoded at a single gene locus.
www.nature.com/articles/s41...
👇 Bluetorial
👉 We discover how sex and development signals are decoded at a single gene locus.
www.nature.com/articles/s41...
👇 Bluetorial
Reposted by Ruifeng Hu
💫NEW: @sarawickstrom.bsky.social @katemiro.bsky.social & co show that mechano-osmotic changes in the #nucleus induce general #transcriptional repression and prime #chromatin for cell fate transitions by relieving repression of specific differentiation genes. #pluripotency
bit.ly/3VMcyNZ
bit.ly/3VMcyNZ
Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells - Nature Cell Biology
McCreery, Stubb et al. show that mechano-osmotic changes in the nucleus induce general transcriptional repression and prime chromatin for cell fate transitions by relieving repression of specific differentiation genes.
bit.ly
October 4, 2025 at 2:40 PM
💫NEW: @sarawickstrom.bsky.social @katemiro.bsky.social & co show that mechano-osmotic changes in the #nucleus induce general #transcriptional repression and prime #chromatin for cell fate transitions by relieving repression of specific differentiation genes. #pluripotency
bit.ly/3VMcyNZ
bit.ly/3VMcyNZ
Reposted by Ruifeng Hu
Taking a snippet of genetic code that is unique to humans and inserting it into mice helps them grow bigger brains than usual
https://go.nature.com/3GOTQkz
https://go.nature.com/3GOTQkz
Mice grow bigger brains when given this stretch of human DNA
Finding adds to the bigger picture of how humans developed such large brains.
go.nature.com
May 14, 2025 at 3:41 PM
Taking a snippet of genetic code that is unique to humans and inserting it into mice helps them grow bigger brains than usual
https://go.nature.com/3GOTQkz
https://go.nature.com/3GOTQkz
Reposted by Ruifeng Hu
Nature research paper: A human-specific enhancer fine-tunes radial glia potency and corticogenesis
https://go.nature.com/4kfH6BC
https://go.nature.com/4kfH6BC
A human-specific enhancer fine-tunes radial glia potency and corticogenesis - Nature
HARE5, a human accelerated region enhancer, modulates cortical development by influencing neural progenitor cell behaviour, leading to an enlarged neocortex with increased functional independence between cortical regions through amplified WNT signalling.
go.nature.com
May 19, 2025 at 11:13 AM
Nature research paper: A human-specific enhancer fine-tunes radial glia potency and corticogenesis
https://go.nature.com/4kfH6BC
https://go.nature.com/4kfH6BC
Reposted by Ruifeng Hu
Collective challenges need collective solutions. Happy to share the insights we've gained from the way our cells handle this: www.nature.com/articles/s41... and its summary www.crick.ac.uk/news/2025-09....
LinkedIn
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lnkd.in
September 24, 2025 at 4:25 PM
Collective challenges need collective solutions. Happy to share the insights we've gained from the way our cells handle this: www.nature.com/articles/s41... and its summary www.crick.ac.uk/news/2025-09....
Reposted by Ruifeng Hu
💫NEW: Djeghloul, Cheriyamkunnel et al. apply chromosome sorting to isolate active and inactive X chromosomes and report a role for Hbo1 and Msl histone acetyltransferase complexes in preserving active X #chromosomes in female cells during #mitosis.
bit.ly/4pIA0ta
bit.ly/4pIA0ta
Hbo1 and Msl complexes preserve differential compaction and H3K27me3 marking of active and inactive X chromosomes during mitosis - Nature Cell Biology
Djeghloul, Cheriyamkunnel et al. apply chromosome sorting to isolate active and inactive X chromosomes and report a role for Hbo1 and Msl histone acetyltransferase complexes in preserving active X chromosomes in female cells during mitosis.
bit.ly
September 24, 2025 at 6:34 AM
💫NEW: Djeghloul, Cheriyamkunnel et al. apply chromosome sorting to isolate active and inactive X chromosomes and report a role for Hbo1 and Msl histone acetyltransferase complexes in preserving active X #chromosomes in female cells during #mitosis.
bit.ly/4pIA0ta
bit.ly/4pIA0ta
Reposted by Ruifeng Hu
Nature research paper: CRISPR activation for SCN2A-related neurodevelopmental disorders
go.nature.com/3VmV1vp
go.nature.com/3VmV1vp
CRISPR activation for SCN2A-related neurodevelopmental disorders - Nature
Using SCN2A haploinsufficiency as a proof-of-concept, upregulation of the existing functional gene copy through CRISPR activation was able to rescue neurological-associated phenotypes in Scn2a haploinsufficient mice and human neurons.
go.nature.com
September 24, 2025 at 7:34 AM
Nature research paper: CRISPR activation for SCN2A-related neurodevelopmental disorders
go.nature.com/3VmV1vp
go.nature.com/3VmV1vp
Reposted by Ruifeng Hu
Our reporter hopping scaled up to thousands of integrations in a single locus, to produce high-resolution functional maps, with plenty of interesting insights: www.science.org/doi/10.1126/...
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...
www.science.org
September 24, 2025 at 8:56 AM
Our reporter hopping scaled up to thousands of integrations in a single locus, to produce high-resolution functional maps, with plenty of interesting insights: www.science.org/doi/10.1126/...
Reposted by Ruifeng Hu
Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication.
www.biorxiv.org/content/10.1...
A🧵👇
www.biorxiv.org/content/10.1...
A🧵👇
September 24, 2025 at 9:45 PM
Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication.
www.biorxiv.org/content/10.1...
A🧵👇
www.biorxiv.org/content/10.1...
A🧵👇
Reposted by Ruifeng Hu
@science.org🧬🔬Kinetic organization of the #genome revealed by ultraresolution multiscale live #imaging | Science www.science.org/doi/10.1126/...
Kinetic organization of the genome revealed by ultraresolution multiscale live imaging
Genome function requires regulated genome motion. However, tools to directly observe this motion in vivo have been limited in coverage and resolution. Here we introduce an approach to tile mammalian c...
www.science.org
September 22, 2025 at 7:43 PM
@science.org🧬🔬Kinetic organization of the #genome revealed by ultraresolution multiscale live #imaging | Science www.science.org/doi/10.1126/...
Reposted by Ruifeng Hu
#1 Centromeres are epigenetic loci defined by CENP-A, positioned in unmethylated DNA flanked by highly methylated regions. Our work, published in @natgenet.nature.com in collaboration with @naltemose.bsky.social investigates the role of DNAme at human centromeres www.nature.com/articles/s41...
DNA methylation influences human centromere positioning and function - Nature Genetics
Genome-wide and targeted perturbation of DNA methylation at centromeres affects CENP-A positioning and centromere structure, resulting in aneuploidy and reduced cell viability.
www.nature.com
September 4, 2025 at 1:10 PM
#1 Centromeres are epigenetic loci defined by CENP-A, positioned in unmethylated DNA flanked by highly methylated regions. Our work, published in @natgenet.nature.com in collaboration with @naltemose.bsky.social investigates the role of DNAme at human centromeres www.nature.com/articles/s41...
Reposted by Ruifeng Hu
Mechanistic and Epigenetic Partitioning of Lamina-Associated Chromatin Revealed by a Genome-Wide Imaging Screen https://www.biorxiv.org/content/10.1101/2025.08.13.670143v1
August 14, 2025 at 6:30 PM
Mechanistic and Epigenetic Partitioning of Lamina-Associated Chromatin Revealed by a Genome-Wide Imaging Screen https://www.biorxiv.org/content/10.1101/2025.08.13.670143v1
Reposted by Ruifeng Hu
Excited to share our work on the specificity of PRC2 subcomplexes in stem cell and differentiation. We show that PRC2.1 and PRC2.2 exhibit distinct H3K27 methylation specificity in human pluripotent stem cells and opposing role in differentiation. Now online at Mol Cell: www.cell.com/molecular-ce...
Distinct specificity and functions of PRC2 subcomplexes in human stem cells and cardiac differentiation
Much et al. reveal that the PRC2 subcomplexes PRC2.1 and PRC2.2 play distinct roles
in the epigenetic repression of developmental genes in human stem cells. Interactions
between the PRC2 core and its ...
www.cell.com
August 12, 2025 at 3:38 PM
Excited to share our work on the specificity of PRC2 subcomplexes in stem cell and differentiation. We show that PRC2.1 and PRC2.2 exhibit distinct H3K27 methylation specificity in human pluripotent stem cells and opposing role in differentiation. Now online at Mol Cell: www.cell.com/molecular-ce...
Reposted by Ruifeng Hu
Check out new paper on single-molecule live-cell imaging of SMCHD1 binding to an inactive X chromosome by Flavia Constantinescu from Neil Brockdorff's team! :)
www.biorxiv.org
June 18, 2025 at 3:53 PM
Check out new paper on single-molecule live-cell imaging of SMCHD1 binding to an inactive X chromosome by Flavia Constantinescu from Neil Brockdorff's team! :)
Reposted by Ruifeng Hu
🍹 @thomasclarke.bsky.social, Mostoslavsky & co identify chromatin factor ZNF280A, which is recruited to damaged chromatin to promote long-range DNA-end resection. Loss of ZNF280A is linked to genome instability in patients with 22q11.2 distal deletion syndrome.
👉https://rdcu.be/ezdPR
bit.ly/46Cpr3L
👉https://rdcu.be/ezdPR
bit.ly/46Cpr3L
ZNF280A links DNA double-strand break repair to human 22q11.2 distal deletion syndrome - Nature Cell Biology
Clarke et al. identify chromatin factor ZNF280A, which is recruited to damaged chromatin where it promotes long-range DNA-end resection. Loss of ZNF280A is linked to genome instability in patients wit...
bit.ly
August 4, 2025 at 5:01 PM
🍹 @thomasclarke.bsky.social, Mostoslavsky & co identify chromatin factor ZNF280A, which is recruited to damaged chromatin to promote long-range DNA-end resection. Loss of ZNF280A is linked to genome instability in patients with 22q11.2 distal deletion syndrome.
👉https://rdcu.be/ezdPR
bit.ly/46Cpr3L
👉https://rdcu.be/ezdPR
bit.ly/46Cpr3L
Congrats Job and all the authors!
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....
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...
www.nature.com
July 11, 2025 at 6:54 AM
Congrats Job and all the authors!
Reposted by Ruifeng Hu
Nature research paper: Probing condensate microenvironments with a micropeptide killswitch
https://go.nature.com/4mMlGyc
https://go.nature.com/4mMlGyc
Probing condensate microenvironments with a micropeptide killswitch - Nature
Targeting a non-natural micropeptide ‘killswitch’ to several biomolecular condensates altered condensate compositions and revealed condensate functions in human cells
go.nature.com
June 9, 2025 at 12:34 PM
Nature research paper: Probing condensate microenvironments with a micropeptide killswitch
https://go.nature.com/4mMlGyc
https://go.nature.com/4mMlGyc