Chong Xie
@chongxie7.bsky.social
IMPRS-GS PhD student in genome organization and Transcription | Akis Papantonis's lab @UMG Göttingen
Reposted by Chong Xie
Want to shape the future of genome science? 🧬 PhD positions available at Max Planck Institute & Uni Göttingen (IMPRS-GS/GönomiX)! Join a vibrant, interdisciplinary research community. Apply by Jan 14, 2026: www.uni-goettingen.de/de/applicati... #GenomeScience #Research
November 28, 2025 at 12:23 PM
Want to shape the future of genome science? 🧬 PhD positions available at Max Planck Institute & Uni Göttingen (IMPRS-GS/GönomiX)! Join a vibrant, interdisciplinary research community. Apply by Jan 14, 2026: www.uni-goettingen.de/de/applicati... #GenomeScience #Research
Reposted by Chong Xie
Wonderful to see the beautiful preprint from Sabate et al now published - TADs are also dynamic structures in human cells, with remarkably similar parameters between mESCs and HCT116 cells
www.nature.com/articles/s41...
www.nature.com/articles/s41...
November 15, 2025 at 5:24 PM
Wonderful to see the beautiful preprint from Sabate et al now published - TADs are also dynamic structures in human cells, with remarkably similar parameters between mESCs and HCT116 cells
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Chong Xie
Sequential verification of transcription by Integrator and Restrictor
Sequential verification of transcription by Integrator and Restrictor
Estell and Łazowski et al. show that Integrator and Restrictor form distinct pathways for early attenuation of RNA polymerase II: Integrator acts at the promoter-proximal pause site, whereas Restrictor acts over a downstream “restriction zone.” For transcription to proceed, CDK7/9 oppose Integrator, while U1 snRNP counteracts both Integrator and Restrictor.
dlvr.it
November 7, 2025 at 11:58 PM
Sequential verification of transcription by Integrator and Restrictor
Reposted by Chong Xie
New Online! DNA looping regulates transcription
DNA looping regulates transcription
Nature Reviews Molecular Cell Biology, Published online: 03 November 2025; doi:10.1038/s41580-025-00924-2Siyuan (Steven) Wang discusses a 1984 study that reported that transcriptional regulation (in this case, in bacteria) depends on the formation of DNA loops.
bit.ly
November 3, 2025 at 11:09 AM
New Online! DNA looping regulates transcription
Reposted by Chong Xie
🎯 We are so thrilled our new paper @narjournal.bsky.social is out! Fantastic collab with the labs of Gordon Hager NIH & Franck Dequiedt. Heaviest lifting from Greg Fettweiss, Kaustub Wagh, Diana Stavreva & Alba Jiménez-Panizo. Big thanks to Andrea Alegre-Marti JdC 🥳✨️
academic.oup.com/nar/article/...
academic.oup.com/nar/article/...
May 16, 2025 at 3:06 PM
🎯 We are so thrilled our new paper @narjournal.bsky.social is out! Fantastic collab with the labs of Gordon Hager NIH & Franck Dequiedt. Heaviest lifting from Greg Fettweiss, Kaustub Wagh, Diana Stavreva & Alba Jiménez-Panizo. Big thanks to Andrea Alegre-Marti JdC 🥳✨️
academic.oup.com/nar/article/...
academic.oup.com/nar/article/...
Reposted by Chong Xie
Epigenetics Update - Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIP go.nature.com/43sr811
#Epigenetics #Chromatin
---
Discover the breakthrough at epigenometech.com
#Epigenetics #Chromatin
---
Discover the breakthrough at epigenometech.com
October 27, 2025 at 12:35 PM
Epigenetics Update - Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIP go.nature.com/43sr811
#Epigenetics #Chromatin
---
Discover the breakthrough at epigenometech.com
#Epigenetics #Chromatin
---
Discover the breakthrough at epigenometech.com
Reposted by Chong Xie
Our collab w. V Goel, @nicholas-aboreden.bsky.social , J Jusuf, G Blobel, L Mirny, @irate-physicist.bsky.social out in @natsmb.nature.com www.nature.com/articles/s41...
Was co-submitted with @allanaschooley.bsky.social @jobdekker.bsky.social whose paper should also come out soon
Brief thread 👇
Was co-submitted with @allanaschooley.bsky.social @jobdekker.bsky.social whose paper should also come out soon
Brief thread 👇
October 20, 2025 at 6:36 PM
Our collab w. V Goel, @nicholas-aboreden.bsky.social , J Jusuf, G Blobel, L Mirny, @irate-physicist.bsky.social out in @natsmb.nature.com www.nature.com/articles/s41...
Was co-submitted with @allanaschooley.bsky.social @jobdekker.bsky.social whose paper should also come out soon
Brief thread 👇
Was co-submitted with @allanaschooley.bsky.social @jobdekker.bsky.social whose paper should also come out soon
Brief thread 👇
Reposted by Chong Xie
New online: Dynamics of microcompartment formation at the mitosis-to-G1 transition
Dynamics of microcompartment formation at the mitosis-to-G1 transition
Nature Structural & Molecular Biology, Published online: 17 October 2025; doi:10.1038/s41594-025-01687-2Goel et al. produce high-resolution three-dimensional genome structure mapping from mitosis to G1 phase to show unseen interactions between enhancers and promoters in prometaphase. Polymer modeling indicates the interactions are facilitated by chromosome compaction.
go.nature.com
October 17, 2025 at 9:59 AM
New online: Dynamics of microcompartment formation at the mitosis-to-G1 transition
Reposted by Chong Xie
Biochemical reconstitution of sister chromatid cohesion establishment during DNA replication
Biochemical reconstitution of sister chromatid cohesion establishment during DNA replication
Genome inheritance during cell divisions relies on replicated sister DNAs being connected by cohesin rings. Minamino et al. reconstitute sister chromatid cohesion establishment during DNA replication using purified budding yeast proteins. The experiments yield molecular insight into more than one way in which sister chromatid cohesion can be built.
dlvr.it
October 2, 2025 at 3:19 PM
Biochemical reconstitution of sister chromatid cohesion establishment during DNA replication
Reposted by Chong Xie
New work from my lab with the Brown lab on how genome folding changes during motor neuron maturation, and how this process goes awry in ALS motor neurons. Led by Dr. Ozgun Uyan.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Dynamic changes in chromosome and nuclear architecture during maturation of normal and ALS C9orf72 motor neurons
We have investigated changes in chromosome conformation, nuclear organization, and transcription during differentiation and maturation of control and mutant motor neurons harboring hexanucleotide expa...
www.biorxiv.org
September 23, 2025 at 9:13 PM
New work from my lab with the Brown lab on how genome folding changes during motor neuron maturation, and how this process goes awry in ALS motor neurons. Led by Dr. Ozgun Uyan.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Chong Xie
🍰Interested in reading more about the study? Here's the N&Vs article written by Ann Dean.
👉https://rdcu.be/eHUxZ
bit.ly/424Iel9
👉https://rdcu.be/eHUxZ
bit.ly/424Iel9
RNA-binding proteins pull in chromatin loops - Nature Cell Biology
During development as cells exit a pluripotent state, chromatin looping interactions are strengthened, but the mechanism for this is unknown. A study now shows that CTCF–RBP interactions increase upon differentiation of embryonic stem cells to neural stem cells, and that the non-coding RNA Pantr1 collaborates with CTCF and RBPs to contract the genome.
bit.ly
September 24, 2025 at 6:41 AM
🍰Interested in reading more about the study? Here's the N&Vs article written by Ann Dean.
👉https://rdcu.be/eHUxZ
bit.ly/424Iel9
👉https://rdcu.be/eHUxZ
bit.ly/424Iel9
Reposted by Chong Xie
REVIEW: Timing is everything: transcription bursting in development
By Jee Min Kim and Daniel Larson
➡️ https://tinyurl.com/gd352465
#transcription #molecularbiology #transcriptionbursting #embryonicdevelopment #stemcell #differentiation #mRNA #development #molecularmechanism
By Jee Min Kim and Daniel Larson
➡️ https://tinyurl.com/gd352465
#transcription #molecularbiology #transcriptionbursting #embryonicdevelopment #stemcell #differentiation #mRNA #development #molecularmechanism
September 8, 2025 at 3:06 PM
REVIEW: Timing is everything: transcription bursting in development
By Jee Min Kim and Daniel Larson
➡️ https://tinyurl.com/gd352465
#transcription #molecularbiology #transcriptionbursting #embryonicdevelopment #stemcell #differentiation #mRNA #development #molecularmechanism
By Jee Min Kim and Daniel Larson
➡️ https://tinyurl.com/gd352465
#transcription #molecularbiology #transcriptionbursting #embryonicdevelopment #stemcell #differentiation #mRNA #development #molecularmechanism
Reposted by Chong Xie
(1/n) DNA-PAINT imaging inside the nucleus at single antibody resolution using TIRF? Ultrathin sectioning makes it happen!
Grateful to share my postdoctoral work introducing “tomographic & kinetically-enhanced DNA-PAINT” or in brief: tkPAINT. Out in @pnas.org!
doi.org/10.1073/pnas...
👇🧵
Grateful to share my postdoctoral work introducing “tomographic & kinetically-enhanced DNA-PAINT” or in brief: tkPAINT. Out in @pnas.org!
doi.org/10.1073/pnas...
👇🧵
August 13, 2025 at 2:19 PM
(1/n) DNA-PAINT imaging inside the nucleus at single antibody resolution using TIRF? Ultrathin sectioning makes it happen!
Grateful to share my postdoctoral work introducing “tomographic & kinetically-enhanced DNA-PAINT” or in brief: tkPAINT. Out in @pnas.org!
doi.org/10.1073/pnas...
👇🧵
Grateful to share my postdoctoral work introducing “tomographic & kinetically-enhanced DNA-PAINT” or in brief: tkPAINT. Out in @pnas.org!
doi.org/10.1073/pnas...
👇🧵
Reposted by Chong Xie
Congratulations to Masahiro Nagano on his new paper on STAG3-cohesin.
STAG3-cohesin has a much shorter residence time which leads to altered 3D genome organization and STAG3-cohesin is important for male germ cell differentiation.
www.nature.com/articles/s41...
STAG3-cohesin has a much shorter residence time which leads to altered 3D genome organization and STAG3-cohesin is important for male germ cell differentiation.
www.nature.com/articles/s41...
August 26, 2025 at 4:18 PM
Congratulations to Masahiro Nagano on his new paper on STAG3-cohesin.
STAG3-cohesin has a much shorter residence time which leads to altered 3D genome organization and STAG3-cohesin is important for male germ cell differentiation.
www.nature.com/articles/s41...
STAG3-cohesin has a much shorter residence time which leads to altered 3D genome organization and STAG3-cohesin is important for male germ cell differentiation.
www.nature.com/articles/s41...
Reposted by Chong Xie
Online Now: Single-stranded DNA-binding proteins are essential components of the architectural LDB1 protein complex Online now:
Single-stranded DNA-binding proteins are essential components of the architectural LDB1 protein complex
Wang et al. show that the architectural protein LDB1 forms a complex with single-stranded DNA-binding proteins (SSBPs) in vitro and in vivo. SSBP3 stabilizes LDB1 self-interactions to support chromatin loop formation.
dlvr.it
August 12, 2025 at 7:14 PM
Online Now: Single-stranded DNA-binding proteins are essential components of the architectural LDB1 protein complex Online now:
Reposted by Chong Xie
Killing liquid condensates with a micropeptide toward modulating condensatopathies
Killing liquid condensates with a micropeptide toward modulating condensatopathies
In a recent Nature article, Zhang et al. develop a non-natural micropeptide killswitch that modulates the material properties and biomolecular composition of target condensates, enabling direct regulation of cellular processes in condensatopathies.
dlvr.it
August 11, 2025 at 7:14 PM
Killing liquid condensates with a micropeptide toward modulating condensatopathies
Reposted by Chong Xie
We found a new asymmetry in the large-scale chromosome structure: sister chromatids are systematically shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! The work was led by Flavia Corsi, in close collaboration with the Daniel Gerlich lab.
www.biorxiv.org/content/10.1...
1/
www.biorxiv.org/content/10.1...
1/
July 15, 2025 at 8:11 AM
We found a new asymmetry in the large-scale chromosome structure: sister chromatids are systematically shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! The work was led by Flavia Corsi, in close collaboration with the Daniel Gerlich lab.
www.biorxiv.org/content/10.1...
1/
www.biorxiv.org/content/10.1...
1/
Reposted by Chong Xie
Online Now: Reconciling competing models on the roles of condensates and soluble complexes in transcription factor function Online now:
Reconciling competing models on the roles of condensates and soluble complexes in transcription factor function
Bremer et al. compare two competing models for how transcription factors mediate gene regulation: via phase separation or via soluble complex formation. They demonstrate that Gcn4 sequence variants can function as soluble complexes as well as heterotypic condensates but that condensates formed by variants with high affinities can dampen activities.
dlvr.it
July 3, 2025 at 11:32 AM
Online Now: Reconciling competing models on the roles of condensates and soluble complexes in transcription factor function Online now:
Reposted by Chong Xie
New online! Structural variants in the 3D genome as drivers of disease
Structural variants in the 3D genome as drivers of disease
Nature Reviews Genetics, Published online: 30 June 2025; doi:10.1038/s41576-025-00862-xDisruption of the 3D genome caused by structural variation contributes to developmental disorders and cancer. The authors review the causes and molecular and clinical consequences of position effects arising from disruptions to the genome architecture.
www.nature.com
June 30, 2025 at 11:30 AM
New online! Structural variants in the 3D genome as drivers of disease
Reposted by Chong Xie
✨OUT TODAY @natgenet.nature.com
📰Disruption of TAD hierarchy promotes LTR co-option in #cancer.
By Elissa W. P. Wong, Ping Chi and colleagues.
⬇️
www.nature.com/articles/s41...
📰Disruption of TAD hierarchy promotes LTR co-option in #cancer.
By Elissa W. P. Wong, Ping Chi and colleagues.
⬇️
www.nature.com/articles/s41...
Disruption of TAD hierarchy promotes LTR co-option in cancer - Nature Genetics
NIPBL perturbation activates long terminal repeat (LTR)-derived alternative promoters due to reorganization of chromatin’s hierarchical structure, leading to LTR co-option and oncogene activation in m...
www.nature.com
June 30, 2025 at 3:36 PM
✨OUT TODAY @natgenet.nature.com
📰Disruption of TAD hierarchy promotes LTR co-option in #cancer.
By Elissa W. P. Wong, Ping Chi and colleagues.
⬇️
www.nature.com/articles/s41...
📰Disruption of TAD hierarchy promotes LTR co-option in #cancer.
By Elissa W. P. Wong, Ping Chi and colleagues.
⬇️
www.nature.com/articles/s41...
Reposted by Chong Xie
📢OUT TODAY @natgenet.nature.com
📰Single-cell Micro-C profiles 3D genome structures at high resolution and characterizes multi-enhancer hubs.
By Honggui Wu, @Xiaoliang Sunney Xie and colleagues.
⬇️
www.nature.com/articles/s41...
📰Single-cell Micro-C profiles 3D genome structures at high resolution and characterizes multi-enhancer hubs.
By Honggui Wu, @Xiaoliang Sunney Xie and colleagues.
⬇️
www.nature.com/articles/s41...
Single-cell Micro-C profiles 3D genome structures at high resolution and characterizes multi-enhancer hubs - Nature Genetics
scMicro-C is a new method that provides high-resolution maps of the 3D genome. scMicro-C identifies structures called ‘promoter stripes’, which link a gene promoter to multiple downstream enhancers.
www.nature.com
July 2, 2025 at 1:02 PM
📢OUT TODAY @natgenet.nature.com
📰Single-cell Micro-C profiles 3D genome structures at high resolution and characterizes multi-enhancer hubs.
By Honggui Wu, @Xiaoliang Sunney Xie and colleagues.
⬇️
www.nature.com/articles/s41...
📰Single-cell Micro-C profiles 3D genome structures at high resolution and characterizes multi-enhancer hubs.
By Honggui Wu, @Xiaoliang Sunney Xie and colleagues.
⬇️
www.nature.com/articles/s41...
Reposted by Chong Xie
(1/n) Excited to present the latest work from the de Wit lab, where we identify and characterise loop extrusion-mediated fountains in mammalian genomes using acute depletion of 3D genome regulators: doi.org/10.1093/nar/.... A Bluetorial🧵:
Extrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriers
Abstract. Interphase chromosomes are mainly shaped by loop extrusion and compartmentalisation mechanisms. However, their temporal component and cause-effec
doi.org
July 1, 2025 at 6:34 AM
(1/n) Excited to present the latest work from the de Wit lab, where we identify and characterise loop extrusion-mediated fountains in mammalian genomes using acute depletion of 3D genome regulators: doi.org/10.1093/nar/.... A Bluetorial🧵:
Reposted by Chong Xie
🧬 @science.org Rules of engagement for condensins and cohesins guide mitotic chromosome formation | Science www.science.org/doi/10.1126/...
@edinburgh-uni.bsky.social @golobor.bsky.social @imbavienna.bsky.social @jobdekker.bsky.social @umasspress.bsky.social @hhmi.org @mitofficial.bsky.social et al.
@edinburgh-uni.bsky.social @golobor.bsky.social @imbavienna.bsky.social @jobdekker.bsky.social @umasspress.bsky.social @hhmi.org @mitofficial.bsky.social et al.
April 14, 2025 at 5:40 AM
🧬 @science.org Rules of engagement for condensins and cohesins guide mitotic chromosome formation | Science www.science.org/doi/10.1126/...
@edinburgh-uni.bsky.social @golobor.bsky.social @imbavienna.bsky.social @jobdekker.bsky.social @umasspress.bsky.social @hhmi.org @mitofficial.bsky.social et al.
@edinburgh-uni.bsky.social @golobor.bsky.social @imbavienna.bsky.social @jobdekker.bsky.social @umasspress.bsky.social @hhmi.org @mitofficial.bsky.social et al.
Reposted by Chong Xie
Nature research paper: Towards accurate differential diagnosis with large language models
https://go.nature.com/4cqHFWz
https://go.nature.com/4cqHFWz
Towards accurate differential diagnosis with large language models - Nature
Diagnostic reasoning using an optimized large language model with a dataset comprising real-world medical cases exhibited improved differential diagnostic performance as an assistive tool for clinicians over search engines and standard medical resources.
go.nature.com
April 14, 2025 at 2:41 PM
Nature research paper: Towards accurate differential diagnosis with large language models
https://go.nature.com/4cqHFWz
https://go.nature.com/4cqHFWz
Reposted by Chong Xie
Online Now: Phosphorylation-dependent charge blocks regulate the relaxation of nuclear speckle networks Online now:
Phosphorylation-dependent charge blocks regulate the relaxation of nuclear speckle networks
Zhang et al. show that the SRRM2 intrinsic disordered region (IDR) is extensively phosphorylated to generate charge blocks, which fine-tune the biophysical properties of nuclear speckles (NSs) to facilitate relaxation. The upstream kinase casein kinase 2 (CK2) phosphorylates SRRM2, which promotes NS relaxation, enhances mRNA splicing efficiency, and safeguards genome stability.
dlvr.it
April 14, 2025 at 3:19 PM
Online Now: Phosphorylation-dependent charge blocks regulate the relaxation of nuclear speckle networks Online now: