Xun Chen (@xunchen85) header
Xun Chen (@xunchen85) profile picture

Xun Chen

@xunchen85

Shanghai Institute of Immunity and Infection (Former Institut Pasteur of Shanghai), CAS

 Shanghai, China
english.siii.cas.cn/en_sourcedb_siii/pi/202404/t20240416_660187.html
Joined April 2015
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Photo by Xun Chen (@xunchen85)Photo by Xun Chen (@xunchen85)Photo by Xun Chen (@xunchen85)Photo by Xun Chen (@xunchen85)Photo by Xun Chen (@xunchen85)Photo by Xun Chen (@xunchen85)Photo by Xun Chen (@xunchen85)
Super excited to share our latest #preprint on the TE classification/annotation and regulatory evolution from our lab @guilbourque at @Ashbi_KyotoU. Check it out here! 🧵 Cryptic endogenous retrovirus subfamilies in the primate lineage doi.org/10.1101/2023.12.07.5…
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New preprint from our lab! Why is not everyone working on Transposons? Loss of H3K9me3 maintenance in human neural progenitor cells leads to transcriptional activation of L1 retrotransposons biorxiv.org/content/10.1101/…
Loss of H3K9me3 maintenance in human neural progenitor cells leads to transcriptional activation of...

Loss of H3K9me3 maintenance in human neural progenitor cells leads to transcriptional activation of...

Heterochromatin is characterised by an inaccessibility to the transcriptional machinery and associated with the histone mark H3K9me3. Heterochromatin erosion is a hallmark of human ageing and H3K9me3...

biorxiv.org
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Capturing cell-type-specific activities of cis-regulatory elements from peak-based single-cell ATAC-seq dlvr.it/TJW2bx
Capturing cell-type-specific activities of cis-regulatory elements from peak-based single-cell...

Capturing cell-type-specific activities of cis-regulatory elements from peak-based single-cell...

Mengjie Chen introduces CREscendo, a framework using Tn5 cleavage and ENCODE CREs to refine scATAC-seq peaks. Applied to PBMCs and mouse cortex, it recovers key regulatory signals that are missed by...

cell.com
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Xun Chen retweeted
nature (@Nature) profile picture
nature
@Nature29 Feb 2024
Why don't humans have tails? A genetics study finds that a mobile genetic sequence inserted into a gene for tail development contributed to tail loss as early apes evolved. go.nature.com/3Te8t4C
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Locus-level L1 DNA methylation profiling reveals the epigenetic and transcriptional interplay between L1s and their integration sites dlvr.it/T2DH8X
Locus-level L1 DNA methylation profiling reveals the epigenetic and transcriptional interplay...

Locus-level L1 DNA methylation profiling reveals the epigenetic and transcriptional interplay...

L1 retrotransposons are abundant sequences in the human genome, implicated in disease and evolution. Lanciano, Philippe et al. profile their DNA methylation patterns at single-locus resolution in...

cell.com
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Our paper on the ancestral genome-assisted TE annotation method/resource is out in @CellGenomics! Enhanced annotation is now available for multiple species, including human and mouse, with ~70% increase in ancient TEs. cell.com/cell-genomics/fullt…
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#Pangenome graphs improve the analysis of SVs for rare genetic diseases. Our new study is out! Great collaboration with the lab of Tomi Pastinen and congrats to @groza_cristian for the amazing work! nature.com/articles/s41467-0…
Pangenome graphs improve the analysis of structural variants in rare genetic diseases

Pangenome graphs improve the analysis of structural variants in rare genetic diseases

Nature Communications - A pangenomic approach, where genome sequences are related to each other in a graph, facilitates analysis of genomic variation between individuals. Here, the authors explore...

nature.com
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I've gotten several requests recently for permission to use the notes from my computational biology class: github.com/pachterlab/BI-BE-… A reminder that they're licensed under CC BY 4.0: you're free to share and adapt, just give appropriate credit and indicate if changes were made.
GitHub - pachterlab/BI-BE-CS-183-2023: Introduction to Computational Biology and Bioinformatics...

GitHub - pachterlab/BI-BE-CS-183-2023: Introduction to Computational Biology and Bioinformatics...

Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023 - pachterlab/BI-BE-CS-183-2023

github.com
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[News release] ASHBi researchers identify and selectively manipulate the neural circuits underlying the balance of risk vs. reward decision-making using optogenetics in primates. ➡️Article science.org/doi/10.1126/scie… ➡️Press Release ashbi.kyoto-u.ac.jp/news/202… @ScienceMagazine
Balancing risk-return decisions by manipulating the mesofrontal circuits in primates

Balancing risk-return decisions by manipulating the mesofrontal circuits in primates

The mesofrontal dopaminergic pathway to ventral Brodmann area 6 is crucial for risk-return decision balance in primates.

science.org
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Genome-wide classification of epigenetic activity reveals regions of enriched heritability in immune-related traits dlvr.it/T0htWb
Genome-wide classification of epigenetic activity reveals regions of enriched heritability in...

Genome-wide classification of epigenetic activity reveals regions of enriched heritability in...

EpiNN is a method that uses epigenetic data to detect genomic regions that are relevant for immune-system function. Regions detected using EpiNN have a high concentration of variants associated with...

cell.com
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🔥🔥How does the LINE-1 retrotransposon jump around in the human genome? Super excited to present my postdoctoral work answering this published today @Nature together with twitterless Kathy Collins's lab and @NogalesLab @UCBerkeley nature.com/articles/s41586-0… A 🧵
Template and target-site recognition by human LINE-1 in retrotransposition

Template and target-site recognition by human LINE-1 in retrotransposition

Nature - Human LINE-1 ORF2p relies on upstream single-stranded target DNA to position the adjacent duplex in the endonuclease active site for nicking of the longer DNA strand, with a single nick...

nature.com
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Check out our latest review | LINE-1 retrotransposition and its deregulation in cancers: implications for therapeutic opportunities by @CarlosMendezPhD. Our thanks to @GenesDev. genesdev.cshlp.org/content/e…
Image from Kathleen Helen Burns (@KathleenHBurns)
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“Transposable elements contribute to nearly 80% of human-specific candidate cis-regulatory elements in cortical cells” 🧠 …🤯 literally! Amazing dataset 🔥 Congrats to all involved! nature.com/articles/s41586-0…
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Very happy to share our new paper on how SOX2 instructs pluripotency program transition in vivo in mouse E3.5-E7.5 embryos. Spearheaded by our super team: Lijia Li, Fangnong Lai, Xiaoyu Hu and Bofeng Liu. Wonderful collaboration with Amy Ralston. (1/n) science.org/doi/10.1126/scie…
Multifaceted SOX2-chromatin interaction underpins pluripotency progression in early embryos

Multifaceted SOX2-chromatin interaction underpins pluripotency progression in early embryos

SOX2 regulatory circuitry in mouse embryos identifies distinct cell states and multifaceted pioneer factor-enhancer interactions.

science.org
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Multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci dlvr.it/T0D5Tk
Multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk...

Multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk...

Hodonsky et al. perform gene expression profiling and a multifaceted genetic analysis of gene regulation in coronary artery tissues from an ancestrally diverse patient cohort. This new resource...

cell.com
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💥 New preprint! Really excited about this work brilliantly led by Manu @manvendr7 & Sabrina Leddy in collab with @TheNixonLab - check it out and let us know what you think!
Manvendra Singh (@manvendr7) profile pictureManvendra Singh@manvendr713 Dec 2023
🎈🎆Beyond thrilled to drop new preprint exploring how #transposons (TEs) contribute to natural resistance to HIV in “Elite Controllers” (ECs) biorxiv.org/content/10.1101/… a work from @TheNixonLab and @CedricFeschotte Lab Please see 🧵till end, it gets better with each 🧵 1/12
Image from Manvendra Singh (@manvendr7)
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We found a high epigenetic heterogeneity per subfamily which was well rearranged by the rooted tree and phyletic groups. And the reconstituted MER11 phyletic groups display a more consistent epigenetic profile compared to the original subfamily annotations.
Image from Xun Chen (@xunchen85)
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Focusing on the youngest phyletic group “MER11_G4”, we revealed the gain of SOX-related motif in this phyletic group was due to a single-nucleotide deletion and occurred in humans and chimpanzees but not in macaques. It also significantly increased their regulatory potential.
Image from Xun Chen (@xunchen85)
Image from Xun Chen (@xunchen85)
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In the end, we applied the approach to other simian-specific LTR subfamilies. Among 53 subfamilies analyzed, we corrected 30% instances from 26 subfamilies. We found that the phyletic groups we characterized were enriched for different epigenetic marks TFs and KRAB-ZNFs.
Image from Xun Chen (@xunchen85)
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We then developed a new annotation approach based on phylogenetic analysis and cross-species conservation to correct it. Focusing on MER11 subfamilies, we reassigned instances from the three subfamilies (MER11A/B/C) into four groups, we defined as “phyletic groups”.
Image from Xun Chen (@xunchen85)
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