Xiao Chen

About

Xiao Chen is a Professor of the Laboratory of Marine Protozoan Biodiversity & Evolution, affiliated with Marine College at Shandong University. His group aims to delineate mechanisms underlying chromatin regulation and genome evolution using eukaryotic cell models. Dr. Chen has been focusing on the epigenetic regulation mechanism of cellular homeostasis maintenance using eukaryotic models including ciliate. The findings are highlighted as follows: 1) Clarified the gene transcription pattern and omics basis for maintaining cellular homeostasis under environmental stress, laying the foundation for further exploration of its epigenetic regulation mechanism; 2) Elucidated the molecular mechanisms by which epigenetic factors alter gene transcription levels and regulate cellular homeostasis, expanding our understanding of the involvement of epigenetic factors in regulating cellular homeostasis; 3) Revealed the pathogenic mechanism of cellular homeostasis imbalance caused by chromatin dysregulation and confirmed the potential diagnostic and therapeutic value of epigenetic regulation of cellular homeostasis. These findings have led to more than 40 publications in high-impact journals including Nature Communications, PNAS, and Molecular Cell. Dr. Chen's work was highly recognized by distinguished experts in chromatin fields as "a crucial discovery that will provide key information for current and future drug development" and "an important study that further illuminates on the role oncohistones have in gene transcription regulation". Currently, the research on the dysregulation of gene transcription by chromatin states has been hampered by a lack of rationalized systems to dig deep into the underlying mechanism. Dr. Chen hereby aims to further explore the roles of histone modifications in regulating gene transcription and maintaining cell physiological and structural stability, in response to the key question of how unicellular eukaryotes maintain cellular homeostasis.

Work

Education

Ocean University of China
China

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PhD

Publications

Epigenetic regulation of p63 blocks squamous-to-neuroendocrine transdifferentiation in esophageal development and malignancy

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Science Advances

Summary

journal-article

Genes and proteins expressed at different life cycle stages in the model protist Euplotes vannus revealed by both transcriptomic and proteomic approaches

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Science China Life Sciences

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journal-article

Rosiglitazone and trametinib exhibit potent anti-tumor activity in a mouse model of muscle invasive bladder cancer

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Nature Communications

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journal-article

Genomic insights into the cellular specialization of predation in raptorial protists

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BMC Biology

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journal-article

Single-cell transcriptomic analysis reveals genome evolution in predatory litostomatean ciliates

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European Journal of Protistology

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journal-article

Decryption of the survival “black box”: gene family expansion promotes the encystment in ciliated protists

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BMC Genomics

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journal-article

Metabolic reprogramming by histone deacetylase inhibition preferentially targets NRF2-activated tumors

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Cell Reports

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journal-article

SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion

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Cell

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journal-article

Recognition of histone methylation and DNA by the PWWP domain: Mechanism and function

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Chromatin Readers in Health and Disease

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book-chapter

Invasion by exogenous RNA: cellular defense strategies and implications for RNA inference

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Marine Life Science & Technology

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journal-article

New evidence of consistency between phylogeny and morphology for two taxa in ciliated protists, the subclasses Oligotrichia and Choreotrichia (Protista, Ciliophora)

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Molecular Phylogenetics and Evolution

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journal-article

Editorial: Biomedical application of DNA modifications

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Frontiers in Genetics

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journal-article

Context-defined cancer co-dependency mapping identifies a functional interplay between PRC2 and MLL-MEN1 complex in lymphoma

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Nature Communications

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journal-article

Single-cell transcriptome reveals cell division-regulated hub genes in the unicellular eukaryote Paramecium

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European Journal of Protistology

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journal-article

Comparative genome analysis of three euplotid protists provides insights into the evolution of nanochromosomes in unicellular eukaryotic organisms

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Marine Life Science & Technology

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journal-article

Single substitution in H3.3G34 alters DNMT3A recruitment to cause progressive neurodegeneration

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Cell

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journal-article

Annotation and evaluation of base editing outcomes in multiple cell types using CRISPRbase.

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Nucleic acids research

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journal-article

Histone methylation antagonism drives tumor immune evasion in squamous cell carcinomas.

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Molecular Cell

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journal-article

Comparative Genome Analysis Reveals Cis-Regulatory Elements on Gene-Sized Chromosomes of Ciliated Protists

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Frontiers in Microbiology

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journal-article

Comparative Genome Analysis Reveals Cis-Regulatory Elements on Gene-Sized Chromosomes of Ciliated Protists

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Frontiers in Microbiology

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journal-article

Comparative Genome Analysis Reveals <i>Cis</i>-Regulatory Elements on Gene-Sized Chromosomes of Ciliated Protists.

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Frontiers in microbiology

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journal-article

The cAMP signaling pathway regulates Epe1 protein levels and heterochromatin assembly

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PLOS Genetics

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journal-article

CHAF1A/B mediate silencing of unintegrated HIV-1 DNAs early in infection

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Proceedings of the National Academy of Sciences

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journal-article

Pparg signaling controls bladder cancer subtype and immune exclusion

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Nature Communications

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journal-article

Histone H3.3 K27M and K36M mutations de-repress transposable elements through perturbation of antagonistic chromatin marks

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Molecular Cell

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journal-article

Growth Inhibition and Induction of Innate Immune Signaling of Chondrosarcomas with Epigenetic Inhibitors.

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Molecular cancer therapeutics

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journal-article

Overview of the Diversity, Phylogeny and Biogeography of Strombidiid Oligotrich Ciliates (Protista, Ciliophora), With a Brief Revision and a Key to the Known Genera.

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Frontiers in microbiology

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journal-article

Chromosome organization and gene expansion in the highly fragmented genome of the ciliate Strombidium stylifer

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Journal of Genetics and Genomics

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journal-article

Two competing mechanisms of DNMT3A recruitment regulate the dynamics of de novo DNA methylation at PRC1-targeted CpG islands.

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Nature genetics

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journal-article

The interplay between DNA and histone methylation: molecular mechanisms and disease implications.

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EMBO Reports

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journal-article

Depletion of H3K36me2 recapitulates epigenomic and phenotypic changes induced by the H3.3K36M oncohistone mutation

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Proc Natl Acad Sci U S A

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journal-article

Chromatin dysregulation associated with NSD1 mutation in head and neck squamous cell carcinoma.

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Cell Reports

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journal-article

Functional interrogation of DNA damage response variants with base editing screens.

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Cell

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journal-article

Single-Cell Genomic Sequencing of Three Peritrichs (Protista, Ciliophora) Reveals Less Biased Stop Codon Usage and More Prevalent Programmed Ribosomal Frameshifting Than in Other Ciliates

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Frontiers in Marine Science

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journal-article

The INO80 Complex Regulates Epigenetic Inheritance of Heterochromatin

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Cell Reports

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journal-article

Characterization of Simple Sequence Repeats (SSRs) in Ciliated Protists Inferred by Comparative Genomics

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Microorganisms

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journal-article

Functional analysis of the methyltransferase SMYD in the single-cell model organism Tetrahymena thermophila

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Marine Life Science & Technology

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journal-article

Pparg promotes differentiation and regulates mitochondrial gene expression in bladder epithelial cells

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Nature Communications

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journal-article

Our recent progress in epigenetic research using the model ciliate, Tetrahymena thermophila

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Marine Life Science & Technology

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journal-article

The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape

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Nature

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journal-article

Further analyses on the evolutionary “key‐protist” Halteria (Protista, Ciliophora) based on transcriptomic data

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Zoologica Scripta

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journal-article

Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors

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Molecular Ecology Resources

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journal-article

RNAi-dependent Polycomb repression controls transposable elements in Tetrahymena

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Genes & Development

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journal-article

Genome analysis of the unicellular eukaryote Euplotes vannus provides insights into mating type determination and tolerance to environmental stresses

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other

GPSit: An automated method for evolutionary analysis of nonculturable ciliated microeukaryotes

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Molecular Ecology Resources

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journal-article

N6-adenine DNA methylation is associated with the linker DNA of H2A.Z-containing well-positioned nucleosomes in Pol II-transcribed genes in Tetrahymena

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Nucleic Acids Research

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journal-article

A comparative study of genome organization and epigenetic mechanisms in model ciliates, with an emphasis on Tetrahymena , Paramecium and Oxytricha

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European Journal of Protistology

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journal-article

A germline-limited piggyBac transposase gene is required for precise excision in Tetrahymena genome rearrangement

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Nucleic Acids Research

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journal-article

Enzymatic and chemical mapping of nucleosome distribution in purified micro- and macronuclei of the ciliated model organism, Tetrahymena thermophila

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Science China Life Sciences

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journal-article

Enzymatic and chemical mapping of nucleosome distribution in purified micro- and macronuclei of the ciliated model organism, Tetrahymena thermophila.

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journal-article

Dissecting relative contributions ofcis- andtrans-determinants to nucleosome distribution by comparingTetrahymenamacronuclear and micronuclear chromatin

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Nucleic Acids Research

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journal-article

Phylogenomics of non-model ciliates based on transcriptomic analyses

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Protein & Cell

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journal-article

Phylogenomics of non-model ciliates based on transcriptomic analyses.

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journal-article

Molecular data suggests the ciliate Mesodinium (Protista: Ciliophora) might represent an undescribed taxon at class level

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Zoological Systematics

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journal-article

New considerations on the phylogeny of cyrtophorian ciliates (Protozoa, Ciliophora): expanded sampling to understand their evolutionary relationships

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Zoologica Scripta

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journal-article