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.

Education

Ocean University of China

China
→
PhD

Publications

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

Science Advances

journal-article

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

Science China Life Sciences

journal-article

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

Nature Communications

journal-article

Genomic insights into the cellular specialization of predation in raptorial protists

BMC Biology

journal-article

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

European Journal of Protistology

journal-article

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

BMC Genomics

journal-article

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

Cell Reports

journal-article

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

Cell

journal-article

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

Chromatin Readers in Health and Disease

book-chapter

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

Marine Life Science & Technology

journal-article

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

Molecular Phylogenetics and Evolution

journal-article

Editorial: Biomedical application of DNA modifications

Frontiers in Genetics

journal-article

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

Nature Communications

journal-article

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

European Journal of Protistology

journal-article

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

Marine Life Science & Technology

journal-article

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

Cell

journal-article

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

Nucleic acids research

journal-article

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

Molecular Cell

journal-article

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

Frontiers in Microbiology

journal-article

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

Frontiers in Microbiology

journal-article

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

Frontiers in microbiology

journal-article

The cAMP signaling pathway regulates Epe1 protein levels and heterochromatin assembly

PLOS Genetics

journal-article

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

Proceedings of the National Academy of Sciences

journal-article

Pparg signaling controls bladder cancer subtype and immune exclusion

Nature Communications

journal-article

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

Molecular Cell

journal-article

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

Molecular cancer therapeutics

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.

Frontiers in microbiology

journal-article

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

Journal of Genetics and Genomics

journal-article

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

Nature genetics

journal-article

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

EMBO Reports

journal-article

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

Proc Natl Acad Sci U S A

journal-article

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

Cell Reports

journal-article

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

Cell

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

Frontiers in Marine Science

journal-article

The INO80 Complex Regulates Epigenetic Inheritance of Heterochromatin

Cell Reports

journal-article

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

Microorganisms

journal-article

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

Marine Life Science & Technology

journal-article

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

Nature Communications

journal-article

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

Marine Life Science & Technology

journal-article

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

Nature

journal-article

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

Zoologica Scripta

journal-article

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

Molecular Ecology Resources

journal-article

RNAi-dependent Polycomb repression controls transposable elements in Tetrahymena

Genes & Development

journal-article

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

other

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

Molecular Ecology Resources

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

Nucleic Acids Research

journal-article

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

European Journal of Protistology

journal-article

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

Nucleic Acids Research

journal-article

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

Science China Life Sciences

journal-article

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

journal-article

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

Nucleic Acids Research

journal-article

Phylogenomics of non-model ciliates based on transcriptomic analyses

Protein & Cell

journal-article

Phylogenomics of non-model ciliates based on transcriptomic analyses.

journal-article

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

Zoological Systematics

journal-article

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

Zoologica Scripta

journal-article