Biography

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.


Profile: https://faculty.sdu.edu.cn/xc/en

Chen Lab: https://faculty.sdu.edu.cn/chenlab/en


Education
  • 2016/10/01-2017/09/30
    University of Michigan
    Medical School
    Visiting scholar
  • 2012/09/01-2018/01/01
    Ocean University of China
    Hydrobiology
    Doctoral Degree
  • 2008/09/01-2012/07/01
    Ocean University of China
    Life Science
    Bachelor
Professional Experience
  • 2024-01 — Now
    Shandong University, Marine College
    Professor (Distinguished)
  • 2022-01 — 2023-12
    Shandong University, Marine College
    Professor (Qilu Young Scholar)
  • 2021-04 — 2021-09
    Columbia University, Dept. of Genet. & Dev.
    Associate Research Scientist
  • 2018-04 — 2021-04
    Columbia University, Dept. of Genet. & Dev.
    Postdoctoral Research Scientist
Working-Papers

Epigenetic Regulation and Evolution of Homeostasis

成果汇总-表观遗传.jpg

Publication
Research direction

1. Epigenetic Regulation of Homeostasis in Eukaryotes

2. Genome and Chromosome Evolution of Eukaryotes

3. Disease-related Chromatin Regulatory Networks

Papers

(1) [Nucleic Acids Research, 2025] Comprehensive genome annotation of the model ciliate Tetrahymena thermophila by in-depth epigenetic and transcriptomic profiling

(2) [Science China Life Sciences, 2025] Unveiling an ancient whole-genome duplication event in Stentor, the model unicellular eukaryotes

(3) [Cell, 2024] SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion

(4) [Science Advances, 2024] Epigenetic regulation of p63 blocks squamous-to-neuroendocrine transdifferentiation in esophageal development and malignancy

(5) [Nature Communications, 2024] Rosiglitazone and trametinib exhibit potent anti-tumor activity in a mouse model of muscle invasive bladder cancer

(6) [Cell Reports, 2024] Metabolic reprogramming by histone deacetylase inhibition preferentially targets NRF2-activated tumors

(7) [Science China Life Sciences, 2024] Genes and proteins expressed at different life cycle stages in the model protist Euplotes vannus revealed by both transcriptomic and proteomic approaches

(8) [BMC Biology, 2024] Genomic insights into the cellular specialization of predation in raptorial protists

(9) [BMC Genomics, 2024] Decryption of the survival "black box": gene family expansion promotes the encystment in ciliated protists

(10) [European Journal of Protistology, 2024] Single-cell transcriptomic analysis reveals genome evolution in predatory litostomatean ciliates

(11) [Cell, 2023] Single substitution in H3.3G34 alters DNMT3A recruitment to cause progressive neurodegeneration

(12) [Nature Communications, 2023] Context-defined cancer co-dependency mapping identifies a functional interplay between PRC2 and MLL-MEN1 complex in lymphoma

(13) [Nucleic Acids Research, 2023] Annotation and evaluation of base editing outcomes in multiple cell types using CRISPRbase

(14) [Molecular Phylogenetics and Evolution, 2023] New evidence of consistency between phylogeny and morphology for two taxa in ciliated protists, the subclasses Oligotrichia and Choreotrichia (Protista, Ciliophora)

(15) [Marine Life Science & Technology, 2023] Comparative genome analysis of three euplotid protists provides insights into the evolution of nanochromosomes in unicellular eukaryotic organisms

(16) [Marine Life Science & Technology, 2023] Invasion by exogenous RNA: cellular defense strategies and implications for RNA inference

(17) [European Journal of Protistology, 2023] Single-cell transcriptome reveals cell division-regulated hub genes in unicellular eukaryote Paramecium

(18) [Molecular Cell, 2022] Histone methylation antagonism drives tumor immune evasion in squamous cell carcinomas

(19) [PNAS, 2022] CHAF1A/B mediate silencing of unintegrated HIV-1 DNAs early in infection

(20) [Cell, 2021] Functional interrogation of DNA damage response variants with base editing screens

(21) [PNAS, 2021] Depletion of H3K36me2 recapitulates epigenomic and phenotypic changes induced by the H3.3K36M oncohistone mutation

(22) [Nature Genetics, 2021] Two competing mechanisms of DNMT3A recruitment regulate the dynamics of de novo DNA methylation at PRC1-targeted CpG islands

(23) [Nature Communications, 2021] Pparg signaling controls bladder cancer subtype and immune exclusion

(24) [Molecular Cell, 2021] Histone H3.3 K27M and K36M mutations de-repress transposable elements through perturbation of antagonistic chromatin marks

(25) [EMBO Reports, 2021] The interplay between DNA and histone methylation: molecular mechanisms and disease implications

(26) [Nature, 2019] The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape

(27) [Molecular Ecology Resources, 2019] Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors

(28) [Molecular Ecology Resources, 2018] GPSit: an automated method for evolutionary analysis of nonculturable ciliated microeukaryotes

(29) [Nucleic Acids Research, 2017] N6-adenine DNA methylation is associated with H2A.Z-containing well-positioned nucleosomes in Pol II-transcribed genes in Tetrahymena

(30) [Science China Life Sciences, 2016] Enzymatic and chemical mapping of nucleosome distribution in purified micro- and macronuclei of the ciliated model organism, Tetrahymena thermophila

(31) [Protein & Cell, 2015] Phylogenomics of non-model ciliates based on transcriptomic analyses

Copyright All Rights Reserved Shandong University Address: No. 27 Shanda South Road, Jinan City, Shandong Province, China: 250100
Information desk: (86) - 0531-88395114
On Duty Telephone: (86) - 0531-88364731 Construction and Maintenance: Information Work Office of Shandong University