Personal profile

Currently, Professor and doctoral supervisor of School of Medicine, Sun Yat-sen University. He graduated from the School of Life Sciences, Sun Yat-sen University in 2006 and received his PhD in 2011. From 2011 to 2015, he worked as a postdoctoral researcher in the laboratory of Professor Jianzhi Zhang at the University of Michigan. At the end of 2015, he was recruited by Sun Yat-sen University's "100 Talent Plan" to introduce talents, and was selected as the National high-level Talent Introduction Youth project in early 2016, and won the Excellent Young People Science Fund project in 2022.
He has published a number of high-impact academic papers as the first author or corresponding author. Published in Science, Nature Genetics, Nat.Ecol.Evol.(2 articles), Mol.Biol.Evol.(6 articles), Genome Biology, PNAS, Cell Systems and other internationally renowned journals.
His research interests focus on the use of high-throughput sequencing technology to study key biological issues, focusing on the important biological process of gene expression, and systematically studying the mechanism of action and evolution of gene expression on cell phenotype from the aspects of chromosome location, gene dose and gene mutation.

Academic achievement

Important academic research achievements and contributions:
Genetic information is transmitted from genotype to phenotype, in which gene expression is a key regulatory step. I systematically studied the influence of gene expression on cell phenotype from three aspects: overexpression, appropriate expression and underexpression, and made the following breakthrough progress:
First, it was demonstrated for the first time that mutations in highly expressed genes produced more of the wrong molecules and caused more damage to the cell's ability to proliferate. This provides direct evidence to explain the theory of slow evolution of highly expressed genes, while revealing that the phenotypic effects of mutations are expression dependent.
Second, it was the first to find that gene integration can cause transcriptional competition, change the expression of neighboring genes, and thus weaken the proliferation ability of cells, revealing that the location of gene integration can not be ignored on the cell phenotype.
Third, it was confirmed that the halved copy number of sex chromosome genes does not mean insufficient gene expression, and the expression sensitivity of genes determines whether gene expression needs to double the evolutionary pattern. At the same time, a new theory of \"sex chromosome insensitivity\" is proposed to explain the evolutionary pattern of sex chromosomes more broadly.
The above original research results have proposed a deeper understanding of the connotation of \"central law\", opened up a new research idea for the improvement of genetic engineering, and provided technical support and theoretical basis for understanding the pathogenicity, epidemic and drug resistance processes of pathogenic microorganisms.

Academic Publication

27.    Wu Z, Cai X, Zhang X, Liu Y, Tian GB, Yang JR, Chen X#. Expression level is a major modifier of the fitness landscape of a protein coding gene. Nat Ecol Evol. 2022 Jan.

26.    Gui Q*，Deng S*，Zhou Z，Cai W，Zhang X，Shi W，Cai X，Jiang W, Cui Z, Hu Z# and Chen X#. Transcriptome Analysis in Yeast Reveals the Externality of Position Effects. Mol. Biol. Evol. 2021 Apr.

25.    Yu G, Zhu H, Chen X# and Yang JR#. Specificity of RNA Folding and its Association with Evolutionarily Adaptive mRNA Secondary Structures. Genom Proteom Bioinf. 2021 Feb.

24.    Mo N, Zhang X, Shi W, Yu G, Chen X # and Yang J#. Bidirectional genetic control of phenotypic heterogeneity and its implication for cancer drug resistance. Mol Biol Evol. 2020 Dec.

23.    Chen J, Wang M, He X, Yang J# and Chen X #. The Evolution of Sex Chromosome Dosage Compensation in Animals. J Genet Genomics. 2020 Nov.

22.     Yuan M, Yang X, Lin J, Cao X, Chen F, Zhang X, Li Z, Zheng G, Wang X, Chen X # and Yang J#. Alignment of Cell Lineage Trees Elucidates Genetic Programs for the Development and Evolution of Cell Types. iScience. 2020 Jul.

21.     Liu L, Wang Y, Zhang D, Chen Z, Chen X, Su Z and He X. The Origin of additive genetic variance driven by positive selection. Mol Biol Evol. 2020 Apr.

20.     Chen F, Wu P, Deng S, Zhang H, Hou Y, Hu Z, Zhang J#, Chen X# and Yang JR#. Dissimilation of synonymous codon usage bias in virus-host coevolution due to translational selection. Nat Ecol Evol. 2020 Mar.

19.     Yang JR# and Chen X#. Dosage sensitivity of X-linked genes in human embryonic single cells. BMC genomics. 2019 Jan.

18.     Duan C*, Huan Q*, Chen X*, Wu S, Carey LB, He X and Qian W. Reduced intrinsic DNA curvature leads to increased mutation rate. Genome Biol. 2018 Sep. (*Co-first authors)

17.     Chen X, Zhang J. The X to autosome expression ratio in haploid and diploid human embryonic stem cells. Mol Biol Evol. 2016 Sep.

16.     Chen X, Zhang J. The genomic landscape of position effects on protein expression level and noise in yeast. Cell Syst. 2016 May.

15.     Chen X, Yang JR, Zhang J. Nascent RNA folding mitigates transcription associated mutagenesis. Genome Res. 2015 Oct.

14.     Chen X, Zhang J. No X-chromosome dosage compensation in human proteomes. Mol Biol Evol. 2015 Feb.

13.     Chen X, Zhang J. Mutation accumulation experiment supports elevated mutation rates at highly transcribed sites. (Letter to Editor) PNAS. 2014 Sep.

12.     Yang JR, Chen X, Zhang J. Codon-by-codon modulation of translational speed and accuracy via mRNA folding. PLoS Biol. 2014 Jul.

11.     Chen X, Zhang J. Why Are Genes Encoded on the Lagging Strand of the Bacterial Genome? Genome Biol Evol. 2013 Nov.

10.     Chen X, Zhang J. No Gene-Specific Optimization of Mutation Rate in Escherichia coli. Mol Biol Evol. 2013 Mar.

9.     Park C, Chen X, Yang JR, Zhang J. Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly. PNAS. 2013 Feb.

8.     Chen X, Zhang J. The ortholog conjecture is untestable by the current Gene Ontology but is supported by RNA sequencing data. PLoS Comput Biol. 2012 Nov.

7.     Chen X, Chen Z, Chen H, Su Z, Yang J, Shi S, He X. Nucleosomes suppress spontaneous mutations base-specifically in eukaryotes. Science. 2012 Mar.

6.     He X, Chen X, Xiong Y, Chen Z, Wang X, Shi S, Wang X, Zhang J. He et al. reply. Nat Genet. 2011 Nov.

5.     Yang G, Zhou R, Tang T, Chen X, Ouyang J, He L, Li W, Chen S, Guo M, Li X, Zhong C, Shi S. Gene expression profiles in response to salt stress in Hibiscus tiliaceus. Plant Mol Biol Rep. 2011 Sep.

4.     Yang G, Chen X, Tang T, Zhou R, Chen S, Li W, Ouyang J , He L, Shi S. Comparative genomics of two ecologically differential populations of Hibiscus tiliaceus under salt stress. Funct Plant Biol. 2011 Mar.

3.     Xiong Y*, Chen X*, Chen Z, Wang X, Shi S, Wang X, Zhang J, He X. RNA sequencing shows no dosage compensation of the active X-chromosome. Nat Genet. 2010 Dec. (*Co-first authors)

2.     Chen X, Shi S, He X. Evidence for gene length as a determinant of gene coexpression in protein complexes. Genetics. 2009 Oct.

1.     Zhou R, Zeng K, Wu W, Chen X, Yang Z, Shi S, Wu CI. Population genetics of speciation in nonmodel organisms: I. Ancestral polymorphism in mangroves. Mol Biol Evol. 2007 Dec.

Award honor

National Key Research and Development Plan \"Research on the Formation and Evolution of Tissue Stem Cell Mutations\" project, sub-project leader (project funding 6.78 million)
Sun Yat-sen University Talent Introduction Project, project leader (project fund 3 million)
National high-level Talent Introduction Youth Project, project leader (project fund 3 million)
National Science Fund for Outstanding Young People (project fund 2 million yuan)
National Natural Science Foundation of China, Project leader (2 projects, project funds 600,000 and 580,000)
Supporting fund of Guangdong Province for National High-level Talent Introduction Youth Project, Project leader (project fund 500,000)