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Assistant Professor307B Mudd Hall Department of Biology Johns Hopkins University 3400 N. Charles Street Baltimore, MD 21218-2685 Email: xchen32 @jhu.eduOffice 410 516-4576 Lab 410 516-6543 Departmental fax 410 516-5213 B.S.University of Science & Technology of China (USTC), Hefei, ChinaPh.D.University of Texas at Austin, TexasPostdoctoralStanford University School of Medicine, California |
Research Interests
Epigenetic regulation of Drosophila germ cell differentiation from a stem cell lineage
A broad definition for “epigenetic phenomenon” refers to effects on gene expression or function that are heritable through many cell divisions without altering the primary DNA sequences. Epigenetic regulation can act through different mechanisms, including post-translational modifications of histones and localization of the chromatin modifiers to particular subnuclear regions. Failure in appropriate epigenetic regulation may lead to abnormalities in development and may also underlie early steps in cancer genesis.
During normal development, the mechanisms that regulate differentiation of cells from undifferentiated precursors play key roles in tissue/organ development and maintenance, such as gametogenesis. Precursor germ cells must commit to differentiate at the right place and with the right timing to generate and maintain the pools of functional gametes. The maintenance of the precursor germ cells in an undifferentiated and proliferative state and the subsequent reversal of these controls to allow terminal differentiation are both critical to continuous production of gametes throughout lifetime.
The Drosophila male germ line provides a powerful model system for studying the mechanisms that regulate differentiation in adult stem cell lineages. My laboratory utilizes it as a model system to study how genetic and epigenetic mechanisms interplay to ensure proper gene expression during spermatogenesis. We use molecular genetics and genomic strategies to systematically study the following questions: (1) Are there genes with stem cell-specific expression? (2) Is the specific expression of these genes maintained by a unique chromatin state? (3) How do the transcription and chromatin landscape change in continuously differentiating germ cells during normal development? (4) How do the epigenomic changes regulate proliferation versus differentiation processes in this lineage? (5) Can GSCs be regenerated if the differentiation process is reversed? Dramatic changes in the transcriptional program and chromatin landscape of male germ cells offer an excellent system to investigate these molecular mechanisms in vivo.
Epigenetic inheritance in germline stem cell lineage
We investigated epigenetic inheritance during GSC asymmetric cell division (Science 338: 679). It has been known for a long time that epigenetic changes are heritable. However, except for DNA methylation, little is known about the molecular mechanisms of epigenetic inheritance. We found that during the asymmetric division of Drosophila male germline stem cell (GSC), the preexisting histones are selectively segregated to the GSC whereas newly synthesized histones during DNA replication are enriched in the differentiating daughter cell. The asymmetric histone inheritance occurs in GSCs but not in symmetrically dividing progenitor cells. Furthermore, if GSCs are genetically manipulated to divide symmetrically, the asymmetric histone inheritance mode is lost. In contrast to canonical histones, the histone variant H3.3 does not exhibit this asymmetric pattern during GSC divisions. Thus, our studies provide the direct evidence that stem cells retain preexisting canonical histones during asymmetric cell divisions in vivo, which may contribute to maintain their epigenetic memory. We are continuing this exciting project by asking: (1) What are the molecular mechanisms underlying asymmetric segregation pattern of H3? (2) What are the consequences of the mis-regulation of such an inheritance mode? Our studies will shed light on a long-standing question regarding whether and how stem cells retain their epigenetic memory.
Representative Publications
Publications related to current work:Research papers:
1. Tarayrah, L., Herz, H-M., Shilatifard, A. and Chen, X. (2013) Histone demethylase dUTX directly antagonizes JAK-STAT signaling to maintain the Drosophila testis niche architecture. Development, 140, 1014-1023.
2. Eun, S., Stoiber, P.M., Wright, H. J., McMurdie, K.E., Choi, C.H., Gan, Q., Lim, C., Chen, X. (2012) MicroRNAs downregulate Bag of marbles to ensure proper terminal differentiation in Drosophila male germline lineage. Development, 140, 23-30.
3. Tran, V.*, Lim, C.*, Xie, J. and Chen, X. (2012) Asymmetric division of Drosophila male germline stem cell shows asymmetric histone distribution. Science 338, 679-682 (* co-first authors).
Featured in Faculty of 1000 Biology.
4. Tran, V., Gan, Q. and Chen, X. (2012) Chromatin immunoprecipitation (ChIP) using Drosophila tissue. Journal of Visualized Experiments (JoVE), pii: 3745. doi: 10.3791/3745.
5. Cuddapah, S.*, Roh, T-Y., Cui, K., Fuller, M.T., Zhao, K. and Chen, X.* (2012) A Polycomb binding site identified in human T cells acts as a functional Polycomb Response Element in Drosophila.
PLoS One 7(5):e36365 (*co-corresponding authors.).
6. Chen, X.*, Lu, C., Morillo, J., Eun, S. and Fuller, M.T.* (2011) Sequential changes at differentiation gene promoters as they become active in a stem cell lineage. Development 138: 2441-2450.
(*co-corresponding authors.) Featured article “In this issue”.
7. Gan, Q.*, Chepelev, I.*, Wei, G., Tarayrah, L., Cui, K., Zhao, K. and Chen, X. (2010) Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq. Cell Research 20(7): 763-783 (*co-first authors).
8. Gan, Q., Schones, D.E., Eun, S., Wei, G., Cui, K., Zhao, K. and Chen, X. (2010) Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis. Genome Biology 11(4): R42.
9. Kracklauer, M.P., Wiora, H.M., Deery, W.J., Chen, X., Bolival, B., Jr., Romanowicz, D., Simonette, R.A., Fuller, M.T., Fischer, J.A., and Beckingham, K.M. (2010) The Drosophila SUN protein Spag4 cooperates with the coiled-coil protein Yuri Gagarin to maintain association of the basal body and spermatid nucleus. Journal of Cell Science 123 (16): 2763- 2772.
10. Krishnamoorthy, T., Chen, X., Govin, J., Cheung, W.L., Dorsey, J., Schindler, K., Winter, E., Allis, C. D., Khochbin, S., Fuller, M. T., and Berger, S. L. (2006) Phosphorylation of histone H4 Ser1 regulates sporulation in yeast and is conserved in fly and mouse spermatogenesis.
Genes and Development 20: 2580–2592.
11. Chen, X., Hiller, M., Sancak, Y. and Fuller, M. T. (2005) Tissue specific TAFs counteract Polycomb to turn on terminal differentiation. Science 310: 869- 872.
This paper was reviewed by Ringrose, L. in BioEssays (2006) 28:330-334; and featured in Faculty of 1000 Biology.
12. Hiller, M., Chen, X., Pringle, M.J., Suchorolski, M., Sancak, Y., Viswanathan, S., Bolival, B., Marino, S. and Fuller, M.T. (2004) Testis-specific TAF homologs collaborate to control a tissue-specific transcription program. Development 131: 5297-5308.
Review articles:
1. Tran,V.*, Feng, L.J.* and Chen, X. (2013) Asymmetric distribution of histones during Drosophila male germline stem cell asymmetric divisions. Invited review to Chromosome Research, in press. (* co-first authors)
2. Lim, C.*, Tarayrah, L.* and Chen, X. (2012) Transcriptional regulation during Drosophila spermatogenesis. Invited review to Spermatogenesis 2:3, 1-9 (* co-first authors).
3. Chepelev, I. and Chen, X. (2012) Switching splicing pattern during stem cell differentiation. Invited review to Frontiers in Biology, doi: 10.1007/s11515-012-1198-y.
4. Eun, S.*, Gan, Q.*, and Chen, X. (2010) Epigenetic regulation of germ cell differentiation. Current Opinion in Cell Biology 22: 737-743 (*co-first authors).
5. Chen, X. (2008) Stem cells- what can we learn from flies? Invited review for Fly. FLY 2-1: 19- 28.
Selected earlier publications:
1. Chen, X., Zhang, B. and Fischer, J. A. (2002) A specific protein substrate for deubiquitinating enzyme: Liquid facets is the substrate of Fat facets. Genes and Development 16: 289-294. One of the cover stories.
2. Chen, X. and Fischer, J. A. (2000) In vivo structure/function analysis of the Drosophila fat facets deubiquitinating enzyme gene. Genetics 156: 1829-1836
3. Chen, X.*, Li, Q.* and Fischer, J. A. (2000) Genetic analysis of the Drosophila DNAprim gene: The function of the 60-kD primase subunit of DNA polymerase opposes the fat facets signaling pathway in the developing eye. Genetics 156: 787-1795. (* indicating authors of equal contribution.)