Center for Plant Cell Biology

Mission

Xuemei Chen

Professor

Mailing Address:

Botany and Plant Sciences
Genomics Building /4234A
University of California
Riverside, CA 92521

Phone: (951) 827-3988
Fax: (951) 827-4294
Email: xuemei.chen@ucr.edu

UCR Living the Promise Profile (2010)

Degree(s):

PhD 1995 Cornell University
BS 1988 Beijing University, China

College/Division Affiliation:

College of Natural and Agricultural Sciences

Center/Inst Affiliation(s):

Center for Plant Cell Biology

Areas Of Expertise:

Plant Development; Small Regulatory RNAs

Awards / Honors:

2013  Election to National Academy of Sciences
2011  HHMI-GBMF (Howard Hughes Medical Institute - Gordon and Betty Moore Foundation) Investigator
2007-2010  University Scholar, UC Riverside
2006  Charles Albert Shull award from American Society of Plant Biologists
2005  Board of Trustees Research Fellowship for Scholarly Excellence, Rutgers University
1995-1997  NIH Postdoctoral Fellowship
1991-1994  Cornell Plant Science Center Fellowship
1992  The Liu Memorial Award and The Hsien Wu and Daisy Yen Wu Scholarship

Research Summary:

The Chen lab is engaged in research in two major directions. In one, we are studying the biogenesis, degradation, modes of action, and biological functions of noncoding RNAs. In the other, we are dissecting the mechanisms underlying stem cell maintenance and/or termination. We mainly use Arabidopsis thaliana as the model, but we also apply insights learned from Arabidopsis to animal systems.

1. Noncoding RNAs

One major focus of our efforts lies in dissecting the mechanisms governing the biogenesis, stability, and modes of action of microRNAs. In the past ten years, the Chen lab has contributed to our understanding of the metabolic pathway of miRNAs by uncovering major players in the transcription of MIR genes, such as Pol II and Mediator, in the processing of miRNA precursors, such as DCL1 and DDL, in the modification of miRNAs, such as the small RNA methyltransferase HEN1, and in the degradation of mature miRNAs, such as SDN1. Our work on HEN1 helped uncover 2’-O-methylation on the 3’ terminal ribose as a conserved metabolic process that occurs on miRNAs and siRNAs in plants, and siRNAs and piRNAs in animals. The analysis of miRNAs and siRNAs in Arabidopsis hen1 mutants revealed two previously unknown processes that target small RNAs for degradation, 3’-to-5’ truncation and 3’ uridylation (the tailing of small RNAs with non-templated U residues). These processes appear to be conserved in plants and animals since 3’ truncation and 3’ uridylation also occur to small RNAs in animal hen1 mutants. Currently, we are studying how miRNA stability is regulated in vivo. In addition, we are actively studying the mode of action of miRNAs, in particular, how miRNAs inhibit the translation of their target mRNAs.

Figure 1. The biogenesis, modification, and degradation of plant miRNAs. Plant MIR genes are transcribed by Pol II, whose recruitment to MIR genes is aided by Mediator, into pri-miRNAs. DCL1processes pri-miRNAs to pre-miRNAs, and then pre-miRNAs to the miRNA/miRNA* duplex. The precision of miRNA processing requires SE and HYL1. The RNA-binding protein DDL probably helps recruits pri-miRNAs to DCL1. The heterodimeric nuclear cap-binding complex (CBC) also promotes miRNA biogenesis. The miRNA/miRNA* duplex is methylated by HEN1 at the 3’ termini, and the miRNA strand is loaded into AGO1. Mature miRNAs are turned over by the SDN1 family of exonucleases.

Another major focus is to understand the metabolism of long noncoding RNAs, especially the ones that impact genome stability through the production or recruitment of endogenous siRNAs that guide DNA methylation. Both forward genetics and reverse genetics approaches are being employed to identify factors that influence the biogenesis and degradation of these long noncodning RNAs. 

2. Floral Stem Cells

The stem cells in a flower are responsible for the production of a defined number of floral organs. They undergo a precise and programmed termination process such that they are no longer stem cells once the primordia for all floral organs have been initiated. We wish to understand the mechanisms underlying this temporally precise termination of floral stem cells. Studies have begun to reveal major players in this process, including transcription factors, such as AGAMOUS (AG), APETALA2 (AP2), and the HD-ZIP proteins PHABOLUSA (PHB) and PHAVOLUTA (PHV), miRNAs, such as miR172 and miR165/166, miRNA effector proteins, such as ARGONAUTE1 (AGO1), and AGO10, and chromatin modification machinery, such as the Polycomb Group (PcG) proteins. These factors all appear to influence the maintenance/termination of floral stem cells through the regulation of the stem cell maintenance gene WUSCHEL (WUS), which is expressed in a group of cells underlying the stem cells. The long term goal is to uncover how the transcription factors, miRNAs, and the PcG work together to ensure the temporally precise termination of WUS expression and how WUS maintenances the stem cells.

Figure 2. Factors that impact the temporally precise termination of floral stem cells. The diagrams represent stage 3 (left) and stage 6 (right) floral meristems. The stem cells and the WUS-expressing cells are in orange and purple, respectively. The shaded region represents where AG is expressed. By stage 6, when the primordia for all floral organs have been initiated, WUS expression is turned off and the stem cells cease to serve as stem cells. This temporally precise regulation of WUS expression and stem cell termination involves genes encoding transcription factors, such as PHB, AP2, AG, and KNU, miRNAs, such as miR172 and miR165/166, and the PcG. The shaded line indicates either a positive or a negative (currently unknown) role in floral stem cell termination.

Related Press Releases:

• UCR April 30, 2013: Plant Cell Biologist Elected to the National Academy of Sciences
• UCR April 25, 2013: Researchers Identify Key Cellular Organelle Involved in Gene Silencing
• UCR June 16, 2011: UC Riverside Botanist Receives High Honor from Howard Hughes Medical Institute
• UCR September 2, 2006: Xuemei Chen Receives the 2006 Charles Albert Shull Award

Selected Publications:

Lijuan Ji, Xigang Liu, Jun Yan, Wenming Wang, Rae Eden Yumul, Yu Ju Kim, Thanh Theresa Dinh, Jun Liu, Xia Cui, Binglian Zheng, Manu Agarwal, Chunyan Liu, Xiaofeng Cao, Guiliang Tang, and Xuemei Chen*. (2011). ARGONAUTE10 and ARGONAUTE1 regulate the termination of floral stem cells through two microRNAs in Arabidopsis. PLoS Genet 7(3): e1001358. doi:10.1371/journal.pgen.1001358.

Yun Ju Kim, Binglian Zheng, Yu Yu, So Youn Won, Beixin Mo, and Xuemei Chen*. (2011). The role of Mediator in small and long noncoding RNA production in Arabidopsis thaliana. EMBO J. 30, 814-822.

Bin Yu, Liu Bi, Jixian Zhai, Manu Agarwal, Shengben Li, Qingfa Wu, Shou-Wei Ding, Blake C. Meyers, Hervé Vaucheret, and Xuemei Chen*. (2010). siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis. Nucleic Acids Res. 38, 5844-50. PMCID: PMC2943618.

Binglian Zheng, Zhengming Wang, Shengben Li, Bin Yu, Jin-Yuan Liu, and Xuemei Chen*. (2009). Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis. Genes & Dev. 23, 2850-2860. PMCID: PMC2800093.

Xuemei Chen*. Small RNAs and their roles in plant development. (2009). Annu. Rev. Cell Dev. Biol. 25, 45-69.

Ying Huang, Lijuan Ji, Qichen Huang, Dmitry G. Vassylyev, Xuemei Chen, Jin-Biao Ma*. (2009). Structural insights into the molecular mechanism of the small RNA methyltransferase HEN1. Nature 461, 823-827.

Vanitharani Ramachandran and Xuemei Chen*. (2008). Degradation of microRNAs by a family of exoribonucleases in Arabidopsis. Science 321, 1490-1492. PMCID: PMC2570778.

Bin Yu, Liu Bi, Binglian Zheng, Lijuan Ji, David Chevalier, Manu Agarwal, Vanitharani Ramachandran, Wanxiang Li, Thierry Lagrange, John C Walker, and Xuemei Chen*.(2008). The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. PNAS 105, 10073-10078. PMCID: PMC2481372.

Julien Curaba and Xuemei Chen*. (2008). Biochemical activities of Arabidopsis RNA-dependent RNA polymerase 6. Journal of Biological Chemistry 283, 3059-3066. PMCID: PMC2629599.

Zhiyong Yang, Yon W. Ebright, Bin Yu, and Xuemei Chen*. (2006). HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2’ OH of the 3’ terminal nucleotide. Nuclei Acids Res. 34, 667-675.

Junjie Li, Zhiyong Yang, Bin Yu, Jun Liu, and Xuemei Chen*. (2005). Methylation protects miRNAs and siRNAs from a 3’ end uridylation activity in Arabidopsis. Current Biology 15, 1501-1507.
Featured in “Editors' Choice: Highlights of the recent literature”. Science 309, 1651.

Bin Yu, Zhiyong Yang, Junjie Li, Svetlana Minakhina, Maocheng Yang, Richard W. Padgett, Ruth Steward, and Xuemei Chen*. (2005). Methylation as a crucial step in plant microRNA biogenesis. Science 307, 932-935.

Jun Liu, Yuehui He, Rick Amasino, and Xuemei Chen*. (2004). SiRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis. Genes Dev., 18, 2873-2878.

Xuemei Chen*. (2004). A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303, 2022-2025.

Yulan Cheng, Naohiro Kato, Wenming Wang, Junjie Li, and Xuemei Chen*. (2003). Two RNA-binding proteins, HEN4 and HUA1, act in the processing of AGAMOUS pre-mRNA in Arabidopsis thaliana. Developmental Cell 4, 53-66.

Wonkeun Park, Junjie Li, Rentao Song, Joachim Messing, and Xuemei Chen*. (2002). CARPEL FACTORY, the Dicer homologue, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Current Biology 12, 1484-1495.

Tamara Western, Yulan Cheng, Jun Liu, and Xuemei Chen*. (2002). HUA ENANCER2, a putative DExH-box RNA helicase, maintains homeotic B and C gene expression in Arabidopsis. Development 129, 1569-1581.

Xuemei Chen*, Jun Liu, Yulan Cheng, and Dongxuan Jia. (2002). HEN1 functions pleiotropically in Arabidopsis development and acts in C function in the flower. Development 129, 1085-1094.

Junjie Li, and Dongxuan Jia, and Xuemei Chen*. (2001). HUA1, a regulator of stamen and carpel identities in Arabidopsis, codes for a nuclear zinc finger protein. Plant Cell 13, 2269-2281.

Xuemei Chen, and Elliot M. Meyerowitz. (1999). HUA1 and HUA2 are two members of the floral homeotic AGAMOUS pathway. Molecular Cell 3, 349-360.

Lab Personnel: 

Gao, Lei

Postdoctoral Researcher —

Li, Shengben

Postdoctoral Researcher —

Liu, Xigang

Postdoctoral Researcher —

Kim, YunKu

Postdoctoral Researcher —

Rogers, Kestrel

Postdoctoral Researcher —

Dinh, Theresa

Graduate Student Researcher — Flower development and small RNA metabolism

Ji, Lijuan

Graduate Student Researcher — Flower development and small RNA metabolism

Li, Shaofang

Graduate Student Researcher —

Yumul, Rae Eden

Graduate Student Researcher —  Plant Development

Won, So Youn

Graduate Student Researcher —  RNA Silencing, Epigenetics

Zhao, YuanYuan

Graduate Student Researcher —  RNA Silencing, Epigenetics

Chow, Matthew; Khoobyuri, Parnian; Orozco, Nikolas; Reimer, Mundy; Luu, Tammy

Undergraduate Student Researchers —