Institute for Integrative Genome Biology


Xuemei ChenXuemei Chen


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)


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 the 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 Arabidopsisto 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

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

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:

Selected Publications:

Selected List of publications from PubMed

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 —

More Information

General Campus Information

University of California, Riverside
900 University Ave.
Riverside, CA 92521
Tel: (951) 827-1012

Career OpportunitiesUCR Libraries
Campus StatusDirections to UCR

Genomics Information

Institute of Integrative Genome Biology
2150 Batchelor Hall

Tel: (951) 827-7177
E-mail: Aurelia Espinoza, Managing Director