RNA is a key molecule in gene expression and is the target of post-transcriptional regulation in gene expression. The Chen lab investigates mechanisms of post-transcriptional regulation in gene expression, with a focus on small RNAs and chemical modifications to mRNAs. We use Arabidopsis thaliana as the model to investigate how small RNA (microRNA and siRNA) metabolism intersects with RNA translation. We also study how microRNAs serve as signaling molecules in plant development, particularly in warm-temperature-induced growth. A second research direction is on noncanonical RNA caps, such as NAD, FAD, and dpCoA. These metabolites can be added to the 5’ end of RNA as a cap and can also be removed by specific enzymes. We have developed LC-MS or enzymatic methods to identify and quantify such RNA caps as well as methods to profile RNAs with the NAD cap. We are developing methods to profile RNAs with FAD and dpCoA caps. We also seek to understand the molecular and biological functions of these noncanonical RNA caps. A third research direction that is in the beginning stage is to understand gene expression in plastids and the signaling between the nucleus and the plastids.

 

(* corresponding authorship)

1.      Qing Sang, Lusheng Fan, Tianxiang Liu, YongjianQiu, Juan Du, Beixin Mo, Meng Chen*, and Xuemei Chen*. (2023). MicroRNA156 conditions auxin sensitivity to enable growth plasticity in response to environmental changes in Arabidopsis. Nature Comm., accepted.

2.     Yuan Wang, Brandon H. Le, Jianqiang Wang, Chenjiang You, Yonghui Zhao, Mary Galli, Ye Xu, Andrea Gallavotti, Thomas Eulgem, Beixin Mo*, and Xuemei Chen*. (2022). A novel factor that recruits and excludes Pol IV-mediated DNA methylation in a site-specific manner. Science Advances 8, DOI: 10.1126/sciadv.adc9454.

3.     Lusheng Fan, Cui Zhang, Yong Zhang, Ethan Stewart, Jakub Jez, Keiji Nakajima, and Xuemei Chen*. (2022). Microtubules promote the non-cell autonomous action of microRNAs by inhibiting their cytoplasmic loading onto ARGONAUTE1 in Arabidopsis. Dev. Cell. 57, 995-1008.

4.     Bailong Zhang, Chenjiang You, Yong Zhang, Liping Zeng, Jun Hu, Minglei Zhao and Xuemei Chen*. (2020). Linking key steps of microRNA biogenesis by TREX-2 and the nuclear pore complex in Arabidopsis. Nature Plants 6, 957–969.

5.     Jianbo Song, Xiaoyan Wang, Bo Song, Lei Gao, Xiaowei Mo, Luming Yue, Haiqi Yang, Jiayun Lu, Guodong Ren, Beixin Mo* and Xuemei Chen*. (2019). Prevalent cytidylation and uridylation of precursor miRNAs in Arabidopsis. Nature Plants 5, 1260-1272.

6.     Shengben Li, Brandon Le, Xuan Ma, Shaofang Li, Chenjiang You, Lin Liu, Lei Gao, Ting Shi, Yonghui Zhao, Beixin Mo, Xiaofeng Cao, and Xuemei Chen*. (2016). Biogenesis of phased siRNAs on membrane-bound polysomes in Arabidopsis. eLife 2016;5:e22750. 

7.     Yuanyuan Zhao, Yu Yu, Jixian Zhai, Vanitharani Ramachandran, Thanh Theresa Dinh, Blake C. Meyers, Beixin Mo*, and Xuemei Chen*. (2012). The Arabidopsis nucleotidyl transferase HESO1 uridylates unmethylated small RNAs to trigger their degradation. Current Biology 22, 689-694.

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

9.     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.

10.   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. 

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

12.   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. 

Selected papers on noncanonical RNA capping 

13.   Hao Hu, Nora Flynn, Hailei Zhang, Chenjiang You, Runlai Hang, Xufeng Wang, Huan Zhong, Zhulong Chan, Yiji Xia*, and Xuemei Chen*. (2021). SPAAC-NAD-seq, a sensitive and accurate method to profile NAD+-capped transcripts. PNAS 118 (13) e2025595118. 

14.   Hailei Zhang, Huan Zhong, Xufeng Wang, Shoudong Zhang, Xiaojian Shao, Hao Hu, Zhiling Yu, Zongwei Cai*, Xuemei Chen* and Yiji Xia*. (2021). Use of NAD tagSeq II to identify growth-phase dependent alterations in E. coli RNA NAD+-capping. PNAS 118 (14) e2026183118.

15.   Hailei Zhang, Huan Zhong, Shoudong Zhang, Xiaojian Shao, Min Ni, Zongwei Cai, Xuemei Chen*, and Yiji Xia*. (2019). NAD tagSeq revealed that NAD⁺-capped RNAs are produced from a large number of protein-coding genes in Arabidopsis. PNAS 116, 12072-12077. 

16.   Yuan Wang, Shaofang Li, Yonghui Zhao, Chenjiang You, Brandon Le, Zhizhong Gong, Beixin Mo, Yiji Xia and Xuemei Chen*. (2019). NAD⁺-capped RNAs are widespread in the Arabidopsis transcriptome and can probably be translated. PNAS 116, 12094-12102.