Faculty
Renyi Liu
Assistant Professor and Evolutionary Genomicist (Ph.D., 2005, University of Georgia)
Office: 3109 Batchelor Hall
Phone: (951) 827-3987
Fax: (951) 827-4437
Email: renyi.liu@ucr.edu
Research Interests
- Computational analysis of high-throughput biological data
- Genome-wide analysis of small RNAs in plant genomes
- DNA methylation and demethylation in plant genomes
- Mechanisms of mRNA decay in plants
- Comparative analysis of plant genomes
Recent Publications
Zhang H, Ma ZY, Zeng L, Tanaka K, Zhang CJ, Ma J, Bai G, Wang P, Zhang SW, Liu ZW, Cai T, Tang K, Liu R, Shi X, He XJ, Zhu JK. 2013. DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV. Proc. Natl. Acad. Sci. USA. doi: 10.1073/pnas.1300585110.
Zhang CJ, Zhou JX, Liu J, Ma ZY, Zhang SW, Dou K, Huang HW, Cai T, Liu R, Zhu JK and He XJ. 2013. The splicing machinery promotes RNA-directed DNA methylation and transcriptional silencing in Arabidopsis. The EMBO Journal advance online publication 22 March 2013; doi:10.1038/emboj.2013.49.
Zhang X, Lii Y, Wu Z, Polishko A, Zhang H, Chinnusamy V, Lonardi S, Zhu JK*, Liu R*, Jin H*. 2013. Mechanisms of small RNA generation from cis-NATs in response to environmental and developmental cues. Molecular Plant. first published online March 15, 2013. doi:10.1093/mp/sst051. *co-corresponding authors.
Guan Q, Wu J, Zhang Y, Jiang C, Liu R, Chai C, Zhu J. 2013. A DEAD box RNA helicase is critical for pre-mRNA splicing, cold-responsive gene regulation, and cold tolerance in Arabidopsis. Plant Cell. originally published online January 31, 2013; DOI 10.1105/tpc.112.108340.
Zhang X, Zhou Y, Ding L, Wu Z, Liu R, Meyerowitz EM. 2013. Transcription Repressor HANABA TARANU Controls Flower Development by Integrating the Actions of Multiple Hormones, Floral Organ Specification Genes, and GATA3 Family Genes in Arabidopsis. Plant Cell. 2013 Jan 18. [Epub ahead of print].
Samir Ben Chaabane*, Renyi Liu*, Viswanathan Chinnusamy, Yerim Kwon, Joo-hyuk Park, Seo Yeon Kim, Jian-Kang Zhu,Seong Wook Yang, Byeong-ha Lee. 2012. STA1, an Arabidopsis pre-mRNA processing factor 6 homolog, is a new player involved in miRNA biogenesis. Nucleic Acids Research. doi: 10.1093/nar/gks1309. * co-first author.
Zhan X, Wang B, Li H, Liu R, Kalia RK, Zhu J-K, and Chinnusamy V. 2012. Arabidopsis proline-rich protein important for development and abiotic stress tolerance is involved in microRNA biogenesis. Proc. Natl. Acad. Sci. U S A; published ahead of print October 15, 2012, doi:10.1073/pnas.1216199109
Liao C, Peng Y, Ma W, Liu R, Li C, Li X. 2012. Proteomic analysis revealed nitrogen-mediated metabolic, developmental, and hormonal regulation of maize (Zea mays L.) ear growth. Journal of Experimental Botany. 63: 5275-5288
Barrera-Figueroa BE, Gao L, Wu Z, Zhou X, Zhu J, Jin H, Liu R*, Zhu JK. 2012. High throughout sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice. BMC Plant Biology. 12:132. *corresponding author
Qian W, Miki D, Zhang H, Liu Y, Zhang X, Tang K, Kan Y, La H, Li X, Li S, Zhu X, Shi X, Zhang K, Pontes O, Chen X, Liu R, Gong Z, Zhu JK. 2012. A histone acetyltransferase regulates active DNA demethylation in Arabidopsis. Science. 336: 1445-1448.
Liao C, Liu R, Zhang F, Li C, Li X. 2012. Nitrogen under- and over-supply induces distinct protein responses in maize (Zea mays L.) xylem sap. Journal of Integrative Plant Biology. 54:374-387.
Zhang X, Xia J, Lii Y, Barrera-Figueroa B, Zhou X, Gao S, Lu L, Niu D, Liang W, Chen Z, Leung C, Wong T, Zhang H, Guo J, Li Y, Liu R, Zhu JK, Zhang W, Jin H. 2012. Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function. Genome Biology. 13:R20.
Barrera-Figueroa BE, Wu Z, Liu R. Abiotic stress-associated microRNAs in plants: discovery, expression analysis, and evolution. 2012. Frontiers in Biology. 2012 Apr 5. [Epub ahead of print].
Lertpanyasampatha M, Gao L, Kongsawadworakul P, Viboonjun U, Chrestin H, Liu R, Chen X, Narangajavana J. 2012. Genome-wide analysis of microRNAs in rubber tree (Hevea brasiliensis L.) using high throughput sequencing. Planta. 2012 Mar 10. [Epub ahead of print]
Martínez-Macías MI, Qian W, Miki D, Pontes O, Liu Y, Tang K, Liu R, Morales-Ruiz T, Ariza RR, Roldán-Arjona T, Zhu JK. 2012. A DNA 3' phosphatase functions in active DNA demethylation in Arabidopsis. Molecular Cell. 45:357-370.
Chaston JM et al. 2011. The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes. Plos ONE. 6: e27909.
Barrera-Figueroa BE, Gao L, Diop NN, Wu Z, Ehlers JD, Roberts PA, Close TJ, Zhu J-K, Liu R. 2011. Identification and comparative analysis of drought-associated microRNAs in two cowpea genotypes. BMC Plant Biology 11:127.
Liu R. 2009. Origin and evolution of the bacterial flagellar system. In: Ken F. Jarrell (Ed.). Pili and Flagella: Current research and future trends. Caister Academic Press, Norfolk, UK. pp.207-214.
DeBarry J, Liu R, Bennetzen JL. 2008. Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm. BMC Bioinformatics. 9:235.
Liu, R. and Ochman, H. 2007. The origins of flagellar gene operons and secondary flagellar systems. J. Bacteriol. doi:10.1128/JB.00643-07.
Liu, R., Vitte, C., Ma, J., Mahama, A.A., Dhliwayo, T., Lee, M. and Bennetzen, J.L. 2007. A GeneTrek analysis of the maize genome. Proc. Natl. Acad. Sci. U S A 104:11844-49.
Liu, R. and Asmussen, M.A. 2007. Cytonuclear dynamics of selfing populations under selection. Theor. Popul. Biol. 71:445-53.
Liu R. and Ochman, H. 2007. Stepwise formation of the bacterial flagellar system. Proc. Natl. Acad. Sci. U S A 104:7116-21.
Ochman, H., Liu, R. and Rocha, E.P.C. 2007. Erosion of interaction networks in reduced and degraded genomes. J. Exp. Zool. (Mol. Dev. Evol.) 308B:97-103.