The long-term research interest of my laboratory is to understand the molecular mechanisms underlying small RNA metabolism and function. Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are 20 to 24 nucleotide (nt) RNAs that function as sequence-specific regulators of gene expression at both transcriptional and post-transcriptional levels in eukaryotes. These small RNAs are involved in numerous cellular processes including development, differentiation, proliferation, apoptosis, and stress responses. We currently employ a combination of genetic, biochemical, cell biological, and genomic approaches to identify and characterize components involved in small RNA metabolism in Arabidopsis thaliana.
- Xie M, Zhang S and Yu B (2014) microRNA biogenesis, degradation and activity in plants. Cel. Mol. Life Sci. Doi/10.1007/s00018-014-1728-7
- Ren G, Chen X and Yu B (2014) Small RNAs meet their targets: when methylation defends miRNAs from uridylation. RNA Biology. Doi/10.4161/rna.36243
- Zhang S, Liu Y and Yu B (2014) PRL1, an RNA-Binding Protein, Positively Regulates theAccumulation of miRNAs and siRNAs in Arabidopsis. Plos Genetics 10: e1004841
- Ren G, Xie M, Zhang X, Vinovskis C, Chen X and Yu B (2014) Methylation protects microRNAs from an AGO1-associated activity that uridylates 5′ RNA fragments generated by AGO1 cleavage. PNAS 111:6365-6370
- Narayanan LA, Mukherjee D, Zhang S, Yu B, Chevalier D (2013) Mutational analyses of a ForkHead Associated domain protein, DAWDLE, in Arabidopsis thaliana. American Journal of Plant Sciences 5:2811-2822
- Liu X, Lu T, Yu B, Zhang C (2013) Identification of RNA silencing components in Soybean and Sorghum. BMC bioinformatics (In press)
- Zhang S, Xie M, Ren G and Yu B (2013) CDC5, a MYB-related protein, positively regulates posttranscriptional processing and/or transcription of pri-miRNAs. PNAS
- Zhai J, Zhao Y, Simon SA, Huang S, Petsch K, Arikit S, Pillay M, Ji L, Xie M, Cao X, Yu B, Timmermans M, Yang B, Chen X and Meyers B (2013) Plant MicroRNAs Display Differential 3’-Truncation and Tailing, Modifications Which Are ARGONAUTE1-Dependent and Conserved ‘Across Species. Plant Cell. Doi/10.1105/tpc.113.114603.
- Ren G and Yu B (2012) Critical roles of RNA-binding proteins in miRNA biogenesis in Arabidopsis. RNA Biology 9:1424-28
- Ren G and Yu B (2012) Post-transcriptional control of miRNA abundance in Arabidopsis. Plant Signal Behav 11:1443-1446
- Ren G, Xie M, Dou Y, Zhang C and Yu B (2012) Regulation of miRNA abundance by RNA binding protein TOUGH in Arabidopsis. PNAS. 109:12817-12821
- Xie M, Ren G, Pedro C, Pontes O, Yu B (2012) A subgroup of SGS3-LIKE proteins act redundantly in RNA-directed DNA methylation. Nucleic Acid Research. 40:4422-31
- Xie M. Ren G, Zhang C, and Yu B (2012) The DNA- and RNA-binding protein FACTOR of DNA METHYLATION 1 requires XH domain-mediated complex formation for its function in RNA-directed DNA methylation. The Plant Journal. 72:491–500
- Ren G, Chen X, Yu B (2012) Uridylation of miRNAs by HEN1 SUPPRESSOR 1 in Arabidopsis. Current Biology 22:695-70
- Xu Y, Santamaria RR, Virdi KS, Arrieta-Montiel MP, Razvi F, Li S, Ren G, Yu B, Guo L, Feng X, Dweikat I and Mackenzie S (2012) The chloroplast triggers developmental reprogramming when MUTS HOMOLOG1 is suppressed in plants. Plant Physiology 159:710-720
- Yu B, Liu B, Zhai J, Agarwal M, Li S, Wu Q, Ding S, Meyers B, Vaucheret H, Chen X (2010) siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis. Nucleic Acid Research. 38:5844-50
- Yu B and Chen X. (2010) Analysis of miRNA modification. Methods in Molecular Biology.592:137-48.
- Yu B and Wang H. (2010) Translational inhibition by miRNAs in Plants. Prog Mol Subcell Biol. 50:41-57.
- Zheng B, Wang Z, Li S, Yu B, Liu J, Chen X (2009) Intergenic transcription by RNA Polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis. Genes & Development. 23: 2850-2860.
- Song D, Yang Y, Yu B, Zheng B, Deng Z, Lu B, Chen X, Jiang T (2009) Computational prediction of novel non-coding RNAs in Arabidopsis thaliana. BMC Bioinformatics, 10(Suppl 1):S36
- Yu B, Liu B, Zheng B, Ji Li, Agarwal M, Chevalie D, Lagrange T, Walker JC, Chen X (2008) The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis PNAS. 105:10073-10078
- Yang Z, Vilkaitis G, Yu B, Klimasauskas S, Chen X (2007) Approaches for Studying MicroRNA and Small Interfering RNA Methylation In Vitro and In Vivo. Methods Enzymol. 427:139-54
- Yu B, Chapman EG, Yang Z, Carrington JC, Chen X (2006) Transgenically expressed viral RNA silencing suppressors interfere with microRNA methylation in Arabidopsis. FEBS Lett 580:3117-20
- Yang Z, Ebright YW, Yu B, Chen X (2006) HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2' OH of the 3' terminal nucleotide. Nucleic Acids Res. 34:667-75.
- Xu C, Yu B CornishAJ, Froehlich JE, Benning C (2006) Phosphatidylglycerol biosynthesis in chloroplasts of Arabidopsis mutants deficient in acyl-ACP glycerol-3- phosphate acyltransferase. Plant J. 47:296-309
- Li J, Yang Z, Yu B, Liu J, and Chen X (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.
- Yu B, Yang ZY, Li JJ, Minakhina S, Yang MC, Padgett RW, Steward R, Chen X (2005) Methylation as a crucial step in plant microRNA biogenesis. Science. 307:932-5
- Weber A, Oesterhelt C, Gross W, Bräutigam A, Imboden L, Krassovskaya I, Linka N, Truchina J, Schneidereit J, Voll LM, Zimmermann M, Riekhof WR, Yu B, Garavito RM, Benning C. (2004) EST-analysis of the thermo-acidophilic red microalga Galdieria sulphuraria reveals potential for lipid A biosynthesis and unveils the pathway of carbon export from rhodoplasts. Plant Mol. Biol. 55:17-32.
- Yu B, Wakao S, Fan JL, Benning C. (2004) Loss of plastidic lysophosphatidate:acyl-ACP acyltransferase activity causes embryo lethality in Arabidopsis. Plant & Cell Physiology 45:503-10
- Yu B and Benning C. (2003) Anionic lipids are required for chloroplast structure and function in Arabidopsis. Plant J. 36:762-70.
- Xu C, Hartel H, Wada H, Hagio M, Yu B, Eakin C, Benning C. (2002) The pgp1 mutant locus of Arabidopsis encodes a phosphatidylglycerolphosphate synthase with impaired activity. Plant Physiol. 129:594-604.
- Yu B, Xu C, Benning C. (2002) Arabidopsis disrupted in SQD2 encoding sulfolipid synthase is impaired in phosphate-limited growth. PNAS. 99:5732-7.