Zhixin Xie

Research Interests

Research in my laboratory is directed to understand how multiple small RNA pathways operate in plants using genetic, genomic, and biochemical approaches. 
Most eukaryotic organisms possess highly conserved RNA silencing machinery that generates 21- ~ 24-nucleotide small RNAs from double stranded RNA precursors.  These small RNAs, which include microRNA (miRNA) and several classes of small interfering RNAs (siRNA), play important roles in regulating gene expression, heterochromatin formation, and defense against invading viruses.  The core components of RNA silencing machinery involve several evolutionarily conserved protein families, including DICER (DCR) or DICER-LIKE (DCL), ARGONAUTE (AGO), and, in some cases, RNA-DEPENDENT RNA POLYMERASE (RDR).  Interestingly, unlike many animals, plants encode multiple DCL and RDR proteins.  Recent genetic studies have revealed multiple small RNA pathways in plants; each requires a distinct set of DCL and RDR factors.  Plants, therefore, provide a unique system to study the genetic diversification and functional adaptation of small RNA pathways.

Selected Publications

• Attri K., Zhang Z., Singh A., Sharrock R. A.,Xie Z. (2022) Rapid sequence and functional diversification of a miRNA superfamily targeting calcium signaling components in seed plants. New Phytol 235, 1082-1095 [PDF] https://doi.org/10.1111/nph.18185
  
• Xie Z., Cheng H. (2017) Interplay and transition between small RNA-directed posttranscriptional and transcriptional gene silencing in plants. Indian J Plant Physiol 22, 371-381 [PDF]
• Xie Z ., Jia G., Ghosh, A. (2012) Small RNAs in Plants. In: Sunkar (ed.) MicroRNAs in Plant Development and Stress Responses. Signaling and Communication in Plants  15 , 1-28 [ MORE ]
• Xie Z . (2011) Biogenesis and function of virus-derived small interfering RNAs in plants. In: Erdmann VA and Barciszewski J (eds.) Non-coding RNAs in plants. RNA Technologies 485-498 [ MORE ]
• Xie Z , Khanna K, Ruan S. (2010) Expression of MicroRNAs and Its Regulation in Plants. Semin Cell Dev Biol 21, 790-797 [ PDF ]
• Liu X, Huang J, Wang Y, Khanna K, Xie Z , Owen HA, Zhao D. (2010) The role of floral organs in carpels , an Arabidopsis loss-of-function mutation in MicroRNA160a , in organogenesis and the mechanism regulating its expression. Plant J 62 , 416-28 [ PDF ]
• Xie Z . (2010) Piecing the Puzzle Together: Genetic Requirements for miRNA Biogenesis in Arabidopsis thaliana . In: Meyers BC and Green, PJ (eds.) Plant microRNAs: Methods and Protocols.  Methods Mol Biol 592 ,1-17 [ MORE ]
• Qi X, Bao FS, and Xie Z. (2009) Small RNA Deep Sequencing Reveals Role for Arabidopsis thaliana RNA-Dependent RNA Polymerases in Viral siRNA Biogenesis. PLoS ONE 4 , e4971 [ PDF ]
• Xie Z , and Qi X. (2008) Diverse small RNA-directed silencing pathways in plants. Biochim Biophys Acta 1779 , 720–724 [ PDF ]
• Xie Z , Allen E, Wilken A, Carrington JC. (2005) DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in  Arabidopsis thaliana . Proc Natl Acad Sci U S A  102 , 12984-9 [ PDF ]
• Xie Z , Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC. (2005) Expression of Arabidopsis MIRNA Genes. Plant Physiol 138 , 2145-54 [ PDF ] This article featured High Impact Paper in PLANT PHYSIOLOGY ; see Plant Physiol 146:3-4(2008) 
• Allen E, Xie Z , Gustafson AM, Carrington JC. (2005) microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121 , 207-21 [ PDF ]
• Zilberman D, Cao X, Johansen LK,  Xie Z  , Carrington JC, Jacobsen SE. (2004) Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats.  Curr Biol  14 , 1214-20 [  PDF  ]
• Xie Z  , Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC. (2004) Genetic and functional diversification of small RNA pathways in plants.  PLoS Biol  2 , E104 [  PDF  ] This article featured THOMSON-ISI Fast Breaking Paper in Biology & Biochemistry
• Allen E,  Xie Z  , Gustafson AM, Sung GH, Spatafora JW, Carrington JC. (2004) Evolution of microRNA genes by inverted duplication of target gene sequences in  Arabidopsis thaliana .  Nat Genet  36 , 1282-90 [ PDF  ]
• Chan SW, Zilberman D, Xie Z , Johansen LK, Carrington JC, Jacobsen SE. (2004) RNA silencing genes control de novo DNA methylation. Science 303 , 1336 [ PDF ]
• Xie Z , Kasschau KD, Carrington JC. (2003) Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation. Curr Biol  13 , 784-9[ PDF ]
• Kasschau KD, Xie Z , Allen E, Llave C, Chapman EJ, Krizan KA, Carrington JC. (2003) P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA function. Dev Cell 4 , 205-17 [ PDF ]
• Llave C, Xie Z , Kasschau KD, Carrington JC. (2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297 , 2053-6 [ PDF ]
• Xie Z , Fan, B, Chen, C, and Chen, Z. (2001) An important role of an inducible RNA-dependent RNA polymerase in plant antiviral defense. Proc Natl Acad Sci U S A  98 , 6516-6521 [ PDF ]