Zhixin Xie, Ph.D.

Research Interests

Research in my laboratory focuses on the biology of regulatory small RNAs (sRNAs) in plants.

Eukaryotic organisms possess highly conserved RNA silencing machinery that generates 21- to 24-nucleotide sRNAs from double-stranded RNA precursors. These sRNAs, which include microRNAs (miRNAs) and several classes of small interfering RNAs (siRNAs), play important roles in post-transcriptional regulation of gene expression, heterochromatin formation, and defense against invading viruses. The core RNA-silencing machinery includes 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. Genetic studies have revealed multiple sRNA pathways in plants, each requiring a distinct set of core components. Plants therefore provide unique systems for studying the genetic diversification and functional adaptation of sRNA pathways.

We are particularly interested in how sRNA pathways and sRNA-mediated regulatory networks operate and functionally evolve in plants. Using a combination of genetic, molecular, genomic, biochemical, and computational approaches, we aim to advance our understanding on how sRNA-mediated regulation contributes to plant development, immunity, and environmental adaptation. Specifically, our projects address: (1) how miRNA-mediated regulatory modules evolve through sequence diversification and functional innovation; (2) how sRNA regulatory networks change during major evolutionary transitions such as polyploid formation; and (3) the roles of sRNA-mediated regulation in maintaining genome integrity and chromosome dynamics, among other areas.

Graduate Research Opportunities

Pursuing a graduate degree, especially a doctoral degree, is a substantial commitment, and choosing a laboratory that provides a strong match of research interests and expectations is an important part of this process. Because the graduate program in Biology at Texas Tech University (TTU) does not currently use a laboratory rotation system, prospective students are encouraged to communicate with potential faculty mentors before submitting a formal application.

Prospective students with a strong interest in plant molecular biology, genetics, genomics, and sRNA biology are encouraged to inquire about opportunities in the lab. Particularly important qualities include:

(1) Attention to detail in experimental observations, record keeping, data analysis, and data management. (2) Strong written and verbal communication skills. (3) A solid foundation in cell and molecular biology and genetics. (4) Curiosity, initiative, and a willingness to learn both experimental and computational approaches.

Prior experience in programming, bioinformatics, or computational biology (e.g., Python) is an advantage but is not required.

Prospective graduate students are strongly encouraged to contact me by email before submitting a formal application to the TTU Graduate School. An initial inquiry should include:

(1) A current résumé or CV, including English-proficiency test scores, if applicable. (2) A brief description of your research background and interests.

(3) A brief explanation of why you are interested in sRNA biology and in pursuing graduate research in our laboratory. Rather than relying on general statements that your interests "align" with those of the laboratory, explain what aspects of sRNA biology interest you, what scientific questions you would like to explore, and how graduate training in our laboratory could contribute to your longer-term research and career goals.

Applicants whose backgrounds and research interests appear to be a strong match will usually be invited to a virtual meeting to discuss potential research directions, expectations, and graduate training.

Selected Publications (Available upon request)

• Ibrahim BM, Ali R., Xie Z. (2026) Keeping UTRs in their place: clarifying transcript-genomic boundaries. Physiol Plant 178, e70899
• Xie Z. and Attri K. (2025) Plant microRNAs enter the scene of calcium signaling. Trends Plant Sci 30, 1119-1129  
• 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  
  
• 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 
• 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 
• 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
• Xie Z, Khanna K, Ruan S. (2010) Expression of MicroRNAs and Its Regulation in Plants. Semin Cell Dev Biol 21, 790-797 
• 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 
• 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 
• 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 
• Xie Z, and Qi X. (2008) Diverse small RNA-directed silencing pathways in plants. Biochim Biophys Acta 1779, 720–724 
• 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 USA  102, 12984-9 
• Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC. (2005) Expression of Arabidopsis MIRNA Genes. Plant Physiol 138, 2145-54 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 
• 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.
• 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  
• 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 
• Chan SW, Zilberman D, Xie Z, Johansen LK, Carrington JC, Jacobsen SE. (2004) RNA silencing genes control de novo DNA methylation. Science 303, 1336 
• 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.
• 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.
• 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.
• 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 USA  98, 6516-6521.