Lei Li, Ph.D.
Functional study of plant microRNA genes
Assistant Professor, School of Advanced Agricultural Sciences, Peking University
tel：
Postcode：010-62754427
E-mail：lei.li@pku.edu.cn
1.Structure and function of microRNA networks in model plants
2.Comparative and evolutionary analysis of the microRNA networks
3.Application of the microRNA networks in biotechnology
MicroRNAs (miRNAs) are a class of sequence-specific, trans-acting small RNAs that post-transcriptionally modulate gene expression. Despite a recent surge of interest in miRNA biology, our knowledge on transcriptional control of miRNA expression, full miRNA target spectrum, and their general and specific function in shaping the transcriptome and hence the phenome is still sparse. Our group is using high throughput approaches to map the structure, molecular genetics to sort out the function, and comparative genomics to trace the evolutionary changes of the miRNA networks in perse plants. An intriguing discovery from our reconstructed transcription factor-miRNA-target network is that co－regulated miRNAs are able to independently excite large overlapping portions of the transcriptome. This finding leads us to propose that in addition to target cleavage and translation inhibition, a cohort of miRNAs may act through intermediate trans-acting small interfering RNAs to exert sophisticated control over a biological process.
Further, by developing a novel computational tool and extensive deep sequencing data mining, we cataloged more than 6000 miRNA genes including the cis-regulatory elements, precursor sequences and mature miRNAs. We found that each of the more than 20 examined plant species has a repertoire of unique miRNAs. We showed that incorporating miRNAs into the regulatory network constitutes a yet fully elucidated mechanisms for generating phenotypic persity during plant evolution. Together our results indicate that miRNAs are powerful and versatile regulators of plant metabolism and development. Tapping into miRNAs mediated gene circuits and regulatory routes will provide not only important insights into the molecular basis for adaptation and phenotypic persity in plants, but also excellent opportunities for genetically engineering traits of agricultural importance.
Hao YZ, Yang YH, Tu H, Guo ZL, Chen PC, Chao XT, Yuan Y, Wang ZM, Miao XL, Zou SL, Li D, Yang YZ, Wu CY, Li B, Li L, Cai HQ. (2024) A transcription factor complex in Dictyostelium enables adaptive changes in macropinocytosis during the growth-to-development transition. Dev. Cell, 59: 645-660.
Yang YZ, Xu L, Hao C, Wan MM, Tao YH, Zhuang Y, Su YN, Li L. (2024) The microRNA408-plantacyanin module balances plant growth and drought resistance by regulating reactive oxygen species homeostasis in guard cells. Plant Cell, 36: 4338-4355.
Xu DB, Tang WS, Ma YA, Wang X, Yang YZ, Wang XT, Xie LA, Huang S, Qin TF, Tang WL, Xu ZS, Li L, Tang YM, Chen M, Ma YZ. (2024) Arabidopsis G-protein β subunit AGB1 represses abscisic acid signaling via attenuation of the MPK3-VIP1 phosphorylation cascade. J. Exp. Bot., 75: 1615-1632.
Guo ZL, Xu ZX, Li L, Xu KW. (2024) Species-Specific miRNAs contribute to the pergence between deciduous and evergreen species in ilex. Plants, 13: 1429.
Xu ZX, Wei HK, Li MY, Qiu YJ, Li L, Xu KW, Guo ZL. (2024) Impact of chromosomal fusion and transposable elements on the genomic evolution and genetic persity of Ilex species. Plants, 13: 2649.
Shen F, Qin YJ, Wang R, Huang X, Wang Y, Gao TG, He JN, Zhou Y, Jiao YN, Wei JH, Li L, Yang XZ. (2023) Comparative genomics reveals a unique nitrogen-carbon balance system in Asteraceae. Nat. Commun., 14: 4334.
Xu L,Tang YM,Yang YZ,Wang DZ,Wang HJ,Du JM,Bai YJ,Su SC,Zhao CP,Li L. (2023)Microspore expressed SCULP1 is required for p-coumaroylation of sporopollenin, exine integrity, and pollen development in wheat.New Phytol.,239: 102-115.
Guo YY, Wang SF, Yu KJ, Wang HL, Xu HM, Song CW, Zhao YY, Wen JL, Fu CX, Li Y, Wang SZ, Zhang X, Zhang Y, Cao Y, Shao FJ, Wang XH, Deng X, Chen T, Zhao Q, Li L, Wang GD, Grünhofer P, Schreiber L, Li Y, Song GY, Dixon RA, Lin JX. (2023) Manipulating microRNA miR408 enhances both biomass yield and saccharification efficiency in poplar. Nat. Commun., 14: 4285.
Guo ZL, Li B, Du JJ, Shen F, Zhao YX, Deng Y, Kuang Z, Tao YJ, Wan MM, Lu XJ, Wang D, Wang Y, Han YY, Wei JH, Li L, Guo XY, Zhao CJ, Yang XZ. (2023) LettuceGDB: the community database for lettuce genetics and omics. Plant Commun., 4: 100425.
Guo ZZ, Kuang Z, Tao YH, Wang HT, Wan MM, Hao C, Shen F, Yang XZ, Li L (2022) Miniature inverted-repeat transposable elements drive rapid microRNA persification in angiosperms. Mol. Biol. Evol., 39: msac224.
Guo ZL, Kuang Z, Zhao YX, Deng Y, He H, Wan MM, Tao YH, Wang D, Wei JH, Li L, Yang XZ. (2022) PmiREN2.0: from data annotation to functional exploration of plant microRNAs. Nucl. Acids Res., 50: D1475-D1482.
Hao C, Yang YZ, Du JM, Deng XW, Li L. (2022) The PCY-SAG14 phytocyanin module regulated by PIFs and miR408 promotes dark-induced leaf senescence in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A., 119: e2116623119.
Yang YZ, Hao C, Du JM, Xu L, Guo ZL, Li D, Cai HQ, Guo HW, Li L. (2022) The carboxy terminal transmembrane domain of SPL7 mediates interaction with RAN1 at the endoplasmic reticulum to regulate ethylene signalling in Arabidopsis. New Phytol., 236: 878-892.
Guo ZL, Kuang Z, Deng Y, Li L, Yang XZ. (2022) Identification of species-specific microRNAs provides insights into dynamic evolution of microRNAs in plants. Int. J Mol. Sci., 23: 14273.
Yang XZ, Unver T, Zhang XR, Li L. (2022) Editorial: Roles and regulatory mechanisms of microRNA in plant development, evolution, and adaptation. Front. Plant Sci., 13: 995517.
Zhang YW, Tu H, Hao YZ, Li D, Yang YH, Yuan Y, Guo ZL, Li L, Wang HB, Cai HQ. (2022) Oligopeptide transporter Slc15A modulates macropinocytosis in Dictyostelium by maintaining intracellular nutrient status. J. Cell. Sci., 135: jcs259450.
Zhang H, Guo ZL, Zhuang Y, Suo YZ, Du JM, Gao ZX, Pan JW, Li L, Wang TX, Xiao L, Qin GJ, Jiao YL, Cai HQ, Li L. (2021) MicroRNA775 regulates intrinsic leaf size and reduces cell wall pectin levels by targeting a plactosyltransferase gene in Arabidopsis. Plant Cell, 33: 581-602.
Jiang AL, Guo ZL, Pan JW, Yang YZ, Zhuang Y, Zuo DQ, Hao C, Gao ZX, Xin PY, Chu JF, Zhong SW, Li L. (2021) The PIF1-miR408-PLANTACYANIN repression cascade regulates light-dependent seed germination. Plant Cell, 33: 1506-1529.
Zhao YX, Kuang Z, Wang Y, Li L, Yang XZ. (2021) MicroRNA annotation in plants: current status and challenges. Brief. Bioinform., 22: bbab075.
Yang YH, Li D, Chao XY, Singh SP, Thomason P, Yan YH, Dong MQ, Li L, Insall RH, Cai HQ. (2021) Leep1 interacts with PIP3 and the Scar/WAVE complex to regulate cell migration and macropinocytosis. J Cell Biol., 220: e202010096.
Guo Z, Kuang Z, Wang Y, Zhao Y, Tao Y, Cheng C, Yang J, Lu X, Hao C, Wang T, Cao X, Wei J, Li L, Yang XZ. (2020) PmiREN: a comprehensive encyclopedia of plant miRNAs. Nucleic Acids Res., 48: D1114-D1121.
Zhuang Y, Zuo DQ, Tao YH, Cai HQ, Li L. (2020) Laccase3-based extracellular domain provides possible positional information for directing Casparian strip formation in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A., 117: 15400-15402.
Zhuang Y, Li L. (2020) Are cuproproteins part of the multi-protein framework for making the Casparian strip? Plant Signal. Behav., 15: 1798605.
Wang Y, Kuang Z, Li L, Yang XZ. (2020) A bioinformatics pipeline to accurately and efficiently analyze the microRNA transcriptomes in plants. J. Vis. Exp., 21: 10.3791/59864.
Yangzhi Yang, He Zhang, Chen Hao, Yan Zhuang, Miaomiao Wan, Yajun Bai, Daqing Zuo, Yihan Tao, Zhan Li, Jiahe Zhao, Liang Xiao
