李磊 研究员
植物microRNA网络与功能研究组
北京大学 生命科学学院 研究员，博士生导师
电话：
E-mail：lei.li@pku.edu.cn
1、模式植物中microRNA网络的构建与功能研究
2、植物演化中microRNA网络的变化
3、microRNA网络在生物技术中的应用
本研究组主要致力于阐明植物如何通过遗传网络对内源信号和外源刺激协同应答以实现最优化生长，并希望通过对基因网络的解析与功能研究来改良作物性状。近五年来，围绕microRNA这一类小的非编码调控因子，通过microRNA相关基因网络的构建和分析，开展了两个方向的研究。一是在模式植物拟南芥中整合转录因子染色质免疫沉淀测序数据、microRNA基因启动子分析、microRNA靶基因谱，构建转录因子-microRNA-靶基因网络。针对不同的microRNA模块（例如HY5介导的光响应模块与SPL7调控的铜稳态模块），结合分子遗传学、细胞生物学、基因组学、数学建模等研究手段，解析以microRNA为中心的调控网络，加深和拓展对植物microRNA调控范畴的认知，通过诠释转录、转录后水平基因调控的有机耦合，旨在深入阐明microRNA在植物生长发育与环境适应中广泛而重要的作用。
另一个研究方向是通过比较基因组学阐明microRNA在遗传多样性中的作用。运用一个基于生物信息学与高通量测序的方法，系统鉴定了包括苔藓、蕨类、双子叶和单子叶在内20余种陆生植物中的6000多个microRNA基因的调控元件、前体结构与成熟microRNA序列。揭示了植物基因组中microRNA密度与蛋白基因密度的正相关性，表明microRNA基因相比目前普遍认可的观点具有更强的进化流动性。通过比较基因组学筛选出大量禾本科特异的microRNA，在水稻、小麦中开展了分子遗传实验，旨在证明将这些microRNA基因以世系特异的方式整合到基因调控网络之中，是禾本科特异植物形态和生命周期的重要遗传基础，为生物多样性资源、生物技术在农业上的应用提供新的材料与思路。
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 divergence 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 diversity 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 diversification 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.
杨彦芝、张禾、郝宸、庄严、万苗苗、柏亚君、左大庆、陶奕含、李展、赵佳禾、肖亮
