陆剑 教授
群体和进化基因组学研究组
北京大学 生命科学学院 教授，博士生导师
电话：
E-mail：luj@pku.edu.cn
1、非编码RNA的起源、进化、以及驱动新非编码RNA基因进化的机理。
2、利用RNA-Seq, ribosome profiling, 基因编辑和比较基因组学等方法研究非编码 RNA的功能。
3、转录水平调控相关的功能基因组学研究。
miRNA的功能和进化研究。miRNA是一类在动植物中广泛存在的非编码小RNA, miRNA参与调控许多重要生命过程。miRNA通过降解靶基因mRNA或抑制靶基因翻译等方式调控靶基因表达。我们以多种miRNA的突变体果蝇为研究对象, 利用RNA-seq、核糖体图谱分析 ，找出miRNA在转录水平和翻译水平调控的靶基因，同时研究miRNA和靶位点上突变对miRNA:mRNA互补匹配模式的改变和影响，找出miRNA 调节基因表达的一般规律。通过不同发育阶段以及在逆境胁迫中miRNA的表达差异，研究miRNA调控对果蝇转录组和翻译组稳定性的缓冲作用，以及在逆境胁迫的应答。
转座元件和piRNA的共进化。在黑腹果蝇中，转座元件的随机跳跃对寄主有害，而基因组也发展出了非编码RNA （主要是piRNA和siRNA）来抑制转座元件的活性，其中在生殖腺中piRNA的抑制作用尤其重要。我们的研究假设是：一个转座元件侵入群体后，将很快产生抑制这个转座元件家族的piRNA，转座元件和piRNA存在一个共进化过程。利用实验室已有的基因组已经测序的源于世界5大洲的92个黑腹果蝇品系，我们对其基因组中转座元件的组成、插入位点和频率分布进行了探索，找到了每个果蝇品系的新的插入与缺失位点。结果显示不同的种群的转座元件的组成和插入是种群特异性的。同时我们将其piRNA进行了测序，分析结果表明绝大多数由活性的转座元件都有相对应的piRNA。piRNA的产生与转座元件的插入呈正相关的关系，同时也与性别，重组率，染色质的修饰等因素有关。
Wu XK, Xu MZ, Yang JR, Lu J. (2024) Genome-wide impact of codon usage bias on translation optimization in Drosophila melanogaster. Nat. Commun., 15: 8329.
Chen JH, Liu CL, Li WX, Zhang WX, Wang YR, Clark AG, Lu J. (2024) From sub-saharan africa to China: evolutionary history and adaptation of Drosophila melanogaster revealed by population genomics.Sci. Adv., 10: eadh3425.
Yao ZC, Zhang L, Duan YE, Tang XL, Lu J. (2024) Molecular insights into the adaptive evolution of SARS-CoV-2 spike protein. J. Infect., 88: 106121.
Wu CC, Ruhan A, Ye S, Ye F, Huo WB, Lu RJ, Tang Y, Yang JW, Meng XH, Tang Y, Chen S, Zhao L, Huang BY, Zhang ZX, Chen YD, Li DF, Wang WL, Shan KJ, Lu J, Tan WJ. (2024) Rapid identification of full-length genome and tracing variations of monkeypox virus in clinical specimens based on mNGS and amplicon sequencing. Virol. Sin., 39: 134-143.
Wang YR, Tang XL, Lu J.(2024) Convergent and divergent evolution of microRNA-mediated regulation in metazoans. Biol. Rev., 99: 525-545.
Shan KJ, Wu CC, Tang XL, Lu RJ, Hu YL, Tan WJ, Lu J. (2024) Molecular evolution of protein sequences and codon usage in monkeypox viruses. Genom. Proteom. Bioinform., 22: qzad003.
Jin KC, Tang XL, Qian ZH, Wu ZQ, Yang ZF, Qian T, Hon C, Lu J. (2024) Modeling viral evolution: A novel SIRSVIDE framework with application to SARS-CoV-2 dynamics. hLife, 2: 227-245.
Wu XK, Shan KJ, Zan FW, Tang XL, Qian ZH, Lu J. (2023) Optimization and deoptimization of codons in SARS-CoV-2 and related implications for vaccine development. Adv. Sci., 10: e2205445.
Tang XL, Qian ZH, Lu XM, Lu J. (2023) Adaptive evolution of the spike protein in coronaviruses. Mol. Biol. Evol., 40: msad089.
Ou XY, Xu G, Li P, Liu Y, Zan FW, Liu P, Hu JX, Lu X, Dong SW, Zhou Y, Mu ZX, Wu ZQ, Wang JW, Jin Q, Liu PH, Lu J, Wang XX, Qian ZH. (2023) Host susceptibility and structural and immunological insight of S proteins of two SARS-CoV-2 closely related bat coronaviruses. Cell Discov., 9: 78.
Li P, Hu JX, Liu Y#, Ou XY, Mu ZX, Lu X, Zan FW, Cao MM, Tan L, Dong SW, Zhou Y, Lu J, Jin Q, Wang JW, Wu ZQ, Zhang YT, Qian ZH (2023) Effect of polymorphism in Rhinolophus affinis ACE2 on entry of SARS-CoV-2 related bat coronaviruses. PLoS Pathog., 19: e1011116.
Hu SX, Wu CL, Wu XK, Ma XH, Shu C, Chen Q, Zheng AQ, Yang HT, Lu J, Du P, Gao GF, Wang QH. (2023) Classification of five SARS-CoV-2 serotypes based on RBD antigenicities. Sci. Bull., 68: 3003-3012.
Duan YG, Tang XL, Lu J. (2022) Evolutionary driving forces of A-to-I editing in metazoans. Wiley Interdiscip. Rev.-RNA, 13: e1666.
Ruan YS, Hou M, Tang XL, He XL, Lu XM, Lu J, Wu CI, Wen HJ. (2022) The runaway evolution of SARS-CoV-2 leading to the highly evolved delta strain. Mol. Biol. Evol., 39: msac046.
Sun Q, Shu C, Shi W, Luo Y, Fan G, Nie J, Bi Y, Wang Q, Qi J, Lu J, Zhou Y, Shen Z, Meng Z, Zhang X, Yu Z, Gao S, Wu L, Ma J, Hu S. (2022) VarEPS: an evaluation and prewarning system of known and virtual variations of SARS-CoV-2 genomes. Nucl. Acids Res., 50: D888-D897.
Qian ZH, Li P, Tang XL, Lu J. (2022) Evolutionary dynamics of the severe acute respiratory syndrome coronavirus 2 genomes. Med. Rev., 2: 3-22.
Hu B, Liu R, Tang XL, Pan YC, Wang M, Tong YQ, Ye GM, Shen GG, Ying RC, Fu AS, Li D, Zhao WX, Peng J, Guo J, Men D, Yao XM, Wang YR, Zhang H, Feng ZH, Yu JP, Chen LJ, Deng ZX, Lu XM, Zhang YP, Li YR, Liu BD, Yu LL, Li Y, Lu J, Liu TG. (2021) The concordance between the evolutionary trend and the clinical manifestation of the two SARS-CoV-2 variants. Natl. Sci. Rev., 8: nwab073.
Ruan YS, Luo ZD, Tang XL, Li GH, Wen HJ, He XL, Lu XM, Lu J, Wu CI. (2021) On the founder effect in COVID-19 outbreaks: how many infected travelers may have started them all? Natl. Sci. Rev., 8: nwaa246.
Yu TX, Huang X, Dou SQ, Tang XL, Luo SQ, Theurkauf WE, Lu J, Weng ZP. (2021) A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies. Nucleic Acids Res., 49: e44.
Zhang H, Wang YR, Wu XK, Tang XL, Wu CC, Lu J. (2021) Determinants of genome-wide distribution and evolution of uORFs in eukaryotes. Nat. Commun., 12: 1076.
Tang XL, Ying RC, Yao XM, Li GH, Wu CC, Tang YYL, Li ZD, Kuang BS, Wu F, Chi CS, Du XM, Qin Y, Gao SH, Hu SNA, Ma JC, Liu TG, Pang XH, Wang JW, Zhao GP, Tan WJ, Zhang YP, Lu XM, Lu J. (2021) Evolutionary analysis and lineage designation of SARS-CoV-2 genomes. Sci. Bull., 66: 2297-2311.
Zhang H, Wang YR, Tang XL, Dou SQ, Sun YQ, Zhang Q, Lu J. (2021) Combinatorial regulation of gene expression by uORFs and microRNAs in Drosophila. Sci. Bull., 66: 225-228.
Duan YG, Tang XL, Lu J. (2021) Evolutionary driving forces of A-to-I editing in metazoans. Wiley Interdiscip. Rev.-RNA, e1666.
Duan YG, Dou SQ, Porath HT, Huang JX, Eisenberg E, Lu J. (2021) A-to-I RNA editing in honeybees shows signals of adaptation and convergent evolution. iScience, 24: 101983.
Peng MS, Li JB, Cai ZF, Liu H, Tang X, Ying R, Zhang JN, Tao JJ, Yin TT, Zhang T, Hu JY, Wu RN, Zhou ZY, Zhang ZG, Yu L, Yao YG, Shi ZL, Lu XM, Lu J, Zhang YP. (2021) The high diversity of SARS-CoV-2-related coronaviruses in pangolins alerts potential ecological risks. Zool. Res., 42: 834-844.
Wu Z, Jin Q, Wu G, Lu J, Li M, Guo D, Lan K, Feng L, Qian Z, Ren L, Tan W, Xu W, Yang W, Wang J, Wang C.(2021)SARS-CoV-2's origin should be investigated worldwide for pandemic prevention. Lancet., 398: 1299-1303.
Feng YQ, Xu HZ, Liu JH, Xie N, Gao L, He YY, Yao Y, Lv FX, Zhang Y, Lu J, Zhang W, Li CY, Hu XL, Yang ZH, Xiao RP. (2021) Functional and adaptive significance of promoter mutations that affect divergent myocardial expressions ofTRIM72in primates. Mol. Biol. Evol., 38: 2930-2945.
Wu CI, Wen H, Lu J, Su XD, Hughes AC, Zhai W, Chen C, Chen H, Li M, Song S, Qian Z, Wang Q, Chen B, Guo Z, Ruan Y, Lu X, Wei F, Jin L, Kang L, Xue Y, Zhao G, Zhang YP. (2021) On the origin of SARS-CoV-2-The blind watchmaker argument. Sci. China-Life Sci., 64: 1560-1563.
Tang XL, Wu CC, Li X, Song YH, Yao XM, Wu XK, Duan YG, Zhang H, Wang YR, Qian ZH, Cui J, Lu J. (2020) On the origin and continuing evolution of SARS-CoV-2. Natl. Sci. Rev., 7: 1012-1023.
Wang Y, Zhang H, Lu J. (2020) Recent advances in ribosome profiling for deciphering translational regulation. Methods., 176:46-54.
Li T, Tang XL, Wu CC, Yao XM, Wang YR, Lu XM, Lu J. (2020) The use of SARS-CoV-2-related coronaviruses from bats and pangolins to polarize mutations in SARS-Cov-2. Sci. China Life Sci., 63: 1608-1611.
Luo SQ, Zhang H, Duan YG, Yao XM, Clark AG, Lu J. (2020) The evolutionary arms race between transposable elements and piRNAs in Drosophila melanogaster. BMC Evol. Biol., 20: 14.
王志娟、陈俊豪、唐小鹿、单科家、姚欣敏、陈心悦、应若晨、刘晨露、李伟轩、汪海蓉、高培翔、高大可、靳垲淳、徐启姮、董馨宁、张林、徐梦泽
