01
单分子 RNA
基于纳米孔测序读取全长转录本，在单分子水平直接测量 RNA 加工状态与 poly(A) 尾。
FLEP-seq2 · 长读长 RNA · 新生 RNA4.22亿+小鼠 poly(A) 图谱中的长读长数据
20植物界 poly(A) 图谱覆盖物种
20万+昼夜节律单细胞图谱中的细胞核
研究方向
跨尺度解析 RNA 调控。
课题组将实验技术创新与定量分析相结合，研究不同生物体系中 RNA 的加工、加尾、翻译与调控。
02
单细胞系统
利用单核与空间组学解析不同组织和生物体系中的细胞身份、动态状态及调控程序。
单核 · 空间组学 · 时间序列03
Poly(A) 与 RNA 命运
研究 poly(A) 尾动态如何跨器官、跨物种调节 RNA 稳定性、翻译与转录后调控。
Poly(A) · 翻译 · RNA 降解04
图谱与算法
将大规模数据转化为可复现的分析流程、可检索图谱和面向学术共同体的开放资源。
数据整合 · 在线数据库 · 开放科学技术平台
- 纳米孔测序
- 单细胞 RNA 测序
- 空间转录组
- Poly(A) 图谱
- 核糖体图谱
- 计算图谱
整合 RNA 生物学
从一个 RNA 分子到完整生物体系。
我们的技术保留传统平均测量中丢失的信息，将分子异质性与细胞状态、组织功能和个体调控联系起来。
01信号离子电流 · 成像
02分子RNA 异构体 · Poly(A) 尾
03细胞身份 · 状态 · 时间
04系统组织 · 器官 · 个体
论文发表
完整论文目录。
以下按年份倒序列出课题组公开论文记录，涵盖近期单分子与单细胞研究，以及早期 RNA 和表观遗传学工作。
109篇论文
2006–2026* 共同第一作者 · # 通讯作者2026
7 篇论文Molecular basis of plant DCL4 action that outcompetes DCL2
Molecular basis of DRB4-assisted long RNA processing and 21-nucleotide siRNA biogenesis by DCL4 in plants
The plant ontology of cell types
2025
8 篇论文Systematic characterization of the composition and dynamics of processing body-associated mRNAs
Empowering low-crosstalk, dynamic-decision random access of DNA storage via 384-multiplexed nanopore signatures
Structural insights into plant DNA CG methylation maintenance by MET1
Pre-mRNA processing factors differentially impact coordination between cotranscriptional cleavage and transcription termination
De novo non-canonical nanopore basecalling enables private communication using heavily-modified DNA data at single-molecule level
48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis
Comparative single-nucleus RNA-seq analysis revealed localized and cell type-specific pathways governing rootmicrobiome interactions
Epigenetics in the modern era of crop improvements
2024
7 篇论文Focus on epigenetics
A repertoire of intronic lariat RNAs reveals tissue-specific regulation and target mimicry potential in plants
A telomere-to-telomere cotton genome assembly reveals centromere evolution and a Mutator transposon-linked module regulating embryo development
Composite Hedges Nanopores codec system for rapid and portable DNA data readout with high INDEL-Correction
Analysis of DNA 5-methylcytosine Using Nanopore Sequencing
Light controls mesophyll-specific post-transcriptional splicing of photoregulatory genes by AtPRMT5
2023
5 篇论文Genome evolution and initial breeding of the Triticeae grass Leymus chinensis dominating the Eurasian Steppe
Cell type–specific cytonuclear coevolution in three allopolyploid plant species
Single-nucleus transcriptomes reveal spatiotemporal symbiotic perception and early response in Medicago
Single-molecule targeted accessibility and methylation sequencing of centromeres, telomeres and rDNAs in Arabidopsis
Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation
2022
11 篇论文MCIBox: A Toolkit for Single-molecule Multi-way Chromatin Interaction Visualization and Micro-Domains Identification
Interplay of phytohormones and epigenetic regulation: a recipe for plant development and plasticity
Genome-wide characterization of nascent RNA processing in plants
An atlas of plant full-length RNA reveals tissue-specific and monocots–dicots conserved regulation of poly(A) tail length
Safeguard DCL2-Dependent 22-nt siRNA generation by DCL1
Induced Mutation in GmCOP1b Enhances the Performance of Soybean under Dense Planting Conditions
A SYBR Gold-based Label-free in vitro Dicing Assay
Pore-C Simultaneously Captures Genome-wide Multi-way Chromatin Interaction and Associated DNA Methylation Status in Arabidopsis
Plant Public RNA-seq Database: a comprehensive online database for expression analysis of ~45 000 plant public RNA-Seq libraries
Regulation of DNA Methylation During Plant Endosperm Development
2021
9 篇论文Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing
Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation
FLEP-seq: simultaneous detection of RNA polymerase II position, splicing status, polyadenylation site and poly(A) tail length at genome-wide scale by single-molecule nascent RNA sequencing
Multiplex CRISPR-Cas9 editing of DNA methyltransferases in rice uncovers a class of non-CG methylation specific for GC-rich regions
Substrate deformation regulates DRM2-mediated DNA methylation in plants
sRNAanno—a database repository of uniformly annotated small RNAs in plants
FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants
2020
9 篇论文Soybean DICER-LIKE2 Regulates Seed Coat Color via Production of Primary 22-Nucleotide Small Interfering RNAs from Long Inverted Repeats
A comprehensive online database for exploring ∼20,000 public Arabidopsis RNA-Seq libraries
Post-transcriptional splicing of nascent RNA contributes to widespread intron retention in plants
The characterization of Mediator 12 and 13 as conditional positive gene regulators in Arabidopsis
Plant 22-nt siRNAs mediate translational repression and stress adaptation
The Dynamic Kaleidoscope of RNA Biology in Plants
An online database for exploring over 2,000 Arabidopsis small RNA libraries
2019
2 篇论文Widespread long-range cis-regulatory elements in the maize genome
A Phytophthora Effector Suppresses Trans-Kingdom RNAi to Promote Disease Susceptibility
2018
3 篇论文RNA-directed DNA methylation involves co-transcriptional small RNA-guided slicing of Pol V transcripts in Arabidopsis
Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis
2017
4 篇论文ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis
MS23, a master basic helix-loop-helix factor, regulates the specification and development of the tapetum in maize
2016
2 篇论文MTHFD1 controls DNA methylation in Arabidopsis
DNA methylome of the 20-gigabase Norway spruce genome
2015
8 篇论文A 'One precursor, One siRNA' model for PolIV-dependent siRNA Biogenesis
Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction
CG gene body DNA methylation changes and evolution of duplicated genes in cassava
Distinct and cooperative activities of HESO1 and URT1 nucleotidyl transferases in microRNA turnover in Arabidopsis
Coordination of MicroRNAs, PhasiRNAs, and NB-LRR Genes in Immune Responses: Insights from analyses of Soybean Rps Gene Near-Isogenic Lines
2014
7 篇论文An atlas of soybean small RNAs demonstrates regulation by phased siRNAs of hundreds of coding genes
Genome-wide Hi-C analyses in wild type and mutants reveal high-resolution chromatin interactions in Arabidopsis
Rapid construction of parallel analysis of RNA end (PARE) libraries for Illumina sequencing
Reprint of: Construction of Specific Parallel Amplification of RNA Ends (SPARE) libraries for the systematic identification of plant microRNA processing intermediates
miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis
Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice
2013
9 篇论文Plant microRNAs display differential 3'-truncation and tailing, modifications which are ARGONAUTE1-dependent and conserved across species
Deep Sequencing from hen1 Mutants to Identify Small RNA 3′ Modifications
Parallel Analysis of RNA Ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon
The Amborella Genome and the Evolution of Flowering Plants
Comprehensive investigation of miRNAs enhanced by analysis of sequence variants, expression patterns, AGO loading and target cleavage
Physiological stressors and invasive plant infections alter the small RNA transcriptome of the rice blast fungus Magnaporthe oryzae
Multiple RNA recognition patterns during microRNA biogenesis in plants
Biogenesis and function of rice small RNAs from non-coding RNA precursors
2012
2 篇论文RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats
HESO1, a nucleotidyl transferase in Arabidopsis, uridylates unmethylated miRNAs and siRNAs to trigger their degradation
2011
4 篇论文MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs
Roles of DCL4 and DCL3b in rice phased small RNA biogenesis
The Medicago genome provides insight into the evolution of rhizobial symbioses
Massive analysis of rice small RNAs: Mechanistic implications of regulated miRNAs and variants for differential target RNA cleavage
2010
4 篇论文siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis
Genome sequencing and analysis of the model grass Brachypodium distachyon
MicroRNA processing: battle of the bulge
Conservation and divergence in eukaryotic DNA methylation
2009
3 篇论文Short-read sequencing technologies for transcriptional analyses
Highly efficient gene silencing using perfect complementary artificial miRNA targeting AP1 or heteromeric artificial miRNA targeting AP1 and CAL genes
Distinct extremely abundant si
2008
2 篇论文Small RNA-directed epigenetic natural variation in Arabidopsis thaliana
The cornucopia of small RNAs in plant genomes
2007
2 篇论文Mutations in the Type II protein arginine methyltransferase AtPRMT5 result in pleiotropic developmental defects in Arabidopsis
SDG714, a histone H3K9 methyltransferase, is involved in Tos17 DNA methylation and transposition in rice
2006
1 篇论文ROR1/RPA2A, a putative replication protein A2, functions in epigenetic gene silencing and in regulation of meristem development in Arabidopsis
课题组成员
课题组的现在与传承。
主页直接展示公开名录中的全部现任成员与毕业成员，研究方向涵盖实验生物学、组学技术与计算研究。
现任成员
12 人
Wenqin Lu
研究助理教授
植物单细胞 RNA 测序
Bo Liu
博士后
分子生物学与表观遗传学
Yi Shu
博士后
植物表观遗传学与生物信息学
Huajie Lei
博士研究生
表观遗传调控
Xinlong Zhu
博士研究生
RNA 生物学
Siteng Bi
博士研究生
系统生物学
Anqi Su
博士研究生
RNA 生物学
Decai Yuan
博士研究生
Yitian Zhang
硕士研究生
生物信息学与基因组数据分析
Leting Chen
硕士研究生
植物表观遗传学
Yanxin Wang
硕士研究生
Cailiu Liang
科研助理 / 实验室主管
实验室日常运行与管理毕业成员
名录信息依据课题组原公开网站整理。
原科研教师
Yanping Long
Ph.D., Institute of Genetics and Developmental Biology, Chinese Academy of Science · Research Interests: Higher-order structure of chromosome
原科研教师
Jinbu Jia
Professor · College of Agriculture, South China Agricultural University
原科研教师
Xuehua Pan
Ph.D., Biochemistry and Molecular Biology, HongKong Polytechnic University · Research Interests: RNA-based therapeutics, Protein molecular biology
原科研教师
Daoheng Hu
Associate Research Fellow · Department of Medical Genetics, · The First People's Hospital of Yunnan Province
原科研教师
Huihui Fang
Lecturer · College of Horticulture Science, Zhejiang Agriculture and Forestry University
原科研教师
Lidan Xiao
Ph.D., Biomedical Engineering，Zhejiang University · Research Interests: Single-cell sequencing，Kinship research，Epigenetics
原博士后
Yu Zhang
Associate Professor · School of Agriculture, Sun Yat-Sen University
原博士后
Wenjian Yu
Associate senior research · Wuhan Rhegen Biotechnology Co.,Ltd
原博士后
Lu Hongwei
Associate researcher · China National Rice Research Institute
原博士后
Yang Chen
Assistant Professor · College of Life Sciences and Oceanography, Shenzhen University
原博士后
Juzuo Li
Ph.D., College of Life Science, Northeast Normal University · Research Interests: Nanopore-based genomics and transcriptomes sequencing and analysing
原博士后
Zhen Wang
Ph.D., Department of biochemistry and biophysics, Texas A & M University · Research interests: Single-cell omics and Nanopore-based genomics and transcriptomics
原博士研究生
Li Feng
Postdoctoral Fellow · The Sainsbury Laboratory
原博士研究生
Yiming Yu
Postdoctoral Fellow · Institute of Science and Technology Austria (ISTA)
原博士研究生
Dongdong Lu
Associate Research Fellow · Peking University Institute of Advanced Agricultural Sciences
原博士研究生
Zhuowen Li
Tech Sales · SAILGENE TECHNOLOGY (HONGKONG) CO LIMITED
原博士研究生
Weipeng Mo
Postdoc · The First Affiliated Hospital, Sun Yat-sen University
原博士研究生
Zhijian Liu
Research Fellow · Northeast Normal University
原博士研究生
Yuwei Qin
Postdoc · Institute of Genetics and Developmental Biology
原硕士研究生
Hongsen Liu
College of Horticulture, South China Agricultural University
原硕士研究生
Hong Zhang
Army Medical Center of PLA
原硕士研究生
Tie Li
Research Interests: Preparation of nanopores for detection
原硕士研究生
Lihao Zheng
AI Developer · Shenzhen CyberAray Network Technology Company
原硕士研究生
Mengyun Zou
Research Interests: Animal fertility and Bioinformatics
原科研助理
Xu Chen
Shenzhen Mindray Bio-Medical Electronics Co.,Ltd.
原科研助理
Mei Yu
Shenzhen Jielikang Biotechnology Co., Ltd.
原科研助理
Fei Zhang
Michigan State University
原科研助理
Fei Lou
Guangzhou College of Commerce
原科研助理
Yan Zhao
Southern University of Science and Technology
原科研助理
Qiumei Zheng
School of Medicine, Southern University of Science and Technology
原科研助理
Yunjing Ma
Leibniz Institute of plant Biochemistry在线数据库
让发表的数据继续被探索。
课题组随论文发布交互式数据库，将单条 reads、细胞状态与跨器官、跨物种 RNA 调控连接起来。
小鼠 Poly(A) 尾图谱
探索 18 个小鼠器官的 poly(A) 尾长度与表达，并查看单条全长 RNA reads。
植物 Poly(A) 图谱
查询 20 个代表性植物物种的全长 RNA 结构及 poly(A) 尾演化图谱。
昼夜节律单细胞图谱
按细胞类型浏览 24 小时与 48 小时时间序列中的基因表达和节律变化。
植物公共 RNA-seq 数据库
检索超过 7 万个公共植物 RNA-seq 文库中的标准化表达图谱。
PISE
探索拟南芥、玉米、水稻和大豆中的内含子剪接效率。
ASRD
检索 2,024 个公共拟南芥小 RNA 文库中的序列、基因及标准化丰度。
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