RNA regulation across biological systems

Zhai Lab

Single-molecule and Single-cell Transcriptomics

We develop sequencing technologies and computational frameworks to resolve RNA regulation across plants, animals and humans.

Explore research Latest publications

422M+long reads in the mouse poly(A) atlas

20species in the plant poly(A) atlas

200K+nuclei in the circadian single-cell atlas

Research

RNA regulation, resolved across scales.

Our lab links experimental innovation with quantitative analysis to understand how RNA is processed, tailed, translated and regulated in diverse biological systems.

Single-molecule RNA

Nanopore-based methods read full-length transcripts while directly measuring processing states and poly(A) tails molecule by molecule.

FLEP-seq2 · Long-read RNA · Nascent RNA

Single-cell systems

Single-nucleus and spatial omics reveal cell identities, dynamic states and regulatory programs across tissues and organisms.

Single nucleus · Spatial · Time series

Poly(A) and RNA fate

We test how poly(A) tail dynamics shape RNA stability, translation and post-transcriptional regulation across organs and kingdoms.

Poly(A) · Translation · RNA turnover

Atlases and algorithms

Large-scale datasets become reproducible workflows, searchable atlases and open infrastructure for the research community.

Data integration · Databases · Open science

Technology stack

Nanopore sequencing
Single-cell RNA-seq
Spatial transcriptomics
Poly(A) profiling
Ribosome profiling
Computational atlases

Integrated RNA biology

From one RNA molecule to a whole organism.

Our workflows preserve the information that conventional averages erase, connecting molecular heterogeneity to cell state, tissue function and organismal regulation.

01SignalIonic current · imaging

02MoleculeRNA isoform · poly(A) tail

03CellIdentity · state · time

04SystemTissue · organ · organism

Publications

Complete publication record.

The lab's full publication record is listed below in reverse chronological order, from current single-molecule and single-cell studies to foundational work in RNA and epigenetics.

109papers

2006–2026* co-first authors · # corresponding authors

2026

7 papers

109

Science China Life Sciencesdoi: 10.1007/s11427-025-3306-6

Single-nucleus RNA sequencing reveals a spatiotemporal pattern of H2S signaling in Chinese cabbage

Zhang J *, Chen Y *, Liu B, Qin Y, Luan Y, Yin H, Liu W, Chen L, Zhai J, Pei Y #, Long Y #, Jin Z #

108

Nature Communicationsdoi: 10.1038/s41467-026-71703-6

Pan-organ poly(A) atlas reveals a post-transcriptional regulatory layer independent of RNA abundance

Lei H *, Long Y *, Wu S *, Wang X *, Peng Y *, Liu Z, Lu W, Shu Y, Zhu H, Zou M, Gao Y, Xia Y, Li S, Ren L, Fu Y #, Zhang Z #, Li Y #, Zhai J #

107

Genome Biologydoi: 10.1186/s13059-026-04040-y

A kingdom-wide full-length RNA atlas reveals the evolutionary landscapes of plant poly(A) tails

Chen Y *, Lu W *, He H *, Zheng L, Pan X, Sun T, Bu F, Fang Y, Sun Y, Long Y, Wang M, Wu S, Liu L, Jia J, Jiao Y, Hu Z, Zhang Y #, Zhai J #

106

Genome Biologydoi: 10.1186/s13059-026-04024-y

Advances in single-cell and spatial omics for studying symbiotic nitrogen fixation: comparative cellular and evolutionary perspectives

Shi Y *, Liu H *, Yang W #, Zhai J #, Wang H #

105

Nature Plants1-15

Molecular basis of plant DCL4 action that outcompetes DCL2

Liu Y *, Feng L, Wang C, Yan W, Linghu Q, Tan H, Pan Y, Yan S, Zhai J, Du J, Guo H #

104

Nature Plants1-8

Molecular basis of DRB4-assisted long RNA processing and 21-nucleotide siRNA biogenesis by DCL4 in plants

Wang C *, Chi C *, Liu Y, Zhao J, Wang Q, Wang N, Zhang Z, Jiang K, Xue Y, Li Y, Wang P, Zhai J, Guo H, Du J #

103

Molecular Plant19(3): 425-429

The plant ontology of cell types

Chen H *, Liang P *, Lu X, Jiang S, Jin J, Cai J, Lu Y, Zheng D, Yao J, Chu Q, Shou H, Fu C, Lu T, Jing Y, Bai Y, Yang N, Zhong S, Xiao J, Yang F, Guo X, Zhai J, Marand AP, Tian Z, Chen F, Xu J, Jiao Y, Chen D, Cao P, Cui X, Jackson D, Nobori T, Gu X, Wang J, Whelan J, Yan J, Schmitz RJ, Zhang Z, Fan L #

2025

8 papers

102

Nature Communications16(1): 9867

Systematic characterization of the composition and dynamics of processing body-associated mRNAs

Sun Z *, Wen X *, Li Y, Xie X, Dong P, Shu Y, Tian S, Yang J, Lin Y, Wang M, Jiang F, Zhu Q, Cui H, Zhai J, Hu Y, Fang L #, Chen W #

101

Nature Communications16(1): 9233

Empowering low-crosstalk, dynamic-decision random access of DNA storage via 384-multiplexed nanopore signatures

Li J *, Zhao X, Fan Q, Long Y, Liu R, Zhai J, Pan Q, Li Y #

100

Plant Cell37(11): koaf244

Structural insights into plant DNA CG methylation maintenance by MET1

Zhang Z *, Li W *, Liu Y *, Chi C *, Nan J, Wang C, Zhu Y, Zhao J, Xue Y, Li Y, Wang P, Zhai J, Du J #

099

Nature Communications16(1), 7086

Pre-mRNA processing factors differentially impact coordination between cotranscriptional cleavage and transcription termination

Jin X *, Li J *, Lu W, Deng X, Wei Y, Shu Y, Liu B, Liu Z, Long Y, Zhu X, Fei Q, Xia Y, Li Q, Michaels SD, Cao X, Lenhard M, Zhai J #

098

Nature Communications16(1): 4099

De novo non-canonical nanopore basecalling enables private communication using heavily-modified DNA data at single-molecule level

Fan Q *, Zhao X, Li J, Liu R, Liu M, Feng Q, Long Y, Fu Y, Zhai J, Pan Q, Li Y #

097

Nature Communications16(1): 4171

48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis

Qin Y *, Liu Z *, Gao S *, Martínez-Vasallo C *, Long Y *, Zhu X, Liu B, Gao Y, Xu X, Nohales MA #, Xie Q #, Zhai J #

096

Nature Communications16(1): 3169

Comparative single-nucleus RNA-seq analysis revealed localized and cell type-specific pathways governing rootmicrobiome interactions

Yang Q *, Li Z *, Guan K *, Wang Z *, Tang X, Hong Y, Liu Z, Zhai J, Huang A #, Long Y #, Song Y #

095

Science China Life Sciences68(6):1570–1609

Epigenetics in the modern era of crop improvements

Xue Y #, Cao X #, Chen X #, Deng X #, Deng XW #, Ding Y #, Dong A #, Duan CG #, Fang X #, Gong L #, Gong Z #, Gu X #, He C #, He H #, He S #, He XJ #, He Y #, He Y #, Jia G #, Jiang D #, Jiang J #, Lai J #, Lang Z #, Li C #, Li Q #, Li X #, Liu B #, Liu B #, Luo X #, Qi Y #, Qian W #, Ren G #, Song Q #, Song X #, Tian Z #, Wang JW #, Wang Y #, Wu L #, Wu Z #, Xia R #, Xiao J #, Xu L #, Xu ZY #, Yan W #, Yang H #, Zhai J #, Zhang Y #, Zhao Y #, Zhong X #, Zhou DX #, Zhou M #, Zhou Y #, Zhu B #, Zhu JK #, Liu Q #

2024

7 papers

094

Plant Physiology194(4): 1925-1928

Focus on epigenetics

Liu Q #, Ton J, Manavella PA, Komiya R, Zhai J

093

Science China Life Sciences67(6): 1280–1291

A repertoire of intronic lariat RNAs reveals tissue-specific regulation and target mimicry potential in plants

Zhang Y, Zhang X, Tang Q, Li L, Jiang T, Fang Y, Zhang H, Zhai J, Ren G, Zheng B #

092

Nature Genetics56(9): 1953-1963

A telomere-to-telomere cotton genome assembly reveals centromere evolution and a Mutator transposon-linked module regulating embryo development

Huang G #, Bao Z, Feng L, Zhai J, Wendel JF, Cao X, Zhu Y #

091

bioRxiv10.1101/2024.08.15.606762

DeepSME: De Novo Nanopore Basecalling of Motif-insensitive DNA Methylation and Alignment-free Digital Information Decryptions at Single-Molecule Level

Fan Q, Zhao X, Li J, Liu R, Liu M, Feng Q, Long Y, Fu Y, Zhai J, Pan Q #, Li Y #

090

Nature Communications15 (1), 9395

Composite Hedges Nanopores codec system for rapid and portable DNA data readout with high INDEL-Correction

Zhao X, Li J, Fan Q, Dai J, Long Y, Liu R, Zhai, J, Pan Q #, Y Li #

089

Bio-protocol14(3): e4943

Analysis of DNA 5-methylcytosine Using Nanopore Sequencing

Li Z *, Zheng L, Zhai J #, Long Y #

088

PNAS121 (6) e2317408121

Light controls mesophyll-specific post-transcriptional splicing of photoregulatory genes by AtPRMT5

Yan Y *, Luo H *, Qin Y *, Yan T, Jia J, Hou Y, Liu Z, Zhai J, Long Y #, Deng X #, Cao X #

2023

5 papers

087

PNAS120 (44) e2308984120

Genome evolution and initial breeding of the Triticeae grass Leymus chinensis dominating the Eurasian Steppe

Li T *, Tang S *, Li W *, Zhang S, Wang J, Pan D, Lin Z, Ma X, Chang Y, Liu B, Sun J, Wang X, Zhao M, You C, Luo H, Wang M, Ye X, Zhai J, Shen Z, Du H #, Song X #, Huang G #, Cao X #

086

PNAS120 (40) e2310881120

Cell type–specific cytonuclear coevolution in three allopolyploid plant species

Zhang K *, Zhao X *, Zhao Y *, Zhang Z *, Liu Z, Liu Z, Yu Y, Li J, Ma Y, Dong Y, Pang X, Jin X, Li N, Liu B, Wendel JF, Zhai J, Long Y #, Wang T #, Gong L #

085

Nature Plants9(10): 1734-1748

Single-nucleus transcriptomes reveal spatiotemporal symbiotic perception and early response in Medicago

Liu Z *, Yang J *, Long Y *, Zhang C *, Wang D, Zhang X, Dong W, Zhao L, Liu C, Zhai J #, Wang E #

084

Nature Plants9(9): 1439-1450

Single-molecule targeted accessibility and methylation sequencing of centromeres, telomeres and rDNAs in Arabidopsis

Mo W *, Shu Y *, Liu B, Long Y, Li T, Cao X, Deng X #, Zhai J #

083

Nature Plants9(4): 515-524

Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation

Liu Z *, Kong X *, Long Y *, Liu S, Zhang H, Jia J, Cui W, Zhang Z, Song X, Qiu L, Zhai J #, Yan Z #

2022

11 papers

082

Briefings in Bioinformatics23(6):bbac380

MCIBox: A Toolkit for Single-molecule Multi-way Chromatin Interaction Visualization and Micro-Domains Identification

Tian S #, Li G, Ning D, Jing K, Xu Y, Yang Y, Fullwood MJ, Yin P, Huang G, Plewczynski D, Wang W, Zhai J, Wang Z, Dai Z, Lin Y, Chen W #, Zheng M #

081

Science China Life Sciences10.1007/s11427-022-2193-3

Plant Intron-Splicing Efficiency Database (PISE): exploring splicing of ~1,650,000 introns in Arabidopsis, maize, rice, and soybean from ~57,000 public RNA-seq libraries

Zhang H *, Jia J, Zhai J #

080

Journal of Integrative Plant Biology65(2):381-398

Interplay of phytohormones and epigenetic regulation: a recipe for plant development and plasticity

Jiang K * #, Guo H, Zhai J #

079

Current Opinion in Plant Biology69:102294

Genome-wide characterization of nascent RNA processing in plants

Qin Y, Long Y, Zhai J #

078

Nature Plants8(9):1118-1126

An atlas of plant full-length RNA reveals tissue-specific and monocots–dicots conserved regulation of poly(A) tail length

Jia J *, Lu W *, Liu B, Fang H, Yu Y, Mo W, Zhang H, Jin X, Shu Y, Long Y, Pei Y, Zhai J #

077

Biochemical and Biophysical Research Communications605, 97-103

Safeguard DCL2-Dependent 22-nt siRNA generation by DCL1

Lu D *, Feng L *, Zhai J, Li B #, Xi M #

076

International Journal of Molecular Sciences23(10):5394

Induced Mutation in GmCOP1b Enhances the Performance of Soybean under Dense Planting Conditions

Ji R *, Xu X *, Liu J, Zhao T, Li H, Zhai J, Liu B #

075

Bio-protocol12(07): e4382

A SYBR Gold-based Label-free in vitro Dicing Assay

Wang Q *, Xue Y *, Zhang L *, Zhong Z, Feng S, Wang C, Xiao L, Yang Z, Harris CJ, Wu Z, Zhai J, Yang M, Li S #, Jacobsen SE #, Du J #

074

Plant Biotechnology Journal20(6):1009-1011

Pore-C Simultaneously Captures Genome-wide Multi-way Chromatin Interaction and Associated DNA Methylation Status in Arabidopsis

Li Z *, Long Y *, Yu Y, Zhang F, Zhang H, Liu Z, Jia J, Mo W, Tian SZ, Zheng M, Zhai J #

073

Plant Biotechnology Journal20, 806-808

Plant Public RNA-seq Database: a comprehensive online database for expression analysis of ~45 000 plant public RNA-Seq libraries

Yu Y *, Zhang H *, Long Y, Shu Y, Zhai J #

072

Frontiers in Genetics13:760690

Regulation of DNA Methylation During Plant Endosperm Development

Lu D, Zhai J #, Xi M #

2021

9 papers

071

Genome Biology22(1):322

Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing

Mo W *, Liu B *, Zhang H, Jin X, Lu D, Yu Y, Liu Y, Jia J, Long Y, Deng X, Cao X, Guo H, Zhai J #

070

New Phytologistdoi: 10.1111/nph.17853

MicroRNA482/2118, a miRNA superfamily essential for both disease resistance and plant development

Zhang Y *, Waseem M *, Zeng Z, Xu J, Chen C, Liu Y, Zhai J, Xia R #

069

Science374(6571):1152-1157

Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation

Wang Q *, Xue Y *, Zhang L *, Zhong Z, Feng S, Wang S, Xiao L, Yang Z, Harris CJ, Wu Z, Zhai J, Yang M, Li S #, Jacobsen SE #, Du J #

068

Nature Protocols16:4355–4381

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

Long Y *, Jia J *, Mo W, Jin X, Zhai J #

067

Plant Cell33(9):2950-2964

Multiplex CRISPR-Cas9 editing of DNA methyltransferases in rice uncovers a class of non-CG methylation specific for GC-rich regions

Hu D *, Yu Y *, Wang C*, Long Y, Liu Y, Feng L, Lu D, Liu B, Jia J, Xia R, Du J, Zhong X, Gong L, Wang K #, Zhai J #

066

Science Advances7(23):eabd9224

Substrate deformation regulates DRM2-mediated DNA methylation in plants

Fang J *, Leichter SM *, Jiang J *, Biswal M, Lu J, Zhang Z, Ren W, Zhai J, Cui Q, Zhong X #, Song J #

065

Annual Review of Phytopathologydoi.org/10.1146/annurev-phyto-121520-023514

Small RNAs in Plant Immunity and Virulence of Filamentous Pathogens

Qiao Y * #, Xia R, Zhai J, Hou Y, Feng L, Zhai Y, Ma W #

064

Horticulture Research8:45

sRNAanno—a database repository of uniformly annotated small RNAs in plants

Chen C *, Li J *, Feng J, Liu B, Feng L, Yu X, Li G, Zhai J, Meyers BC, Xia R #

063

Genome Biology22(1): 66

FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants

Long Y *, Liu Z *, Jia J *, Mo W, Fang L, Lu D, Liu B, Zhang H, Chen W, Zhai J #

2020

9 papers

062

Nature Plantsdoi.org/10.1038/s41477-020-00803-y

The chromatin will never forget

Yu Y, Zhai J #

061

New Phytologistdoi.org/10.1111/nph.17097

The antagonistic MYB paralogs RH1 and RH2 govern anthocyanin leaf markings in Medicago truncatula

Wang C *, Ji W*, Liu Y, Zhou P, Meng Y, Zhang P, Wen J, Mysore KS, Zhai J, Young ND, Tian Z, Niu L, Lin H #

060

Plant Cell32(12):3662-3673

Soybean DICER-LIKE2 Regulates Seed Coat Color via Production of Primary 22-Nucleotide Small Interfering RNAs from Long Inverted Repeats

Jia J *, Ji R *, Li Z, Yu Y, Nakano M, Long Y, Feng L, Qin C, Lu D, Zhan J, Xia R, Meyers BC, Liu B #, Zhai J #

059

Molecular Plant13(9):1231-1233

A comprehensive online database for exploring ∼20,000 public Arabidopsis RNA-Seq libraries

Zhang H *, Zhang F *, Yu Y *, Feng L, Jia J, Liu B, Li B, Guo H, Zhai J #

058

Nature Plants6(7):780-788

Post-transcriptional splicing of nascent RNA contributes to widespread intron retention in plants

Jia J *, Long Y *, Zhang H, Li Z, Liu Z, Zhao Y, Lu D, Jin X, Deng X, Xia R, Cao X, Zhai J #

057

Nature Communications11(1):2798

The characterization of Mediator 12 and 13 as conditional positive gene regulators in Arabidopsis

Liu Q * #, Bischof S *, Harris CJ Zhong Z, Zhan L, Nguyen C, Rashoff A, Barshop WD, Sun F, Feng S, Potok M, Gallego-Bartolome J, Zhai J, Wohlschlegel JA, Carey MF, Long JA, Jacobsen SE #

056

Nature581(7806):89-93

Plant 22-nt siRNAs mediate translational repression and stress adaptation

Wu H *, Li B *, Iwakawa HO, Pan Y, Tang X, Ling-Hu Q, Liu Y, Sheng S, Feng L, Zhang H, Zhang X, Tang Z, Xia X, Zhai J, Guo H #

055

Plant Physiology182(1):1-9

The Dynamic Kaleidoscope of RNA Biology in Plants

Bailey-Serres J * #, Zhai J, Seki M

054

Plant Physiology182(2):685-691

An online database for exploring over 2,000 Arabidopsis small RNA libraries

Feng L *, Zhang F *, Zhang H, Zhao Y, Meyers BC, Zhai J #

2019

2 papers

053

Nature Plants, 1-13

Widespread long-range cis-regulatory elements in the maize genome

Ricci W. A., Lu Z., Ji L., Marand A. P., Ethridge C. L., Murphy N. G., Noshay J.M., Galli M., Guerra M.K.M, Tatché M.C., Johannes F., Rowley M.J, Corce V.G., Zhai J, Scanlon M.J., Buckler E.S., Gallavotti A., Springer N.M., Schmitz R.J. #, Zhang X #

052

Cell Host & Microbe25(1):153-165

A Phytophthora Effector Suppresses Trans-Kingdom RNAi to Promote Disease Susceptibility

Hou Y *, Zhai Y *, Feng L, Karimi HZ, Rutter BD, Zeng L, Choi DS, Zhang B, Gu W, Chen X, Ye W, Innes RW, Zhai J, Ma W #

2018

3 papers

051

New Phytologistdoi:doi.org/10.1101/243907

Cis-directed cleavage and nonstoichiometric abundances of 21-nt reproductive phasiRNAs in grasses

Tamim S. *, Cai Z *, Mathioni S.M., Zhai J, Teng C, Zhang Q, Meyers B.C. #

050

Nature Plants4, p181–188

RNA-directed DNA methylation involves co-transcriptional small RNA-guided slicing of Pol V transcripts in Arabidopsis

Wanlu Liu *, Sascha Duttke *, Jonathan Hetzel, Martin Groth, Suhua Feng, Javier Gallego-Bartolome, Zhenhui Zhong, Hsuan Yu Kuo, Zhai J, Joanne Chory, and Steve Jacobsen #

049

PNAS115 (5) E1069-E1074

Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis

Yu Zhang *, Jake Harris *, Qikun Liu *, Wanlu Liu, Israel Ausin, Yanping Long, Lidan Xiao, Li Feng, Xu Chen, Yubin Xie, Xinyuan Chen, Lingyu Zhan, Suhua Feng, Jingyi Jessica Li, Haifeng Wang #, Zhai J #, and Steven E. Jacobsen #

2017

4 papers

048

PLoS biology15(2): e2001272

ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis

Yu Yu *, Lijuan Ji *, Brandon H Le *, Zhai J, Jiayi Chen, Elizabeth Luscher, Lei Gao, Chunyan Liu, Xiaofeng Cao, Beixin Mo, Jinbiao Ma, Blake C Meyers, Xuemei Chen #

047

Journal of Genetics and Genomics20;44(1):3-6. doi: 10.1016/j.jgg.2016.10.009

Characteristics and processing of Pol IV-dependent transcripts in Arabidopsis

Kuo HY *, Jacobsen EL *, Long Y, Chen X, Zhai J #

046

Plant JournalJul 3. doi: 10.1111/tpj.13627

The Ca2+/calmodulin2-binding transcription factor TGA3 elevates LCD expression and H2S production to bolster Cr6+ tolerance in Arabidopsis

Fang H *, Liu Z, Long Y, Liang Y, Jin Z, Zhang L, Liu D, Li H, Zhai J #, Pei Y #

045

Development144(1):163-172

MS23, a master basic helix-loop-helix factor, regulates the specification and development of the tapetum in maize

Nan GL #, Zhai J, Arikit S, Morrow D, Fernandes J, Mai L, Nguyen N, Meyers BC, Walbot V #

2016

2 papers

044

Nature CommunicationJun 13;7:11640

MTHFD1 controls DNA methylation in Arabidopsis

Groth M #, Moissiard G, Wirtz M, Wang H, GarciaSalinas G, Ramos-Parra PA, Bischof S, Feng S, Cokus SJ, John A, Smith DC, Zhai J, Hale CJ, Long JA, Hell R, Garza RID, Jacobsen SE #

043

PNAS113(50):E8106-E8113

DNA methylome of the 20-gigabase Norway spruce genome

Israel Ausin, Suhua Feng, Chaowei Yu, Wanlu Liu, Hsuan Yu Kuo, Elise L. Jacobsen, Zhai J, Javier Gallego-Bartolome, Lin Wang, Ulrika Egertsdotter, Nathaniel R. Street, Steven E. Jacobsen #, Haifeng Wang #

2015

8 papers

042

Cell163, 445–455

A 'One precursor, One siRNA' model for PolIV-dependent siRNA Biogenesis

Zhai J *, Bischof S *, Wang H, Feng S, Lee T, Teng C, Chen X, Park SY, Liu L, Gallego-Bartolome J, Liu W, Henderson I, Meyers BC, Ausin I #, Jacobsen SE #

041

PNAS112(10): 3146-51

Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction

Zhai J *, Zhang H *, Arikit S, Huang K, Nan G, Walbot V #, Meyers BC #

040

PNAS112(44):13729-34

CG gene body DNA methylation changes and evolution of duplicated genes in cassava

Wang H, Beyene G, Zhai J, Feng S, Fahlgren N, Taylor N, Bart R, Carrington JC, Jacobsen SE #, Ausin I #

039

Plant Biotechnology Journal10.1111/pbi.12387

Identification and functional characterization of soybean root hair microRNAs expressed in response to Bradyrhizobium japonicum infection

Yan Z *, Hossain MS *, Valdés-López O, Hoang NT, Zhai J, Wang J, Libault M, Joshi T, Brechenmacher L, Findley S, Qiu L, Sherrier DJ, Meyers BC, Xu D, Stacey G #

038

PLoS Genetics11(4): e1005119

Distinct and cooperative activities of HESO1 and URT1 nucleotidyl transferases in microRNA turnover in Arabidopsis

Tu B *, Xu C *, Liu L *, Zhai J, Li S, Lopez MA, Zhao Y, Yu Y, Ren G, Yu B, Li S, Meyers BC, Mo B #, Chen X #

037

New Phytologist10.1111/nph.13365

Identification of MicroRNAs and their mRNA targets during soybean nodule development: Functional analysis of the role of miR393* in soybean nodulation

Yan Z *, Hossain MS *, Arikit S, Valdé O, Zhai J, Wang J, Libault M, Ji T, Qiu L, Meyers BC, Stacey G #

036

The Plant Genome10.3835

Coordination of MicroRNAs, PhasiRNAs, and NB-LRR Genes in Immune Responses: Insights from analyses of Soybean Rps Gene Near-Isogenic Lines

Zhao M, Cai C, Zhai J, Lin F, Zhao M, Baumann DD, Ping J, Sun L, Liu Y, Zhang B, Tang Z, Hughes E, Doerge RW, Hughes TJ, Ma J #

035

Plant Biology10.1111/plb.12215

Efficient transformation and artificial miRNA gene silencing in Lemna minor

Cantó-Pastor A, Mollá-Morales A, Ernst E, Dahl W, Zhai J, Yan Y, Meyers BC, Shanklin J, Martienssen RA

2014

7 papers

034

The Plant Cell26: 4584-4601

An atlas of soybean small RNAs demonstrates regulation by phased siRNAs of hundreds of coding genes

Arikit S, Xia R, Kakrana A, Huang K, Zhai J, Yan Z, Valdés-López O, Prince S, Musket TA, Nguyen HT, Stacey G, Meyers BC #

033

Molecular Cell55(5):694-707

Genome-wide Hi-C analyses in wild type and mutants reveal high-resolution chromatin interactions in Arabidopsis

Feng S *, Cokus SJ *, Schubert V, Zhai J, Pellegrini M, Jacobsen SE #

032

The Plant Journal10.1111/tpj.12590

Roles of Small RNAs in Soybean Defense against Phytophthora sojae Infection

Wong J, Gao L, Yang Y, Zhai J, Arikit S, Yu Y, Duan S, Xiong Q, Yan J, Li S, Liu R, Wang Y, Tang G, Meyers BC, Chen X, Ma W #

031

Methods67(1),84-90

Rapid construction of parallel analysis of RNA end (PARE) libraries for Illumina sequencing

Zhai J *, S Arikit *, SA Simon, BF Kingham, BC Meyers #

030

Methods67(1):36-44

Reprint of: Construction of Specific Parallel Amplification of RNA Ends (SPARE) libraries for the systematic identification of plant microRNA processing intermediates

Schapire AL *, Bologna NG *, Moro B, Zhai J, Meyers BC, Palatnik JF #

029

Nature508 (7496):411-5

miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis

Creasey KM, Zhai J, Borges F, Van EF, Meyers BC, Martienssen RA #

028

PNAS111(10):3877-82

Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice

Wei L *, Gu L *, Song X *, Cui X, Lua Z, Zhou M, Wang L, Hu F, Zhai J, Meyers BC, Cao X #

2013

9 papers

027

The Plant Cell25(7):2417-28

Plant microRNAs display differential 3'-truncation and tailing, modifications which are ARGONAUTE1-dependent and conserved across species

Zhai J, Zhao Y, Simon SA, Huang S, Petsch K, Arikit S, Pillay L, Ji L, Xie M, Cao X, Yu B, Timmermans M, Yang B, Chen X, Meyers BC #

026

Cold Spring Harb Symp Quant Biol1943-4456

Deep Sequencing from hen1 Mutants to Identify Small RNA 3′ Modifications

Zhai J and Meyers BC #

025

Methodsdoi:10.1016/j.ymeth.2013.08.032

Construction of Specific Parallel Amplification of RNA Ends (SPARE) libraries for the systematic identification of plant microRNA processing intermediates

Schapire A *, Bologna NG *, Moro B, Zhai J, Meyers BC, Palatnik JF #

024

Genome Biology14(12):R145

Parallel Analysis of RNA Ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon

Jeong DH, Schmidt SA, Rymarquis LA, Park S, Ganssmann M, German MA, Accerbi M, Zhai J, Paoli ED, Fahlgren N, Fox SE, Garvin DF, Mockler TC, Carrington JC, Meyers BC, and Green PJ #

023

Science342(6165):1241089

The Amborella Genome and the Evolution of Flowering Plants

Amborella Genome Project

022

Plant Physiology162(3):1225

Comprehensive investigation of miRNAs enhanced by analysis of sequence variants, expression patterns, AGO loading and target cleavage

Jeong DH *, Thatcher SR *, Brown RS, Zhai J, Park S, Meyers BC, Green PJ #

021

BMC Genomics14:326

Physiological stressors and invasive plant infections alter the small RNA transcriptome of the rice blast fungus Magnaporthe oryzae

Raman V *, Simon SA *, Romag A, Demirci F, Mathioni SM, Zhai J, Meyers BC, Donofrio NM #

020

Genome Research(10):1675-89

Multiple RNA recognition patterns during microRNA biogenesis in plants

Bologna NG, Schapire AL, Zhai J, Chorostecki U, Boisbouvier J, Meyers BC, Palatnik J #

019

Current Opinion in Plant Biology16(2):170-9

Biogenesis and function of rice small RNAs from non-coding RNA precursors

Arikit S, Zhai J, Meyers BC #

2012

2 papers

018

Epigenetics7(7):781-95

RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats

Lee TF, Gurazada SG, Zhai J, Li S, Simon SA, Matzke MA, Chen X, Meyers BC #

017

Current Biology22(8):689-94

HESO1, a nucleotidyl transferase in Arabidopsis, uridylates unmethylated miRNAs and siRNAs to trigger their degradation

Zhao Y *, Yu Y *, Zhai J, Ramachandran V, Dinh T, Meyers BC, Mo B #, Chen X #

2011

4 papers

016

Genes & Development25(23):2540-53

MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs

Zhai J, Jeong D-H, Paoli ED, Park S, Rosen BD, Li Y, González AJ, Yan Z, Kitto Sherry L, Grusak Michael A, Jackson Scott A, Stacey Gary, Cook Douglas R, Green Pamela J, Sherrier D Janine, Meyers Blake C #

015

The Plant Journal69, 462-474

Roles of DCL4 and DCL3b in rice phased small RNA biogenesis

Song X *, Li P *, Zhai J *, Zhou M*, Ma L, Liu B, Jeong DH, Nakano M, Cao S, Liu C, Chu C, Wang X, Green P,Meyers BC, Cao X #

014

Nature480, 520-524

The Medicago genome provides insight into the evolution of rhizobial symbioses

The_International_Medicago_Initiative

013

The Plant Cell23(12):4185-207

Massive analysis of rice small RNAs: Mechanistic implications of regulated miRNAs and variants for differential target RNA cleavage

Jeong D-H, Park S, Zhai J, Gurazada SGR, Paoli ED, Meyers BC, Green PJ #

2010

4 papers

012

Nucleic Acids Research38(17):5844-5850

siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis

Yu B, Bi L, Zhai J, Agarwal M, Li S, Wu Q, Ding SW, Meyers BC, Vaucheret H, Chen X #

011

Nature463(7282):763-768

Genome sequencing and analysis of the model grass Brachypodium distachyon

The International Brachypodium Initiative

010

Current Biology20(2):R68-70. (review)

MicroRNA processing: battle of the bulge

Meyers BC, Simon SA, Zhai J

009

PNAS107(20):9027-9028. (review)

Conservation and divergence in eukaryotic DNA methylation

Lee TF, Zhai J, Meyers BC #

2009

3 papers

008

Annual Review Plant Biology60:305-333. (review)

Short-read sequencing technologies for transcriptional analyses

Simon SA, Zhai J, Nandety RS, McCormick KP, Zeng J, Mejia D, Meyers BC #

007

Plant Cell Rep28(3):469-480

Highly efficient gene silencing using perfect complementary artificial miRNA targeting AP1 or heteromeric artificial miRNA targeting AP1 and CAL genes

Park W, Zhai J, Lee JY #

006

RNAs associated with cosuppression in petunia. RNA 15(11):1965-1970

Distinct extremely abundant si

De Paoli E, Dorantes-Acosta A, Zhai J, Accerbi M, Jeong DH, Park S, Meyers BC, Jorgensen RA, Green PJ

2008

2 papers

005

PLoS Genetics4, e1000056

Small RNA-directed epigenetic natural variation in Arabidopsis thaliana

Zhai J, Liu J, Liu B, Li P, Meyers BC, Chen X, Cao X #

004

Rice1(1):52-62. (review)

The cornucopia of small RNAs in plant genomes

Simon SA, Zhai J, Zeng J, Meyers BC #

2007

2 papers

003

Plant Physiology144, 1913-1923

Mutations in the Type II protein arginine methyltransferase AtPRMT5 result in pleiotropic developmental defects in Arabidopsis

Pei Y *, Niu L *, Lu F *, Liu C*, Zhai J, Kong X, Cao X #

002

The Plant Cell19, 9-22

SDG714, a histone H3K9 methyltransferase, is involved in Tos17 DNA methylation and transposition in rice

Ding Y, Wang X, Su L, Zhai J, Cao S, Zhang D, Liu C, Bi Y, Qian Q, Cheng Z, Chu C #, Cao X #

2006

1 papers

001

The Plant Cell18, 85-103

ROR1/RPA2A, a putative replication protein A2, functions in epigenetic gene silencing and in regulation of meristem development in Arabidopsis

Xia R *, Wang J *, Liu C, Wang Y, Zhai J, Liu J, Hong X, Cao X, Zhu JK, Gong Z #

People

The whole lab, past and present.

Meet every current member and alumnus in the lab's public directory, spanning experimental biology, genomics and computational research.

Principal investigator

Jixian Zhai, PhD

Professor · School of Life Sciences · SUSTech

Single-molecule RNA biology, single-cell omics and poly(A)-mediated regulation across biological systems.

Email Faculty profile

Current members

12 people

Wenqin Lu

Research Assistant Professor

Single-cell RNA sequencing in Plant

Bo Liu

Postdoctoral Researcher

Molecular Biology and Epigenetics

Yi Shu

Postdoctoral Researcher

Plant epigenetics, Bioinformatics

Huajie Lei

PhD Student

Epigenetic regulation

Xinlong Zhu

PhD Student

RNA biology

Siteng Bi

PhD Student

Systems biology

Anqi Su

PhD Student

RNA biology

Decai Yuan

PhD Student

12591004@mail.sustech.edu.cn

Yitian Zhang

Master's Student

Bioinformatics, Genomic data analysis

Leting Chen

Master's Student

Plant epigenetics

Yanxin Wang

Master's Student

12532900@mail.sustech.edu.cn

Cailiu Liang

Research Assistant / Lab Manager

Daily Management

Alumni

Directory information follows the lab's existing public website.

31 people

Former research faculty

Yanping Long

Ph.D., Institute of Genetics and Developmental Biology, Chinese Academy of Science · Research Interests: Higher-order structure of chromosome

Former research faculty

Jinbu Jia

Professor · College of Agriculture, South China Agricultural University

Former research faculty

Xuehua Pan

Ph.D., Biochemistry and Molecular Biology, HongKong Polytechnic University · Research Interests: RNA-based therapeutics, Protein molecular biology

Former research faculty

Daoheng Hu

Associate Research Fellow · Department of Medical Genetics, · The First People's Hospital of Yunnan Province

Former research faculty

Huihui Fang

Lecturer · College of Horticulture Science, Zhejiang Agriculture and Forestry University

Former research faculty

Lidan Xiao

Ph.D., Biomedical Engineering，Zhejiang University · Research Interests: Single-cell sequencing，Kinship research，Epigenetics