Plant synthetic epigenomic engineering for crop improvement

RNA N6-methyladenosine modification promotes auxin biosynthesis required for male meiosis in rice

(2022) Peng Cheng et al.   DEVELOPMENTAL CELL

FIONA1‐Mediated m 6 A Modification Regulates the Floral Transition in Arabidopsis

(2022) Tao Xu et al.   Advanced Science

SMOC: a smart model for open chromatin region prediction in rice genomes

(2022) Weijun Guo et al.   Journal of Genetics and Genomics

A histone H3K27me3 reader cooperates with a family of PHD finger‐containing proteins to regulate flowering time in Arabidopsis

(2021) Feng Qian et al.   Journal of Integrative Plant Biology

Efficient assembly of nanopore reads via highly accurate and intact error correction

(2021) Ying Chen et al.   Nature Communications

Genome engineering for crop improvement and future agriculture

(2021) Caixia Gao   CELL

Reorganization of the 3D chromatin architecture of rice genomes during heat stress

(2021) Zhe Liang et al.   BMC BIOLOGY

Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing

(2021) James K. Nuñez et al.   CELL

A cis-regulatory atlas in maize at single-cell resolution

(2021) Alexandre P. Marand et al.   CELL

CRISPR/dCas-mediated transcriptional and epigenetic regulation in plants

(2021) Changtian Pan et al.   CURRENT OPINION IN PLANT BIOLOGY

Arabidopsis N6-methyladenosine reader CPSF30-L recognizes FUE signals to control polyadenylation site choice in liquid-like nuclear bodies

(2021) Peizhe Song et al.   Molecular Plant

CPSF30-L-mediated recognition of mRNA m6A modification controls alternative polyadenylation of nitrate signaling-related gene transcripts in Arabidopsis

(2021) Yifeng Hou et al.   Molecular Plant

N 6 ‐Methyladenosine mRNA methylation is important for salt stress tolerance in Arabidopsis

(2021) Jianzhong Hu et al.   PLANT JOURNAL

Single-cell transcriptome atlas and chromatin accessibility landscape reveal differentiation trajectories in the rice root

(2021) Tian-Qi Zhang et al.   Nature Communications

OsEDM2L mediates m 6 A of EAT1 transcript for proper alternative splicing and polyadenylation regulating rice tapetal degradation

(2021) Kun Ma et al.   Journal of Integrative Plant Biology

Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore

(2021) Ploy N. Pratanwanich et al.   NATURE BIOTECHNOLOGY

RNA demethylation increases the yield and biomass of rice and potato plants in field trials

(2021) Qiong Yu et al.   NATURE BIOTECHNOLOGY

A deep learning approach to automate whole‐genome prediction of diverse epigenomic modifications in plants

(2021) Yifan Wang et al.   NEW PHYTOLOGIST

Targeted DNA demethylation produces heritable epialleles in rice

(2021) Shanjie Tang et al.   Science China-Life Sciences

Precise editing of methylated cytosine in Arabidopsis thaliana using a human APOBEC3Bctd-Cas9 fusion

(2021) Zhi-Hong Liu et al.   Science China-Life Sciences

Crosstalk between epitranscriptomic and epigenetic mechanisms in gene regulation

(2021) Ryan L. Kan et al.   TRENDS IN GENETICS

Rice functional genomics: decades’ efforts and roads ahead

(2021) Rongzhi Chen et al.   Science China-Life Sciences

Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives

(2020) Wanneng Yang et al.   Molecular Plant

eRice: a refined epigenomic platform for japonica and indica rice

(2020) Pingxian Zhang et al.   PLANT BIOTECHNOLOGY JOURNAL

Enhanced sustainable green revolution yield via nitrogen-responsive chromatin modulation in rice

(2020) Kun Wu et al.   SCIENCE

OsNSUN2-Mediated 5-Methylcytosine mRNA Modification Enhances Rice Adaptation to High Temperature

(2020) Yongyan Tang et al.   DEVELOPMENTAL CELL

Design of orthogonal regulatory systems for modulating gene expression in plants

(2020) Michael S. Belcher et al.   Nature Chemical Biology

Genomic Prediction of Maize Micro‐Phenotypes Provides Insights for Optimizing Selection and Mining Diversity

(2020) Xiaoqing Yu et al.   PLANT BIOTECHNOLOGY JOURNAL

High‐throughput phenotyping accelerates the dissection of the dynamic genetic architecture of plant growth and yield improvement in rapeseed

(2020) Haitao Li et al.   PLANT BIOTECHNOLOGY JOURNAL

Light-powered CO2 fixation in a chloroplast mimic with natural and synthetic parts

(2020) Tarryn E. Miller et al.   SCIENCE

Integrative analysis of reference epigenomes in 20 rice varieties

(2020) Lun Zhao et al.   Nature Communications

Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors

(2020) Andrew V. Anzalone et al.   NATURE BIOTECHNOLOGY

Optogenetic control of gene expression in plants in the presence of ambient white light

(2020) Rocio Ochoa-Fernandez et al.   NATURE METHODS

Using synthetic biology to overcome barriers to stable expression of nitrogenase in eukaryotic organelles

(2020) Nan Xiang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA 5-Methylcytosine Controls Plant Development and Environmental Adaptation

(2020) Pingxian Zhang et al.   TRENDS IN PLANT SCIENCE

DNA N6-Methyladenine Modification in Wild and Cultivated Soybeans Reveals Different Patterns in Nucleus and Cytoplasm

(2020) De-Hui Yuan et al.   Frontiers in Genetics

Intrinsic and Extrinsic Programming of Product Chain Length and Release Mode in Fungal Collaborating Iterative Polyketide Synthases

(2020) Chen Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Identification of the human DPR core promoter element using machine learning

(2020) Long Vo ngoc et al.   NATURE

Predicting the efficiency of prime editing guide RNAs in human cells

(2020) Hui Kwon Kim et al.   NATURE BIOTECHNOLOGY

Applications of CRISPR–Cas in agriculture and plant biotechnology

(2020) Haocheng Zhu et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Installation of C 4 photosynthetic pathway enzymes in rice using a single construct

(2020) Maria Ermakova et al.   PLANT BIOTECHNOLOGY JOURNAL

A DNA Methylation Reader-Chaperone Regulator-Transcription Factor Complex Activates OsHKT1;5 Expression during Salinity Stress

(2020) Jie Wang et al.   PLANT CELL

Ligand-recognizing motifs in plant LysM receptors are major determinants of specificity

(2020) Zoltan Bozsoki et al.   SCIENCE

Transcriptional landscape of rice roots at the single-cell resolution

(2020) Qing Liu et al.   Molecular Plant

An SHR–SCR module specifies legume cortical cell fate to enable nodulation

(2020) Wentao Dong et al.   NATURE

Engineering 6-phosphogluconate dehydrogenase improves grain yield in heat-stressed maize

(2020) Camila Ribeiro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering a New Chloroplastic Photorespiratory Bypass to Increase Photosynthetic Efficiency and Productivity in Rice

(2019) Bo-Ran Shen et al.   Molecular Plant

Synthetic glycolate metabolism pathways stimulate crop growth and productivity in the field

(2019) Paul F. South et al.   SCIENCE

Artificial photosynthetic cell producing energy for protein synthesis

(2019) Samuel Berhanu et al.   Nature Communications

The Arabidopsis H3K27me3 demethylase JUMONJI 13 is a temperature and photoperiod dependent flowering repressor

(2019) Shuzhi Zheng et al.   Nature Communications

Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems

(2019) Ashot Papikian et al.   Nature Communications

Single gametophyte sequencing reveals that crossover events differ between sexes in maize

(2019) Cheng Luo et al.   Nature Communications

Optogenetic manipulation of stomatal kinetics improves carbon assimilation, water use, and growth

(2019) M. Papanatsiou et al.   SCIENCE

Histone H3 trimethylation at lysine 36 guides m6A RNA modification co-transcriptionally

(2019) Huilin Huang et al.   NATURE

A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root

(2019) Tian-Qi Zhang et al.   Molecular Plant

Arabidopsis histone H3K4 demethylase JMJ 17 functions in dehydration stress response

(2019) Shuangzhan Huang et al.   NEW PHYTOLOGIST

The subunit of RNA N6-methyladenosine methyltransferase OsFIP regulates early degeneration of microspores in rice

(2019) Fan Zhang et al.   PLoS Genetics

Advances in epigenetics link genetics to the environment and disease

(2019) Giacomo Cavalli et al.   NATURE

Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data

(2019) Qian Liu et al.   Nature Communications

m5C Methylation Guides Systemic Transport of Messenger RNA over Graft Junctions in Plants

(2019) Lei Yang et al.   CURRENT BIOLOGY

Programmable RNA N6-methyladenosine editing by CRISPR-Cas9 conjugates

(2019) Xiao-Min Liu et al.   Nature Chemical Biology

Functional interpretation of genetic variants using deep learning predicts impact on chromatin accessibility and histone modification

(2019) Gabriel E Hoffman et al.   NUCLEIC ACIDS RESEARCH

Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation

(2019) Lun Zhao et al.   Nature Communications

Role of Mammalian DNA Methyltransferases in Development

(2019) Zhiyuan Chen et al.   Annual Review of Biochemistry

Epigenetic Modifications of mRNA and DNA in Plants

(2019) Zhe Liang et al.   Molecular Plant

DNA N 6 -Adenine Methylation in Arabidopsis thaliana

(2018) Zhe Liang et al.   DEVELOPMENTAL CELL

Mapping and characterizing N6-methyladenine in eukaryotic genomes using single-molecule real-time sequencing

(2018) Shijia Zhu et al.   GENOME RESEARCH

N 6 -Methyladenine DNA Modification in the Human Genome

(2018) Chuan-Le Xiao et al.   MOLECULAR CELL

Genome-Wide Association Studies of Image Traits Reveal Genetic Architecture of Drought Resistance in Rice

(2018) Zilong Guo et al.   Molecular Plant

Telobox motifs recruit CLF/SWN–PRC2 for H3K27me3 deposition via TRB factors in Arabidopsis

(2018) Yue Zhou et al.   NATURE GENETICS

Dynamics and function of DNA methylation in plants

(2018) Huiming Zhang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

An m6A-YTH Module Controls Developmental Timing and Morphogenesis in Arabidopsis

(2018) Laura Arribas-Hernández et al.   PLANT CELL

The m6A Reader ECT2 Controls Trichome Morphology by Affecting mRNA Stability in Arabidopsis

(2018) Lian-Huan Wei et al.   PLANT CELL

Targeted DNA demethylation of theArabidopsisgenome using the human TET1 catalytic domain

(2018) Javier Gallego-Bartolomé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL

(2018) Shuiming Qian et al.   Nature Communications

Polycomb-mediated gene silencing by the BAH–EMF1 complex in plants

(2018) Zicong Li et al.   NATURE GENETICS

Unexpected synergistic HIV neutralization by a triple microbicide produced in rice endosperm

(2018) Evangelia Vamvaka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mre11 complex links sister chromatids to promote repair of a collapsed replication fork

(2018) Min Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering Epigenetic Regulation Using Synthetic Read-Write Modules

(2018) Minhee Park et al.   CELL

N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses

(2018) Qian Zhang et al.   Molecular Plant

From Golden Rice to aSTARice: Bioengineering Astaxanthin Biosynthesis in Rice Endosperm

(2018) Qinlong Zhu et al.   Molecular Plant

De novo genome assembly of the stress tolerant forest species Casuarina equisetifolia provides insight into secondary growth

(2018) Gongfu Ye et al.   PLANT JOURNAL

Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA

(2018) Xinyue Zhao et al.   Nature Communications

NSUN2-Mediated m5C Methylation and METTL3/METTL14-Mediated m6A Methylation Cooperatively Enhance p21 Translation

(2017) Qiu Li et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

5-Methylcytosine RNA Methylation in Arabidopsis Thaliana

(2017) Xuean Cui et al.   Molecular Plant

Development of “Purple Endosperm Rice” by Engineering Anthocyanin Biosynthesis in the Endosperm with a High-Efficiency Transgene Stacking System

(2017) Qinlong Zhu et al.   Molecular Plant

Identification of factors required for m6 A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

(2017) Kamil Růžička et al.   NEW PHYTOLOGIST

ALKBH10B Is an RNAN6-Methyladenosine Demethylase Affecting Arabidopsis Floral Transition

(2017) Hong-Chao Duan et al.   PLANT CELL

Transcriptome-Wide Mapping of RNA 5-Methylcytosine in Arabidopsis mRNAs and Noncoding RNAs

(2017) Rakesh David et al.   PLANT CELL

Arabidopsism6A demethylase activity modulates viral infection of a plant virus and the m6A abundance in its genomic RNAs

(2017) Mireya Martínez-Pérez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance

(2017) Yiwen Deng et al.   SCIENCE

A natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice

(2017) Lin Zhang et al.   Nature Communications

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

(2016) Taiji Kawakatsu et al.   CELL

N 6 -Methyladenosine RNA Modification Regulates Shoot Stem Cell Fate in Arabidopsis

(2016) Lisha Shen et al.   DEVELOPMENTAL CELL

Agrochemical control of plant water use using engineered abscisic acid receptors

(2015) Sang-Youl Park et al.   NATURE

PcG and trxG in plants – friends or foes

(2015) Li Pu et al.   TRENDS IN GENETICS

SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation

(2014) Lianna M. Johnson et al.   NATURE

Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state

(2014) Pedro Crevillén et al.   NATURE

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility

(2012) Guanqun Zheng et al.   MOLECULAR CELL

Synthetic Reversal of Epigenetic Silencing

(2011) Karmella A. Haynes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO

(2011) Guifang Jia et al.   Nature Chemical Biology

Epigenome-wide association studies for common human diseases

(2011) Vardhman K. Rakyan et al.   NATURE REVIEWS GENETICS

A synthetic mammalian gene circuit reveals antituberculosis compounds

(2008) W. Weber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA