Integrating ATAC-seq and RNA-seq Reveals the Dynamics of Chromatin Accessibility and Gene Expression in Apple Response to Drought

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

(2021) Zhe Liang et al.   BMC BIOLOGY

Characterization of Chromatin Accessibility and Gene Expression upon Cold Stress Reveals that the RAV1 Transcription Factor Functions in Cold Response in Vitis Amurensis

(2021) Chong Ren et al.   PLANT AND CELL PHYSIOLOGY

Open chromatin in grapevine marks candidate CREs and with other chromatin features correlates with gene expression

(2021) Rachel Schwope et al.   PLANT JOURNAL

Transcription Factors Interact with ABA through Gene Expression and Signaling Pathways to Mitigate Drought and Salinity Stress

(2021) Quaid Hussain et al.   Biomolecules

Genome-wide characterization of Brassica napus INDETERMINATE DOMAIN genes reveals a negative role for BnA08.IDD7 in plant development

(2021) Bangyang Sun et al.   INDUSTRIAL CROPS AND PRODUCTS

Abiotic stress responses in plants

(2021) Huiming Zhang et al.   NATURE REVIEWS GENETICS

A lamin‐like protein OsNMCP1 regulates drought resistance and root growth through chromatin accessibility modulation by interacting with a chromatin remodeler OsSWI3C in rice

(2020) Jun Yang et al.   NEW PHYTOLOGIST

The physiology of plant responses to drought

(2020) Aditi Gupta et al.   SCIENCE

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

(2020) Chengjie Chen et al.   Molecular Plant

GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5′ and 3′ ends of its target genes

(2020) Soonkap Kim et al.   NUCLEIC ACIDS RESEARCH

Transcription factors as key molecular target to strengthen the drought stress tolerance in plants

(2020) Mrinalini Manna et al.   PHYSIOLOGIA PLANTARUM

A novel ABA functional analogue B2 enhances drought tolerance in wheat

(2019) Yuyi Zhou et al.   Scientific Reports

The AP2/ERF Transcription Factor TINY Modulates Brassinosteroid-Regulated Plant Growth and Drought Responses in Arabidopsis

(2019) Zhouli Xie et al.   PLANT CELL

Contribution of methylation regulation of MpDREB2A promoter to drought resistance of Mauls prunifolia

(2019) Xuewei Li et al.   PLANT AND SOIL

Redox‐sensitive bZIP 68 plays a role in balancing stress tolerance with growth in Arabidopsis

(2019) Yimin Li et al.   PLANT JOURNAL

Physiological and transcriptomic analyses of roots from Malus sieversii under drought stress

(2019) Da-li GENG et al.   Journal of Integrative Agriculture

The Polycomb protein LHP 1 regulates Arabidopsis thaliana stress responses through the repression of the MYC 2‐dependent branch of immunity

(2019) J.S. Ramirez‐Prado et al.   PLANT JOURNAL

Epigenetic regulation in plant abiotic stress responses

(2019) Ya‐Nan Chang et al.   Journal of Integrative Plant Biology

Changes in chromatin accessibility between Arabidopsis stem cells and mesophyll cells illuminate cell type-specific transcription factor networks

(2018) Paja Sijacic et al.   PLANT JOURNAL

Meta-analysis of transcriptomic responses to biotic and abiotic stress in tomato

(2018) Elham Ashrafi-Dehkordi et al.   PeerJ

MdMYB88 and MdMYB124 Enhance Drought Tolerance by Modulating Root Vessels and Cell Walls in Apple

(2018) Dali Geng et al.   PLANT PHYSIOLOGY

Identification of water use efficiency related genes in ‘Garnem’ almond-peach rootstock using time-course transcriptome analysis

(2018) Beatriz Bielsa et al.   PLoS One

Phytohormones enhanced drought tolerance in plants: a coping strategy

(2018) Abid Ullah et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

WRKY transcription factors in plant responses to stresses

(2017) Jingjing Jiang et al.   Journal of Integrative Plant Biology

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

(2017) Nicolas Daccord et al.   NATURE GENETICS

Single-base methylome analysis reveals dynamic epigenomic differences associated with water deficit in apple

(2017) Jidi Xu et al.   PLANT BIOTECHNOLOGY JOURNAL

Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules

(2017) Kelsey A. Maher et al.   PLANT CELL

SPL13 regulates shoot branching and flowering time in Medicago sativa

(2017) Ruimin Gao et al.   PLANT MOLECULAR BIOLOGY

MicroRNA156 improves drought stress tolerance in alfalfa ( Medicago sativa ) by silencing SPL13

(2017) Muhammad Arshad et al.   PLANT SCIENCE

Longitudinal patterning in roots: a GATA2–auxin interaction underlies and maintains the root transition domain

(2017) Keni Jiang et al.   PLANTA

Genome-Wide Investigation of WRKY Transcription Factors Involved in Terminal Drought Stress Response in Common Bean

(2017) Jing Wu et al.   Frontiers in Plant Science

The MAPKKK gene family in cassava: Genome-wide identification and expression analysis against drought stress

(2017) Jianqiu Ye et al.   Scientific Reports

A Direct Link between Abscisic Acid Sensing and the Chromatin-Remodeling ATPase BRAHMA via Core ABA Signaling Pathway Components

(2016) Marta Peirats-Llobet et al.   Molecular Plant

Transcription factors involved in drought tolerance and their possible role in developing drought tolerant cultivars with emphasis on wheat (Triticum aestivum L.)

(2016) Vijay Gahlaut et al.   THEORETICAL AND APPLIED GENETICS

The Plant Heat Stress Transcription Factors (HSFs): Structure, Regulation, and Function in Response to Abiotic Stresses

(2016) Meng Guo et al.   Frontiers in Plant Science

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Arabidopsis thalianaHomeoBox 1 (AtHB1), a Homedomain-Leucine Zipper I (HD-Zip I) transcription factor, is regulated by PHYTOCHROME-INTERACTING FACTOR 1 to promote hypocotyl elongation

(2015) Matías Capella et al.   NEW PHYTOLOGIST

Erratum: OsTCP19 influences developmental and abiotic stress signaling by modulating ABI4-mediated pathways

(2015) Pradipto Mukhopadhyay et al.   Scientific Reports

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Reference genes for transcriptional analysis of flowering and fruit ripening stages in apple (Malus × domestica Borkh.)

(2014) Pâmela Perini et al.   MOLECULAR BREEDING

Tandem CCCH Zinc Finger Proteins in Plant Growth, Development and Stress Response

(2014) Srimathi P. Bogamuwa et al.   PLANT AND CELL PHYSIOLOGY

Role of chromatin in water stress responses in plants

(2013) Soon-Ki Han et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

Functional study of TCP23 in Arabidopsis thaliana during plant development

(2013) Emilia Balsemão-Pires et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Analysis of the role of Arabidopsis class I TCP genes AtTCP7, AtTCP8, AtTCP22, and AtTCP23 in leaf development

(2013) José A. Aguilar-Martínez et al.   Frontiers in Plant Science

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SWI2/SNF2 Chromatin Remodeling ATPase BRAHMA Represses Abscisic Acid Responses in the Absence of the Stress Stimulus in Arabidopsis

(2012) S.-K. Han et al.   PLANT CELL

The homeodomain-leucine zipper (HD-Zip) class I transcription factors ATHB7 and ATHB12 modulate abscisic acid signalling by regulating protein phosphatase 2C and abscisic acid receptor gene activities

(2012) Ana Elisa Valdés et al.   PLANT MOLECULAR BIOLOGY

Identification of a MYB3R gene involved in drought, salt and cold stress in wheat (Triticum aestivum L.)

(2011) Hongsheng Cai et al.   GENE

WRKY transcription factors: key components in abscisic acid signalling

(2011) Deena L. Rushton et al.   PLANT BIOTECHNOLOGY JOURNAL

The Jasmonate-ZIM Domain Proteins Interact with the R2R3-MYB Transcription Factors MYB21 and MYB24 to Affect Jasmonate-Regulated Stamen Development in Arabidopsis

(2011) S. Song et al.   PLANT CELL

Arabidopsis thaliana WRKY25, WRKY26, and WRKY33 coordinate induction of plant thermotolerance

(2011) Shujia Li et al.   PLANTA

Integration of Light- and Brassinosteroid-Signaling Pathways by a GATA Transcription Factor in Arabidopsis

(2010) Xiao-Min Luo et al.   DEVELOPMENTAL CELL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The Phytochrome-Interacting Factor PIF7 Negatively Regulates DREB1 Expression under Circadian Control in Arabidopsis

(2009) S. Kidokoro et al.   PLANT PHYSIOLOGY

Abscisic Acid-mediated Epigenetic Processes in Plant Development and Stress Responses

(2008) Viswanathan Chinnusamy et al.   Journal of Integrative Plant Biology

HAB1-SWI3B Interaction Reveals a Link between Abscisic Acid Signaling and Putative SWI/SNF Chromatin-Remodeling Complexes in Arabidopsis

(2008) A. Saez et al.   PLANT CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY