Integrating ATAC-seq and RNA-seq to identify differentially expressed genes with chromatin-accessible changes during photosynthetic establishment in Populus leaves

HY5: A Pivotal Regulator of Light-Dependent Development in Higher Plants

(2022) Yuntao Xiao et al.   Frontiers in Plant Science

PdeHCA2 affects biomass in Populus by regulating plant architecture, the transition from primary to secondary growth, and photosynthesis

(2022) Biligen-Gaowa Zhao et al.   PLANTA

FLOWERING LOCUS T paralogs control the annual growth cycle in Populus trees

(2022) Domenique André et al.   CURRENT BIOLOGY

From genes to networks: The genetic control of leaf development

(2021) Hongfeng Wang et al.   Journal of Integrative Plant Biology

Plant-specific Dof transcription factors VASCULAR-RELATED DOF1 and VASCULAR-RELATED DOF2 regulate vascular cell differentiation and lignin biosynthesis in Arabidopsis

(2020) Vasagi Ramachandran et al.   PLANT MOLECULAR BIOLOGY

Plastome Sequences Help to Resolve Deep-Level Relationships of Populus in the Family Salicaceae

(2019) Dan Zong et al.   Frontiers in Plant Science

The transcription factor GATA10 regulates fertility conversion of a two‐line hybrid tms5 mutant rice via the modulation of Ub L40 expression

(2019) Jing Jin et al.   Journal of Integrative Plant Biology

The developmental dynamics of the Populus stem transcriptome

(2018) Qing Chao et al.   PLANT BIOTECHNOLOGY JOURNAL

Genetic architecture underlying the lignin biosynthesis pathway involves noncoding RNAs and transcription factors for growth and wood properties in Populus

(2018) Mingyang Quan et al.   PLANT BIOTECHNOLOGY JOURNAL

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

Prospects for enhancing leaf photosynthetic capacity by manipulating mesophyll cell morphology

(2018) Tao Ren et al.   JOURNAL OF EXPERIMENTAL BOTANY

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

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

The light response of mesophyll conductance is controlled by structure across leaf profiles

(2017) Guillaume Théroux-Rancourt et al.   PLANT CELL AND ENVIRONMENT

Cell density and airspace patterning in the leaf can be manipulated to increase leaf photosynthetic capacity

(2017) Christoph Lehmeier et al.   PLANT JOURNAL

Increasing Leaf Vein Density via Mutagenesis in Rice Results in an Enhanced Rate of Photosynthesis, Smaller Cell Sizes and Can Reduce Interveinal Mesophyll Cell Number

(2017) Aryo B. Feldman et al.   Frontiers in Plant Science

Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes

(2016) Zefu Lu et al.   NUCLEIC ACIDS RESEARCH

EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments

(2016) Olivia Wilkins et al.   PLANT CELL

Active suppression of a leaf meristem orchestrates determinate leaf growth

(2016) John Paul Alvarez et al.   eLife

Plant expansins: diversity and interactions with plant cell walls

(2015) Daniel J Cosgrove   CURRENT OPINION IN PLANT BIOLOGY

Leaf expansion in Arabidopsis is controlled by a TCP-NGA regulatory module likely conserved in distantly related species

(2015) Patricia Ballester et al.   PHYSIOLOGIA PLANTARUM

SCARECROW, SCR-LIKE 23 and SHORT-ROOT control bundle sheath cell fate and function inArabidopsis thaliana

(2014) Hongchang Cui et al.   PLANT JOURNAL

Genome-Wide Analysis of Histone Modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica

(2013) Zhou Du et al.   Molecular Plant

PtrHB7, a class III HD-Zip Gene, Plays a Critical Role in Regulation of Vascular Cambium Differentiation in Populus

(2013) Yingying Zhu et al.   Molecular Plant

The homeodomain-leucine zipper ATHB23, a phytochrome B-interacting protein, is important for phytochrome B-mediated red light signaling

(2013) Hyunmo Choi et al.   PHYSIOLOGIA PLANTARUM

Constitutively Elevated Salicylic Acid Levels Alter Photosynthesis and Oxidative State but Not Growth in Transgenic Populus

(2013) L.-J. Xue et al.   PLANT CELL

Functional characterization of a plastid-specific ribosomal protein PSRP2 in Arabidopsis thaliana under abiotic stress conditions

(2013) Tao Xu et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate

(2013) Toshiyuki Takai et al.   Scientific Reports

Exit from Proliferation during Leaf Development in Arabidopsis thaliana: A Not-So-Gradual Process

(2012) Megan Andriankaja et al.   DEVELOPMENTAL CELL

Knockdown expression of Apc11 leads to cell-cycle distribution reduction in G2/M phase

(2012) Y.-J. Shi et al.   GENETICS AND MOLECULAR RESEARCH

Deletion of MP/ARF5 domains III and IV reveals a requirement for Aux/IAA regulation in Arabidopsis leaf vascular patterning

(2012) Naden T. Krogan et al.   NEW PHYTOLOGIST

Opinion: Prospects for improving photosynthesis by altering leaf anatomy

(2012) Danny Tholen et al.   PLANT SCIENCE

Hypersalinity effects on leaf ultrastructure and physiology in the mangrove Avicennia marina

(2011) Gonasageran Naidoo et al.   FLORA

Leaf and root pectin methylesterase activity and 13C/12C stable isotopic ratio measurements of methanol emissions give insight into methanol production in Lycopersicon esculentum

(2011) Patricia Yoshino Oikawa et al.   NEW PHYTOLOGIST

Characterization of the plasma membrane proteins and receptor-like kinases associated with secondary vascular differentiation in poplar

(2011) Dongliang Song et al.   PLANT MOLECULAR BIOLOGY

Organ Size Regulation in Plants: Insights from Compensation

(2011) Gorou Horiguchi et al.   Frontiers in Plant Science

Regulatory Mechanisms for Specification and Patterning of Plant Vascular Tissues

(2010) Ana Caño-Delgado et al.   Annual Review of Cell and Developmental Biology

An R package for spatial coverage sampling and random sampling from compact geographical strata by k-means

(2010) D.J.J. Walvoort et al.   COMPUTERS & GEOSCIENCES

Regulation of plant biomass production

(2010) Taku Demura et al.   CURRENT OPINION IN PLANT BIOLOGY

Simultaneous activation of SHR and ATHB8 expression defines switch to preprocambial cell state in Arabidopsis leaf development

(2010) Jason Gardiner et al.   DEVELOPMENTAL DYNAMICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The signalling peptide EPFL9 is a positive regulator of stomatal development

(2010) Lee Hunt et al.   NEW PHYTOLOGIST

Leaf Functional Anatomy in Relation to Photosynthesis

(2010) I. Terashima et al.   PLANT PHYSIOLOGY

Evolutionary conservation of the transcriptional network regulating secondary cell wall biosynthesis

(2010) Ruiqin Zhong et al.   TRENDS IN PLANT SCIENCE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Overexpression of the NAC transcription factor family gene ANAC036 results in a dwarf phenotype in Arabidopsis thaliana

(2009) Hiroaki Kato et al.   JOURNAL OF PLANT PHYSIOLOGY

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

The DOF transcription factor OBP1 is involved in cell cycle regulation inArabidopsis thaliana

(2008) Aleksandra Skirycz et al.   PLANT JOURNAL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY