4.6 Article

PIF4 enhances DNA binding of CDF2 to co-regulate target gene expression and promote Arabidopsis hypocotyl cell elongation

Related references

Note: Only part of the references are listed.
Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

Article Multidisciplinary Sciences

Spatial regulation of thermomorphogenesis by HY5 and PIF4 in Arabidopsis

Sanghwa Lee et al.

Summary: Plants undergo morphological changes collectively termed thermomorphogenesis when exposed to elevated temperature. Here the authors show that the SPA1 kinase regulates distinct thermomorphogenic responses according to tissue type by interactions with PIF4 and HY5 in shoots and roots, respectively.

NATURE COMMUNICATIONS (2021)

Article Multidisciplinary Sciences

The epidermis coordinates thermoresponsive growth through the phyB-PIF4-auxin pathway

Sara Kim et al.

NATURE COMMUNICATIONS (2020)

Review Plant Sciences

The DOF Transcription Factors in Seed and Seedling Development

Veronica Ruta et al.

PLANTS-BASEL (2020)

Review Cell Biology

Structural Biology of RNA Polymerase II Transcription: 20 Years On

Sara Osman et al.

ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 36, 2020 (2020)

Article Biochemistry & Molecular Biology

Circadian Waves of Transcriptional Repression Shape PIF-Regulated Photoperiod-Responsive Growth in Arabidopsis

Guiomar Martin et al.

CURRENT BIOLOGY (2018)

Article Biochemical Research Methods

Salmon provides fast and bias-aware quantification of transcript expression

Rob Patro et al.

NATURE METHODS (2017)

Article Biochemistry & Molecular Biology

A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

Runxuan Zhang et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemical Research Methods

cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing

Andrey Kechin et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2017)

Article Multidisciplinary Sciences

Cryptochrome 1 interacts with PIF4 to regulate high temperature-mediated hypocotyl elongation in response to blue light

Dingbang Ma et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Biochemistry & Molecular Biology

Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light

Ullas V. Pedmale et al.

Article Multidisciplinary Sciences

TOC1-PIF4 interaction mediates the circadian gating of thermoresponsive growth in Arabidopsis

Jia-Ying Zhu et al.

NATURE COMMUNICATIONS (2016)

Letter Biochemical Research Methods

The I-TASSER Suite: protein structure and function prediction

Jianyi Yang et al.

NATURE METHODS (2015)

Review Genetics & Heredity

Integrating circadian dynamics with physiological processes in plants

Kathleen Greenham et al.

NATURE REVIEWS GENETICS (2015)

Article Plant Sciences

A simple and versatile cell wall staining protocol to study plant reproduction

Thomas J. Musielak et al.

PLANT REPRODUCTION (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

Motif-based analysis of large nucleotide data sets using MEME-ChIP

Wenxiu Ma et al.

NATURE PROTOCOLS (2014)

Review Biochemistry & Molecular Biology

PIFs: Systems Integrators in Plant Development

Pablo Leivar et al.

PLANT CELL (2014)

Review Biochemistry & Molecular Biology

Absence of a simple code: how transcription factors read the genome

Matthew Slattery et al.

TRENDS IN BIOCHEMICAL SCIENCES (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Multidisciplinary Sciences

Naturally occurring allele diversity allows potato cultivation in northern latitudes

Bjorn Kloosterman et al.

NATURE (2013)

Article Multidisciplinary Sciences

Probing Allostery Through DNA

Sangjin Kim et al.

SCIENCE (2013)

Article Cell Biology

Linking photoreceptor excitation to changes in plant architecture

Lin Li et al.

GENES & DEVELOPMENT (2012)

Article Multidisciplinary Sciences

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

Caryn S. Ross-Innes et al.

NATURE (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemistry & Molecular Biology

Inferring direct DNA binding from ChIP-seq

Timothy L. Bailey et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

Matthew Slattery et al.

Article Biochemical Research Methods

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

Lihua J. Zhu et al.

BMC BIOINFORMATICS (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

High Temperature-Medated Adaptations in Plant Architecture Require the bHLH Transcription Factor PIF4

Maria A. Koini et al.

CURRENT BIOLOGY (2009)

Article Multidisciplinary Sciences

Combinatorial binding predicts spatio-temporal cis-regulatory activity

Robert P. Zinzen et al.

NATURE (2009)

Article Multidisciplinary Sciences

Mechanistic duality of transcription factor function in phytochrome signaling

Bassern Al-Sady et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Biotechnology & Applied Microbiology

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang et al.

GENOME BIOLOGY (2008)

Article Multidisciplinary Sciences

Rhythmic growth explained by coincidence between internal and external cues

Kazunari Nozue et al.

NATURE (2007)

Article Biochemical Research Methods

Improved scoring of functional groups from gene expression data by decorrelating GO graph structure

Adrian Alexa et al.

BIOINFORMATICS (2006)

Review Cell Biology

Genomic regulatory networks and animal development

A Stathopoulos et al.

DEVELOPMENTAL CELL (2005)

Article Multidisciplinary Sciences

Arabidopsis transcription factors:: Genome-wide comparative analysis among eukaryotes

JL Riechmann et al.

SCIENCE (2000)