(Q50420539)

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Chromatin accessibility changes between Arabidopsis stem cells and mesophyll cells illuminate cell type-specific transcription factor networks

scientific article published on 7 March 2018

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Europe PubMed Central

PubMed publication ID

13 March 2018

http://europepmc.org/abstract/MED/29513366

Chromatin accessibility changes between Arabidopsis stem cells and mesophyll cells illuminate cell type-specific transcription factor networks (English)

1 reference

Europe PubMed Central

PubMed publication ID

13 March 2018

http://europepmc.org/abstract/MED/29513366

author name string

Paja Sijacic

1

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29513366%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Marko Bajic

2

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29513366%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Elizabeth C McKinney

3

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29513366%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Richard B Meagher

4

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29513366%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Roger B Deal

5

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Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29513366%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

publication date

7 March 2018

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Europe PubMed Central

PubMed publication ID

13 March 2018

http://europepmc.org/abstract/MED/29513366

The Plant Journal

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Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29513366%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

94

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Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29513366%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

2

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29513366%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

215-231

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29513366%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The stem cell population of Arabidopsis shoot meristems in maintained by a regulatory loop between the CLAVATA and WUSCHEL genes.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Regulation of CLV3 expression by two homeobox genes in Arabidopsis.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Arabidopsis ERF4 is a transcriptional repressor capable of modulating ethylene and abscisic acid responses

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

TCP transcription factors control the morphology of shoot lateral organs via negative regulation of the expression of boundary-specific genes in Arabidopsis

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Unique and overlapping expression patterns among members of photosynthesis-associated nuclear gene families in Arabidopsis

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Gene expression map of the Arabidopsis shoot apical meristem stem cell niche

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

PIF3 is a repressor of chloroplast development

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The Sequence Alignment/Map format and SAMtools

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Twenty years on: the inner workings of the shoot apical meristem, a developmental dynamo

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

agriGO: a GO analysis toolkit for the agricultural community

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A simple method for gene expression and chromatin profiling of individual cell types within a tissue

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

PIFs: pivotal components in a cellular signaling hub

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A novel aux/IAA28 signaling cascade activates GATA23-dependent specification of lateral root founder cell identity

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Roles of arabidopsis WRKY18, WRKY40 and WRKY60 transcription factors in plant responses to abscisic acid and abiotic stress

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

FIMO: scanning for occurrences of a given motif

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

MEME-ChIP: motif analysis of large DNA datasets

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Organogenesis from stem cells in planta: multiple feedback loops integrating molecular and mechanical signals

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Ethylene-responsive element-binding factor 5, ERF5, is involved in chitin-induced innate immunity response

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Fast gapped-read alignment with Bowtie 2

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Transcription factors: from enhancer binding to developmental control

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The accessible chromatin landscape of the human genome

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Circuitry and dynamics of human transcription factor regulatory networks

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A quartet of PIF bHLH factors provides a transcriptionally centered signaling hub that regulates seedling morphogenesis through differential expression-patterning of shared target genes in Arabidopsis.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Antagonistic basic helix-loop-helix/bZIP transcription factors form transcriptional modules that integrate light and reactive oxygen species signaling in Arabidopsis

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Genome-scale mapping of DNase I hypersensitivity

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Convergence of auxin and gibberellin signaling on the regulation of the GATA transcription factors GNC and GNL in Arabidopsis thaliana

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

PAVIS: a tool for Peak Annotation and Visualization.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The arabidopsis IDD14, IDD15, and IDD16 cooperatively regulate lateral organ morphogenesis and gravitropism by promoting auxin biosynthesis and transport

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Regulation of epidermal cell fate in Arabidopsis roots: the importance of multiple feedback loops

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

DELLA protein functions as a transcriptional activator through the DNA binding of the indeterminate domain family proteins.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The HY5-PIF regulatory module coordinates light and temperature control of photosynthetic gene transcription

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A high-resolution gene expression map of the Arabidopsis shoot meristem stem cell niche

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Combinatorial complexity in a transcriptionally centered signaling hub in Arabidopsis.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Determination and inference of eukaryotic transcription factor sequence specificity

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Chromatin dynamics in the regulation of cell fate allocation during early embryogenesis

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Tissue-specific clocks in Arabidopsis show asymmetric coupling

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Growth control: brassinosteroid activity gets context

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

B-GATA transcription factors - insights into their structure, regulation, and role in plant development

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

RSAT 2015: Regulatory Sequence Analysis Tools.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The Arabidopsis thaliana TCP transcription factors: A broadening horizon beyond development

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Transcriptional control of tissue formation throughout root development

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Versatile roles of brassinosteroid in plants in the context of its homoeostasis, signaling and crosstalks

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mapping nucleosome positions using DNase-seq

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Cell Fate Determination and the Switch from Diffuse Growth to Planar Polarity in Arabidopsis Root Epidermal Cells

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

LLM-Domain Containing B-GATA Factors Control Different Aspects of Cytokinin-Regulated Development in Arabidopsis thaliana

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

deepTools2: a next generation web server for deep-sequencing data analysis

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Active suppression of a leaf meristem orchestrates determinate leaf growth

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

ERF105 is a transcription factor gene of Arabidopsis thaliana required for freezing tolerance and cold acclimation.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Induced Genome-Wide Binding of Three Arabidopsis WRKY Transcription Factors during Early MAMP-Triggered Immunity.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

TCP Transcription Factors at the Interface between Environmental Challenges and the Plant's Growth Responses

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Overexpression of AtERF019 delays plant growth and senescence, and improves drought tolerance in Arabidopsis

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Arabidopsis WRKY46, WRKY54, and WRKY70 Transcription Factors Are Involved in Brassinosteroid-Regulated Plant Growth and Drought Responses

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identification of Open Chromatin Regions in Plant Genomes Using ATAC-Seq

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Profiling of accessible chromatin regions across multiple plant species and cell types reveals common gene regulatory principles and new control modules.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29513366

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1111/TPJ.13882

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29513366%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29513366%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29513366%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

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