ArticlePlant methods2018
Regulatory chromatin landscape in
Article in Plant methods, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 2 of them syntheses that pooled it.
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Who cites it
25 citing papers in PubMed, 2 syntheses or guidelines pooled it, 52 citations in OpenAlex.
- A systematic review of single-cell RNA sequencing applications and insights in Oryza sativa response to environmental stresses.Molecular biology reports · 2025Pooled it
- ChIP-Hub provides an integrative platform for exploring plant regulome.Nature communications · 2022Pooled it
- Article
- Organ-level gene-regulatory networks inferred from transcriptomic data reveal context-specific regulation and highlight novel regulators of ripening and ABA-mediated responses in tomato.Plant communications · 2025Article
- Combination of 3D chromatin architecture and omics analysis provides insight into anthocyanin regulation inHorticulture research · 2025Article
- Chromosome-level genome assembly of the autotetraploid yellow pitaya provides novel insights into evolution of trait patterning in pitaya species with different ploidy.Genome biology · 2025Article
- Dynamic Chromatin Accessibility and Gene Expression Regulation During Maize Leaf Development.Genes · 2024Article
- PeNAC67-PeKAN2-PeSCL23 and B-class MADS-box transcription factors synergistically regulate the specialization process from petal to lip in Phalaenopsis equestris.Molecular horticulture · 2024Article
- Application of Single-Cell Assay for Transposase-Accessible Chromatin with High Throughput Sequencing in Plant Science: Advances, Technical Challenges, and Prospects.International journal of molecular sciences · 2024Review
- Enhancer activation via TCP and HD-ZIP and repression by Dof transcription factors mediate giant cell-specific expression.The Plant cell · 2023Article
- PlantCADB: A Comprehensive Plant Chromatin Accessibility Database.Genomics, proteomics & bioinformatics · 2023Article
- Article
- Chromatin dynamics associated with seed desiccation tolerance/sensitivity at early germination inFrontiers in plant science · 2022Article
- Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species.BMC biology · 2021Article
- Genome accessibility dynamics in response to phosphate limitation is controlled by the PHR1 family of transcription factors inProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Genomic Features of Open Chromatin Regions (OCRs) in Wild Soybean and Their Effects on Gene Expressions.Genes · 2021Article
- H2AK121ub in Arabidopsis associates with a less accessible chromatin state at transcriptional regulation hotspots.Nature communications · 2021Article
- Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective.Frontiers in cell and developmental biology · 2021Review
- Prediction of condition-specific regulatory genes using machine learning.Nucleic acids research · 2020Article
- 3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize.Genome biology · 2020Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThere is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever-growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puzzle. An important mechanism of gene regulation is the binding of transcription factors (TFs) to specific DNA sequence motifs across the genome. However, these sequences are hindered by the packaging of DNA to chromatin. Thus, the accessibility of these loci for TF binding is highly regulated and determines where and when TFs bind. We present a workflow for measuring chromatin accessibility in
resultsWe coupled the recently described isolation of nuclei tagged in specific cell types (INTACT) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) as a genome-wide strategy to uncover accessible regulatory sites in
conclusionsBy coupling INTACT with ATAC-seq methods, we present a feasible pipeline to profile accessible chromatin in plants. We also introduce a rapid measure of the experiment quality. We find that chromatin accessibility at promoter regions is strongly associated with transcription and active histone marks. However, root-specific chromatin accessibility is primarily found at intergenic regions, suggesting their predominance in defining organ identity possibly via long-range chromatin interactions. This workflow can be rapidly applied to study the regulatory landscape in other cell types, plant species and conditions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.