ReviewCurrent opinion in plant biology2020
Considerations in the analysis of plant chromatin accessibility data.
Review in Current opinion in plant biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed, 32 citations in OpenAlex.
- Method for ATAC Sequencing Data Analysis for Understanding Chromatin Biology in Legumes.Methods in molecular biology (Clifton, N.J.) · 2026Article
- ISDH-seq: a robust methodology for profiling and characterization of open chromatin.Plant biotechnology journal · 2025Article
- The regulatory potential of transposable elements in maize.Nature plants · 2025Article
- Expression of Iron Metabolism Genes Is Potentially Regulated by DOF Transcription Factors inInternational journal of molecular sciences · 2024Article
- Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton.Molecular biology and evolution · 2024Article
- A review of artificial intelligence-assisted omics techniques in plant defense: current trends and future directions.Frontiers in plant science · 2024Review
- Optimization of ATAC-seq in wheat seedling roots using INTACT-isolated nuclei.BMC plant biology · 2023Article
- Genome-wide mapping of DNase I hypersensitive sites in pineapple leaves.Frontiers in genetics · 2023Article
- Genome-wide chromatin accessibility analysis unveils open chromatin convergent evolution during polyploidization in cotton.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Quality control and evaluation of plant epigenomics data.The Plant cell · 2022Article
- Chromatin dynamics associated with seed desiccation tolerance/sensitivity at early germination inFrontiers in plant science · 2022Article
- 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
- The native cistrome and sequence motif families of the maize ear.PLoS genetics · 2021Article
- Chromatin accessibility and translational landscapes of tea plants under chilling stress.Horticulture research · 2021Article
- Network-based approaches for understanding gene regulation and function in plants.The Plant journal : for cell and molecular biology · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Transcriptional control is exerted primarily through the binding of transcription factor proteins to regulatory elements in DNA. By virtue of eukaryotic DNA being complexed with histones, transcription factor binding to DNA alters or eliminates histone-DNA contacts, leading to increased accessibility of the DNA region to nuclease enzymes. This hypersensitivity to nuclease digestion has been used to define DNA binding events and regulatory elements across genomes, and to compare these attributes between cell types or conditions. These approaches make it possible to define the regulatory elements in a genome as well as to predict the regulatory networks of transcription factors and their target genes in a given cell state. As these chromatin accessibility assays are increasingly used, it is important to consider how to analyze the resulting data to avoid artifactual results or misinterpretation. In this review, we focus on some of the key technical and computational caveats associated with plant chromatin accessibility data, including strategies for sample preparation, sequencing, read mapping, and downstream analyses.
Indexed as
Identifiers
What OpenQuestion holds
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.