ArticleThe Plant journal : for cell and molecular biology2018
Changes in chromatin accessibility between Arabidopsis stem cells and mesophyll cells illuminate cell type-specific transcription factor networks.
Article in The Plant journal : for cell and molecular biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers, 1 of them a synthesis that pooled it.
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
72 citing papers in PubMed, 1 synthesis or guideline pooled it, 145 citations in OpenAlex.
- ChIP-Hub provides an integrative platform for exploring plant regulome.Nature communications · 2022Pooled it
- Endogenous constitutive promoters with a broad range of transcriptional activities for plant synthetic biology.Plant cell reports · 2026Article
- Cross-species optimization of nuclei isolation in ten plant species.Plant methods · 2026Article
- Big data approaches to understanding gene regulatory networks in the shoot apical meristem andFrontiers in plant science · 2026Review
- ATAC-Seq and RNA-Seq Integration Reveals Chromatin Accessibility and Transcriptional Dynamics During Fruit Color Development in Mulberry.International journal of molecular sciences · 2026Article
- Synthetic promoter design in plants: integration of computational and experimental approaches.Frontiers in plant science · 2026Review
- ISDH-seq: a robust methodology for profiling and characterization of open chromatin.Plant biotechnology journal · 2025Article
- Many transcription factor families have evolutionarily conserved binding motifs in plants.Plant physiology · 2025Article
- The genetic architecture of cell type-specific cis regulation in maize.Science (New York, N.Y.) · 2025Article
- The role of DNA content in shaping chromatin architecture and gene expression.The Plant journal : for cell and molecular biology · 2025Article
- Using Callus as an Ex Vivo System for Chromatin Analysis.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Epigenomic and 3D genomic mapping reveals developmental dynamics and subgenomic asymmetry of transcriptional regulatory architecture in allotetraploid cotton.Nature communications · 2024Article
- Chromatin Accessibility and Gene Expression Vary Between a New and Evolved Autopolyploid of Arabidopsis arenosa.Molecular biology and evolution · 2024Article
- Dual roles of the MPK3 and MPK6 mitogen-activated protein kinases in regulating Arabidopsis stomatal development.The Plant cell · 2024Article
- Computational Reconstruction of the Transcription Factor Regulatory Network Induced by Auxin inPlants (Basel, Switzerland) · 2024Article
- The Function of Florigen in the Vegetative-to-Reproductive Phase Transition in and around the Shoot Apical Meristem.Plant & cell physiology · 2024Review
- Protocol to isolate nuclei from Chlamydomonas reinhardtii for ATAC sequencing.STAR protocols · 2024Article
- An epigenetic timer regulates the transition from cell division to cell expansion during Arabidopsis petal organogenesis.PLoS genetics · 2024Article
- BCL7A and BCL7B potentiate SWI/SNF-complex-mediated chromatin accessibility to regulate gene expression and vegetative phase transition in plants.Nature communications · 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
12 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Cell differentiation is driven by changes in the activity of transcription factors (TFs) and subsequent alterations in transcription. To study this process, differences in TF binding between cell types can be deduced by probing chromatin accessibility. We used cell type-specific nuclear purification followed by the assay for transposase-accessible chromatin (ATAC-seq) to delineate differences in chromatin accessibility and TF regulatory networks between stem cells of the shoot apical meristem (SAM) and differentiated leaf mesophyll cells in Arabidopsis thaliana. Chromatin accessibility profiles of SAM stem cells and leaf mesophyll cells were very similar at a qualitative level, yet thousands of regions having quantitatively different chromatin accessibility were also identified. Analysis of the genomic regions preferentially accessible in each cell type identified hundreds of overrepresented TF-binding motifs, highlighting sets of TFs that are probably important for each cell type. Within these sets, we found evidence for extensive co-regulation of target genes by multiple TFs that are preferentially expressed in each cell type. Interestingly, the TFs within each of these cell type-enriched sets also showed evidence of extensively co-regulating each other. We further found that preferentially accessible chromatin regions in mesophyll cells tended to also be substantially accessible in the stem cells, whereas the converse was not true. This observation suggests that the generally higher accessibility of regulatory elements in stem cells might contribute to their developmental plasticity. This work demonstrates the utility of cell type-specific chromatin accessibility profiling for the rapid development of testable models of regulatory control differences between cell types.
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.