ArticleNature plants2020
Marchantia TCP transcription factor activity correlates with three-dimensional chromatin structure.
Article in Nature plants, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 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
44 citing papers in PubMed, 85 citations in OpenAlex.
- TADs, CGVs, and compartmentalization in genomes: Providing a new way for crop domestication and improvement.Journal of integrative plant biology · 2026Review
- A high-resolution 3D genome map of kiwifruit provides insights into chromatin architecture and transcriptional activity.Horticulture research · 2026Article
- Spatial distribution of isoprenoid enzymes and MpABCG1 transporter influences sesquiterpene accumulation in Marchantia polymorpha oil bodies.Communications biology · 2026Article
- Coordinated epigenomic reprogramming and chromatin-mediated transcriptional regulation during soybean callus development.Frontiers in plant science · 2026Article
- PKL mediates H3K4me2 modification and spatial gene congregation in chromatin regulation.Nucleic acids research · 2025Article
- Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream.Genomics, proteomics & bioinformatics · 2025Article
- BMI1s interact with condensin complexes to regulate chromatin 3D structure and gene expression inaBIOTECH · 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
- Microrchidia ATPases and DNA 6mA demethylase ALKBH1 act antagonistically on PRC2 to control chromatin structure and stress tolerance.Nature plants · 2025Article
- TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation.Science advances · 2025Article
- Topologically associating domains and the evolution of three-dimensional genome architecture in rice.The Plant journal : for cell and molecular biology · 2025Article
- Subfunctionalization and epigenetic regulation of a biosynthetic gene cluster inProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Dynamic changes in 3D chromatin structure during male gametogenesis in Arabidopsis thaliana.Genome biology · 2025Article
- Chromatin Topological Domains Associate With the Rapid Formation of Tandem Duplicates in Plants.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants.GigaScience · 2025Article
- Simultaneous Visualization of Protein and Genomic Regions in Plant Nuclei.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Simultaneous Visualization of Protein and Genomic Regions in Plant Nuclei.Methods in molecular biology (Clifton, N.J.) · 2025Article
- PWOs repress gene transcription by regulating chromatin structures in Arabidopsis.Nucleic acids research · 2024Article
- Mutations of PDS5 genes enhance TAD-like domain formation Arabidopsis thaliana.Nature communications · 2024Article
- Drought-responsive dynamics of H3K9ac-marked 3D chromatin interactions are integrated by OsbZIP23-associated super-enhancer-like promoter regions in rice.Genome biology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
Abstract
Information in the genome is not only encoded within sequence or epigenetic modifications, but is also found in how it folds in three-dimensional space. The formation of self-interacting genomic regions, named topologically associated domains (TADs), is known as a key feature of genome organization beyond the nucleosomal level. However, our understanding of the formation and function of TADs in plants is extremely limited. Here we show that the genome of Marchantia polymorpha, a member of a basal land plant lineage, exhibits TADs with epigenetic features similar to those of higher plants. By analysing various epigenetic marks across Marchantia TADs, we find that these regions generally represent interstitial heterochromatin and their borders are enriched with Marchantia transcription factor TCP1. We also identify a type of TAD that we name 'TCP1-rich TAD', in which genomic regions are highly accessible and are densely bound by TCP1 proteins. Transcription of TCP1 target genes differs on the basis gene location, and those in TCP1-rich TADs clearly show a lower expression level. In tcp1 mutant lines, neither TCP1-bound TAD borders nor TCP1-rich TADs display drastically altered chromatin organization patterns, suggesting that, in Marchantia, TCP1 is dispensable for TAD formation. However, we find that in tcp1 mutants, genes residing in TCP1-rich TADs have a greater extent of expression fold change as opposed to genes that do not belong to these TADs. Our results suggest that, besides standing as spatial chromatin-packing modules, plant TADs function as nuclear microcompartments associated with transcription factor activities.
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.