ArticleNucleic acids research2021
INT-Hi-C reveals distinct chromatin architecture in endosperm and leaf tissues of Arabidopsis.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 33 citations in OpenAlex.
- 3D Chromatin Architecture Provides Insights Into Leaf Trait Variation Among Pear Species.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Bioinformatics insights into plant genomic imprinting: approaches, challenges, and future perspectives.Briefings in functional genomics · 2026Review
- Exploring the untapped potential of single-cell and spatial omics in plant biology.The New phytologist · 2025Review
- Epigenetics and plant hormone dynamics: a functional and methodological perspective.Journal of experimental botany · 2024Review
- Mind the gap: Epigenetic regulation of chromatin accessibility in plants.Plant physiology · 2024Review
- Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition.Nature communications · 2024Article
- Review
- The eINTACT method for studying nuclear changes in host plant cells targeted by bacterial effectors in native infection contexts.Nature protocols · 2023Review
- Role of Epigenetic Factors in Response to Stress and Establishment of Somatic Memory of Stress Exposure in Plants.Plants (Basel, Switzerland) · 2023Review
- Binding by the Polycomb complex component BMI1 and H2A monoubiquitination shape local and long-range interactions in the Arabidopsis genome.The Plant cell · 2023Article
- Isolation of Nuclei Tagged in Specific Cell Types (INTACT) in Arabidopsis.Methods in molecular biology (Clifton, N.J.) · 2023Article
- The maize gene maternal derepression of r1 encodes a DNA glycosylase that demethylates DNA and reduces siRNA expression in the endosperm.The Plant cell · 2022Article
- Dynamic enhancer transcription associates with reprogramming of immune genes during pattern triggered immunity in Arabidopsis.BMC biology · 2022Article
- Interaction between zinc and selenium bio-fortification and toxic metals (loid) accumulation in food crops.Frontiers in plant science · 2022Review
- Modeling the 3D genome of plants.Nucleus (Austin, Tex.) · 2021Article
- Endosperm-Embryo Communications: Recent Advances and Perspectives.Plants (Basel, Switzerland) · 2021Review
- Genome Maintenance Mechanisms at the Chromatin Level.International journal of molecular sciences · 2021Review
- Stress Conditions Modulate the Chromatin Interactions Network inFrontiers in genetics · 2021Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Higher-order chromatin structure undergoes striking changes in response to various developmental and environmental signals, causing distinct cell types to adopt specific chromatin organization. High throughput chromatin conformation capture (Hi-C) allows studying higher-order chromatin structure; however, this technique requires substantial amounts of starting material, which has limited the establishment of cell type-specific higher-order chromatin structure in plants. To overcome this limitation, we established a protocol that is applicable to a limited amount of nuclei by combining the INTACT (isolation of nuclei tagged in specific cell types) method and Hi-C (INT-Hi-C). Using this INT-Hi-C protocol, we generated Hi-C data from INTACT purified endosperm and leaf nuclei. Our INT-Hi-C data from leaf accurately reiterated chromatin interaction patterns derived from conventional leaf Hi-C data. We found that the higher-order chromatin organization of mixed leaf tissues and endosperm differs and that DNA methylation and repressive histone marks positively correlate with the chromatin compaction level. We furthermore found that self-looped interacting genes have increased expression in leaves and endosperm and that interacting intergenic regions negatively impact on gene expression in the endosperm. Last, we identified several imprinted genes involved in long-range and trans interactions exclusively in endosperm. Our study provides evidence that the endosperm adopts a distinct higher-order chromatin structure that differs from other cell types in plants and that chromatin interactions influence transcriptional activity.
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