{"doi":"10.1105/tpc.114.124578","title":"The Functional Topography of the <i>Arabidopsis</i> Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States\n ","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>Chromatin is of major relevance for gene expression, cell division, and differentiation. Here, we determined the landscape of Arabidopsis thaliana chromatin states using 16 features, including DNA sequence, CG methylation, histone variants, and modifications. The combinatorial complexity of chromatin can be reduced to nine states that describe chromatin with high resolution and robustness. Each chromatin state has a strong propensity to associate with a subset of other states defining a discrete number of chromatin motifs. These topographical relationships revealed that an intergenic state, characterized by H3K27me3 and slightly enriched in activation marks, physically separates the canonical Polycomb chromatin and two heterochromatin states from the rest of the euchromatin domains. Genomic elements are distinguished by specific chromatin states: four states span genes from transcriptional start sites (TSS) to termination sites and two contain regulatory regions upstream of TSS. Polycomb regions and the rest of the euchromatin can be connected by two major chromatin paths. Sequential chromatin immunoprecipitation experiments demonstrated the occurrence of H3K27me3 and H3K4me3 in the same chromatin fiber, within a two to three nucleosome size range. Our data provide insight into the Arabidopsis genome topography and the establishment of gene expression patterns, specification of DNA replication origins, and definition of chromatin domains.</jats:p>","journal":"The Plant Cell","year":2014,"id":38718,"datarank":0.896488541110063,"base_score":5.730099782973575,"endowment":5.730099782973575,"self_citation_contribution":0.8595149674460364,"citation_network_contribution":0.03697357366402663,"self_endowment_contribution":0.8595149674460364,"citer_contribution":0.03697357366402663,"corpus_percentile":null,"corpus_rank":null,"citation_count":307,"citer_count":1,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":25,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":191637,"name":"Irene Aragüez","orcid":null,"position":1,"is_corresponding":false},{"id":191638,"name":"Ramón Peiró","orcid":null,"position":2,"is_corresponding":false},{"id":191639,"name":"Raul Mendez-Giraldez","orcid":null,"position":3,"is_corresponding":false},{"id":20859,"name":"Xiaoyu Zhang","orcid":"0000-0002-6033-0525","position":4,"is_corresponding":false},{"id":191640,"name":"Steven E. Jacobsen","orcid":null,"position":5,"is_corresponding":false},{"id":187310,"name":"Ugo Bastolla","orcid":null,"position":6,"is_corresponding":false},{"id":191641,"name":"Crisanto Gutierrez","orcid":null,"position":7,"is_corresponding":false},{"id":191636,"name":"Joana Sequeira-Mendes","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"datacite_reuse_total":25,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"24934173","pmcid":null,"openalex_id":"https://openalex.org/W24934173","authors":[],"funders":[{"funder_name":"NIGMS NIH HHS","grant_id":"R01 GM060398","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"R37 GM060398","title":null}],"total_grants":2,"fwci":0.0,"citation_percentile":0.00437111,"influential_citations":32,"citation_trend":[{"year":2019,"count":1}],"oa_status":"bronze","license":"https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model","oa_locations":[{"url":"http://www.plantcell.org/content/plantcell/26/6/2351.full.pdf","host_type":"BRONZE"},{"url":"http://www.plantcell.org/content/plantcell/26/6/2351.full.pdf","host_type":"publisher"},{"url":"http://academic.oup.com/plcell/article-pdf/26/6/2351/36983806/plcell_v26_6_2351.pdf","host_type":"publisher"},{"url":"https://vuir.vu.edu.au/4206/","host_type":"journal"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4114938","host_type":"repository"}],"fields_of_study":["Digital Storytelling and Education","Art Education and Development","Literacy, Media, and Education","Biology","Medicine","Computer Science"],"mesh_terms":[],"keywords":["Narrative","Visual arts","Aesthetics","History","Art","Computer science","Communication","Sociology","Literature"],"sdg_mappings":[],"linked_datasets":[{"doi":"10.6084/m9.figshare.14173869.v1","title":"Additional file 1 of SDG711 Is Involved in Rice Seed Development through Regulation of Starch Metabolism Gene Expression in Coordination with Other Histone Modifications","publisher":"figshare","resource_type":"Presentation"},{"doi":"10.6084/m9.figshare.14173869","title":"Additional file 1 of SDG711 Is Involved in Rice Seed Development through Regulation of Starch Metabolism Gene Expression in Coordination with Other Histone Modifications","publisher":"figshare","resource_type":"Presentation"},{"doi":"10.6084/m9.figshare.14173872.v1","title":"Additional file 2 of SDG711 Is Involved in Rice Seed Development through Regulation of Starch Metabolism Gene Expression in Coordination with Other Histone Modifications","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.14173872","title":"Additional file 2 of SDG711 Is Involved in Rice Seed Development through Regulation of Starch Metabolism Gene Expression in Coordination with Other Histone Modifications","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.22706063.v1","title":"Additional file 1 of MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.22706078.v1","title":"Additional file 6 of MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.22706063","title":"Additional file 1 of MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.22706078","title":"Additional file 6 of MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.22706081.v1","title":"Additional file 7 of MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.22706081","title":"Additional file 7 of MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.23265206.v1","title":"Additional file 1 of Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.23265206","title":"Additional file 1 of Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.23265224.v1","title":"Additional file 7 of Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.23265224","title":"Additional file 7 of Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.24303441.v1","title":"Additional file 2 of Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.24303441","title":"Additional file 2 of Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.24628024.v1","title":"Additional file 1 of H2A.X promotes endosperm-specific DNA methylation in Arabidopsis thaliana","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.24628024","title":"Additional file 1 of H2A.X promotes endosperm-specific DNA methylation in Arabidopsis thaliana","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.24628151.v1","title":"Additional file 2 of H2A.X promotes endosperm-specific DNA methylation in Arabidopsis thaliana","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.24628151","title":"Additional file 2 of H2A.X promotes endosperm-specific DNA methylation in Arabidopsis thaliana","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.25357862.v1","title":"Additional file 1 of KAKU4 regulates leaf senescence through modulation of H3K27me3 deposition in the Arabidopsis genome","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.25357862","title":"Additional file 1 of KAKU4 regulates leaf senescence through modulation of H3K27me3 deposition in the Arabidopsis genome","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.26626264.v1","title":"Additional file 4 of Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.26626264","title":"Additional file 4 of Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.26690018.v1","title":"Additional file 5 of KAKU4 regulates leaf senescence through modulation of H3K27me3 deposition in the Arabidopsis genome","publisher":"figshare","resource_type":"JournalArticle"}],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-11T05:31:12.382318Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}