[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"detail-sidebar-cat-0-en-105":3,"doc-seo-379857-105":59,"doc-detail-379857-en":130},{"code":4,"msg":5,"data":6},0,"success",[7,13,18,23,28,33,38,43,48,51,55],{"id":8,"doc_module":4,"doc_module_name":9,"category_name":10,"show_sort_weight":11,"slug":12},1,"Document","Story & Novel",90,"story-novel",{"id":14,"doc_module":4,"doc_module_name":9,"category_name":15,"show_sort_weight":16,"slug":17},2,"Literature",80,"literature",{"id":19,"doc_module":4,"doc_module_name":9,"category_name":20,"show_sort_weight":21,"slug":22},4,"Exam",70,"exam",{"id":24,"doc_module":4,"doc_module_name":9,"category_name":25,"show_sort_weight":26,"slug":27},5,"Comic",60,"comic",{"id":29,"doc_module":4,"doc_module_name":9,"category_name":30,"show_sort_weight":31,"slug":32},6,"Technology",50,"technology",{"id":34,"doc_module":4,"doc_module_name":9,"category_name":35,"show_sort_weight":36,"slug":37},7,"Healthcare",40,"healthcare",{"id":39,"doc_module":4,"doc_module_name":9,"category_name":40,"show_sort_weight":41,"slug":42},8,"Research & Report",30,"research-report",{"id":44,"doc_module":4,"doc_module_name":9,"category_name":45,"show_sort_weight":46,"slug":47},9,"Religion & Spirituality",20,"religion-spirituality",{"id":46,"doc_module":4,"doc_module_name":9,"category_name":49,"show_sort_weight":46,"slug":50},"World Cup","world-cup",{"id":52,"doc_module":4,"doc_module_name":9,"category_name":53,"show_sort_weight":52,"slug":54},10,"Lifestyle","lifestyle",{"id":56,"doc_module":4,"doc_module_name":9,"category_name":57,"show_sort_weight":24,"slug":58},19,"General","general",{"code":4,"msg":60,"data":61},"ok",{"site_id":62,"language":63,"slug":64,"title":65,"keywords":66,"description":67,"schema_data":68,"social_meta":123,"head_meta":125,"extra_data":127,"updated_unix":129},105,"en","characterization-of-network-hierarchy-reflects-cell-state-specificity-in-genome-organization","Characterization of network hierarchy reflects cell state specificity in genome organization","","Dynamic chromatin structure governs transcription programs during critical processes such as cancer progression and cell development, yet a unified way to characterize chromatin structural evolution is lacking. This study applies graph inference to Hi-C datasets to derive chromatin contact networks and quantifies information transmission changes. Results show reduced network efficiency in colorectal cancer and T-ALL versus matched controls, shallower hierarchy depths in patient chromatin, early-embryo reversals, and tissue-specific conservation of hierarchy order, with cancer showing attenuated top-down chromatin organization.",{"@graph":69,"@context":122},[70,84,105],{"@type":71,"itemListElement":72},"BreadcrumbList",[73,77,79,82],{"item":74,"name":75,"@type":76,"position":8},"https://docshare.wps.com","Home","ListItem",{"item":78,"name":9,"@type":76,"position":14},"https://docshare.wps.com/document/",{"item":80,"name":40,"@type":76,"position":81},"https://docshare.wps.com/document/research-report/",3,{"item":83,"name":65,"@type":76,"position":19},"https://docshare.wps.com/document/characterization-of-network-hierarchy-reflects-cell-state-specificity-in-genome-organization/379857/",{"url":83,"name":65,"@type":85,"image":86,"author":91,"headline":65,"publisher":94,"fileFormat":97,"inLanguage":63,"description":67,"dateModified":98,"datePublished":99,"encodingFormat":97,"isAccessibleForFree":100,"interactionStatistic":101},"DigitalDocument",{"url":87,"@type":88,"width":89,"height":90},"https://docshare.wps.com/thumbnails/characterization-of-network-hierarchy-reflects-cell-state-specificity-in-genome-organization/379857.png","ImageObject",300,407,{"name":92,"@type":93},"Emma Wilson","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-09-26","2026-09-24",true,{"@type":102,"interactionType":103,"userInteractionCount":8},"InteractionCounter",{"@type":104},"ViewAction",{"@type":106,"mainEntity":107},"FAQPage",[108,114,118],{"name":109,"@type":110,"acceptedAnswer":111},"How does the study characterize chromatin structural evolution?","Question",{"text":112,"@type":113},"It performs graph inferences on Hi-C datasets to derive chromatin contact networks and applies graph statistics and network embedding to quantify hierarchy properties and information transmission.","Answer",{"name":115,"@type":110,"acceptedAnswer":116},"What network-level changes are observed in colorectal cancer and T-ALL?",{"text":117,"@type":113},"Both show significant decreases in information transmission efficiencies compared with corresponding normal controls, and their chromatin hierarchy depths are significantly shallower.",{"name":119,"@type":110,"acceptedAnswer":120},"Are chromatin hierarchy patterns consistent across tissues or developmental stages?",{"text":121,"@type":113},"The study finds tissue-specific conservation of hierarchy order in chromatin contact networks and observes a reverse trend during early embryo development, indicating stage-dependent structural changes.","https://schema.org",{"og:url":83,"og:type":124,"og:title":65,"og:site_name":95,"og:description":67},"article",{"robots":126,"canonical":83},"index,follow",{"doc_id":128,"site_id":62},379857,1790451642,{"code":4,"msg":5,"data":131},{"doc_id":128,"user_id":132,"nickname":92,"user_avatar":133,"doc_module":4,"category_id":39,"category_name":40,"doc_title":65,"doc_description":67,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":8,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":139,"language":140,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":141,"faqs":142,"seo_title":143,"seo_description":67,"update_tm":144,"read_time":145},3848291630094,"https://eur-avatar.wpscdn.com/davatar_085a072bc5b1113ac321206ff7593b45","Characterization of network hierarchy reflects cell state specificity in genome organization  \nJingyao Wang, 1,4 Yue Xue, 1,4 Yueying He, 1 Hui Quan, 1 Jun Zhang, 3 and Yi Qin Gao 1,2,3 1Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China; 2Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China; 3 Changping Laboratory, Beijing, 102206, China  \nDynamic chromatin structure acts as the regulator of transcription program in crucial processes including cancer and cell development, but a unified framework for characterizing chromatin structural evolution remains to be established. Here, we performed graph inferences on Hi-C data sets and derived the chromatin contact networks. We discovered significant decreases in information transmission efficiencies in chromatin of colorectal cancer (CRC) and T-cell acute lymphoblastic leukemia (T-ALL) compared to corresponding normal controls through graph statistics. Using network embedding in the Poincar disk, the hierarchy depths of chromatin from CRC and T-ALL patients were found to be significantly shallower compared to their normal controls. A reverse trend of change in chromatin structure was observed during early embryo development. We found tissue-specific conservation of hierarchy order in chromatin contact networks. Our findings reveal the top-down hierarchy of chromatin organization, which is significantly attenuated in cancer.  \n[Supplemental material is available for this article.]  \nGenome architecture plays an important role in transcription regulation (Liu et al. 2018; Deng et al. 2022; He et al. 2022) . Instead of maintaining a static configuration, chromatin structure is dynamic (Barth et al. 2020) . A large and diverse set of gene regulatory elements in chromatin are found to regulate transcription through long-range interactions. For example, promoter–enhancer interactions regulate the dynamic activation of genes (Cloney 2016), whereas insulators and repressors play the opposite roles (Yang and Corces 2012) . Graph theory has been widely used in deciphering biological networks including protein interaction and gene expression networks (Koutrouli et al. 2020) . Dynamic information transmission in networks is vital for maintaining functionalities (Eisenberg et al. 2000; Brazhnik et al. 2002) .  \nChromatin structure evolves during crucial life processes including cancer and cell development. Although extensive studies have attributed oncogenesis to gene mutations (Fujimoto et al. 1992; Brekelmans et al. 2001; Davies et al. 2002; Sprucket al. 2002), targeting chromatin structure for diagnosis and therapy has increasingly gained attention (Kaur et al. 2019) . Conventional microscopic observation of aberrant chromatin was used for cancer diagnosis (Zink et al. 2004). The recently developed Hi-C technology allows detailed inspection of aberrant chromatin structure in cancer. Pathological cancer tissues were observed to be accompanied by disturbances in compartments and TAD structures in Hi-C (Johnstone et al. 2020; Iyyanki et al. 2021; Yang et al. 2021) . On the other side, the similarity between embryonic stem cells and cancer cells has also attracted attention (Kim and Orkin 2011; Malta et al. 2018; Feng et al. 2021). The characteristics shared by embryonic stem cells and cancer cells include unlimited proliferation and high cellular plasticity (Seftor et al. 2002; Hendrix et al. 2007) . However, the similarity in chromatin  \nstructure between embryo tissues and pathological cancer tissues has not been extensively studied.  \nAlthough a number of methods have been reported to delineate the hierarchy of Hi-C data, they are confined to the notion of nested hierarchy, which describes a containment relationship of units. For example, Soler-Vila et al. introduced TADpole to identify the hierarchical subdivisions of TADs in intrachromosomal Hi-C (Soler-Vila et a","cbCainB6nDoyl6md","https://ap.wps.com/l/cbCainB6nDoyl6md","pdf",15080094,14,"English","# Introduction\n## Dynamic chromatin structure and transcription regulation\n## Hi-C and cancer-associated chromatin disruptions\n## Limitations of nested hierarchy methods\n# Results\n## Graph statistics reveal altered contact networks in cancer and differentiation","[{\"question\":\"How does the study characterize chromatin structural evolution?\",\"answer\":\"It performs graph inferences on Hi-C datasets to derive chromatin contact networks and applies graph statistics and network embedding to quantify hierarchy properties and information transmission.\"},{\"question\":\"What network-level changes are observed in colorectal cancer and T-ALL?\",\"answer\":\"Both show significant decreases in information transmission efficiencies compared with corresponding normal controls, and their chromatin hierarchy depths are significantly shallower.\"},{\"question\":\"Are chromatin hierarchy patterns consistent across tissues or developmental stages?\",\"answer\":\"The study finds tissue-specific conservation of hierarchy order in chromatin contact networks and observes a reverse trend during early embryo development, indicating stage-dependent structural changes.\"}]","Characterization of network hierarchy reflects cell state specificity in genome organization | PDF",1790237777,35]