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Cohesin and condensins, ATP-powered SMC protein complexes, orchestrate chromatin structure, yet genetic loss is lethal. Inducible degradation via the auxin-inducible degradation (AID) system enables rapid, robust analysis of protein depletion phenotypes across cell-cycle phases. This review summarizes how condensins and cohesins shape mitotic chromosome helical organization and interphase chromosome territories, including AID-based studies of TOP2A, KIF4A, and SRBD, and it highlights emerging mitotic-to-interphase transition principles and interphase organization advances revealed by AID approaches.",{"@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/spatial-chromatin-organization-across-the-cell-cycle-insights-from-auxin-inducible-protein-depletion/465513/",{"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/spatial-chromatin-organization-across-the-cell-cycle-insights-from-auxin-inducible-protein-depletion/465513.png","ImageObject",300,407,{"name":92,"@type":93},"Kyle","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-10-04","2026-09-30",true,{"@type":102,"interactionType":103,"userInteractionCount":14},"InteractionCounter",{"@type":104},"ViewAction",{"@type":106,"mainEntity":107},"FAQPage",[108,114,118],{"name":109,"@type":110,"acceptedAnswer":111},"What is the purpose of using the auxin-inducible degradation (AID) system in this review?","Question",{"text":112,"@type":113},"The review explains that AID enables tight, stage-controlled depletion of chromatin proteins, allowing rapid and robust phenotypic analysis across cell-cycle phases.","Answer",{"name":115,"@type":110,"acceptedAnswer":116},"How do cohesin and condensins contribute to chromatin organization?",{"text":117,"@type":113},"They are described as structural maintenance of chromosomes (SMC) complexes acting as ATP-powered loop extrusion motors that help organize chromatin into dynamic interphase loops and condensed mitotic structures.",{"name":119,"@type":110,"acceptedAnswer":120},"Which additional proteins are discussed as targets studied with the AID system during mitosis?",{"text":121,"@type":113},"The abstract highlights studies examining roles of TOP2A, KIF4A, and SRBD during mitosis using AID-based approaches.","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},465513,1791082990,{"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":14,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":41,"language":139,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":140,"faqs":141,"seo_title":142,"seo_description":67,"update_tm":143,"read_time":144},3985741905716,"https://ap-avatar.wpscdn.com/davatar_994ba38a5ba835b3df7d355c54d3ed8d","Review  \nSpatial Chromatin Organization Across the Cell Cycle: Insights from Auxin-Inducible Protein Depletion  \nArtem Nurislamov 1,2 and Anastasia Yunusova 2, *  \nAcademic Editor: Yegor S. Vassetzky  \nReceived: 20 November 2025  \nRevised: 24 December 2025  \nAccepted: 25 December 2025  \nPublished: 26 December 2025  \nCopyright: © 2025 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.  \n1 Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sirius Federal Territory, Sochi 354340, Russia  \n2 Institute of Cytology and Genetics, Novosibirsk 630090, Russia  \n* [Correspondence: yunusova@bionet.nsc.ru](Correspondence: yunusova@bionet.nsc.ru)  \nAbstract  \nMany cellular processes, including gene expression regulation, DNA replication and repair, as well as proper condensation and segregation of chromosomes, require highly coordinated remodeling of chromatin. Cohesin and condensins, the structural maintenance of chromosomes (SMC) protein complexes that function as ATP-powered loop extrusion motors, are key determinants of chromatin structure. The genetic loss of their function is lethal, whereas inducible degradation approaches enable rapid, robust analysis of the depletion phenotype. In this review, we discuss new insights into chromatin folding through each cell cycle phase from the auxin-inducible degradation (AID) system. We review the mechanisms by which condensins and cohesins contribute to the helical organization of mitotic chromosomes and to the maintenance of chromosome territories in interphase. Additionally, we discuss studies examining the roles of TOP2A, KIF4A, and SRBD during mitosis using the AID system. We then outline emerging principles of the mitotic-to-interphase transition and how targeted degradation of chromatin proteins reshapes this process. Finally, we highlight and discuss new advances in understanding interphase chromatin organization revealed by AID-based studies.  \nKeywords: 3D genome; SMC complexes; CTCF; auxin-inducible degradation  \n1. Auxin-Inducible Degron System  \nIn eukaryotic cells, highly ordered chromatin structure plays an essential role in genome regulation and the underlying biological functions of chromosomes. Chromatin architecture is tightly coordinated in a spatiotemporal manner during cell cycle progression: from the relatively diffuse interphase chromatin structure, organized into dynamic DNA loops by cohesin and CTCF, to the highly condensed loop arrays of mitotic chromosomes mediated by condensins. The auxin-inducible degradation (AID) system, which allows the level of the target protein to be tightly controlled, has significantly advanced the knowledge of the key regulators of chromatin architecture and unveiled their novel functions. When combined with cell synchronization protocols, the AID system enables detailed analysis of proteins with stage-specific cellular function [1] . Briefly, this three-component system of protein degradation requires the following: (1) expressing an exogenous E3 ligase adaptor proteins (OsTIR1 or AtAFB2); (2) introducing an AID-tag, a short degron domain on N-or C-terminus of the target protein; and (3), adding the plant hormone auxin, indole-3-acetic acid (IAA), or its chemical analogs. IAA mediates the interaction between the E3 ubiquitin ligase SCF/TIR1 and a degron-fused protein, leading to its ubiquitination and proteasomal  \ndegradation (Figure 1) . The AID system, as an effective approach for protein degradation, was pioneered in 2009, and for now ithas been applied in many model organisms, including Saccharomyces, Drosophila, Caenorhabditis, zebrafish, mouse, chicken, and human cell lines, as has been thoroughly reviewed in [1–3] .  \nFigure 1. Scheme of the AID system. IAA binding to OsTIR1 induces the activity of the SCF/TIR1 complex recruiting an E2 ligase and promoting ","cbCaip4nwdhDDKse","https://ap.wps.com/l/cbCaip4nwdhDDKse","pdf",1701653,"English","# Abstract\n# Auxin-Inducible Degron System\n# Key Regulators of Mitotic Chromatin Architecture\n## Condensins","[{\"question\":\"What is the purpose of using the auxin-inducible degradation (AID) system in this review?\",\"answer\":\"The review explains that AID enables tight, stage-controlled depletion of chromatin proteins, allowing rapid and robust phenotypic analysis across cell-cycle phases.\"},{\"question\":\"How do cohesin and condensins contribute to chromatin organization?\",\"answer\":\"They are described as structural maintenance of chromosomes (SMC) complexes acting as ATP-powered loop extrusion motors that help organize chromatin into dynamic interphase loops and condensed mitotic structures.\"},{\"question\":\"Which additional proteins are discussed as targets studied with the AID system during mitosis?\",\"answer\":\"The abstract highlights studies examining roles of TOP2A, KIF4A, and SRBD during mitosis using AID-based approaches.\"}]","Spatial Chromatin Organization Across the Cell Cycle - Insights from Auxin-Inducible Protein Depletion | PDF",1790769714,76]