{"date_published":"2025-12-26T00:00:00Z","status":"public","publication_status":"epub_ahead","date_updated":"2026-01-05T11:16:11Z","department":[{"_id":"AlMi"}],"date_created":"2026-01-04T23:01:33Z","language":[{"iso":"eng"}],"day":"26","project":[{"name":"Circadian structural transitions of chromatin","grant_number":"101162145","_id":"9136c684-16d5-11f0-9cad-91c0177b365f"}],"has_accepted_license":"1","intvolume":"         7","scopus_import":"1","corr_author":"1","quality_controlled":"1","PlanS_conform":"1","article_number":"104295","doi":"10.1016/j.xpro.2025.104295","oa_version":"Published Version","external_id":{"pmid":["41455105"]},"month":"12","volume":7,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","OA_place":"publisher","year":"2025","publication":"STAR Protocols","publication_identifier":{"eissn":["2666-1667"]},"acknowledgement":"We thank R.H. Kim, A. Casper, and R. Gautsch for sequencing at the NGS facility (RRID:SCR_025746). K.T. is an Honorary Professor at the Department of Biology, Ludwig-Maximilians-University, Munich, Germany. This study was funded by European Research Council grant ERC-CoG-818556 TotipotentZygotChrom (K.T.), Max Planck Society (K.T.), and ERC Starting Grant “ChromaChrono” 101162145 (A.K.M.).","title":"Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination","_id":"20924","author":[{"first_name":"Wataru","full_name":"Kobayashi, Wataru","last_name":"Kobayashi"},{"id":"6437c950-2a03-11ee-914d-d6476dd7b75c","orcid":"0000-0002-6080-839X","last_name":"Michael","full_name":"Michael, Alicia","first_name":"Alicia"},{"last_name":"Ruangroengkulrith","full_name":"Ruangroengkulrith, Siwat","first_name":"Siwat"},{"full_name":"Kümmecke, Maximilian","first_name":"Maximilian","last_name":"Kümmecke"},{"full_name":"Tachibana, Kikuë","first_name":"Kikuë","last_name":"Tachibana"}],"abstract":[{"text":"Pioneer transcription factors (TFs) possess the ability to read out DNA motifs embedded within nucleosomes, driving changes in gene expression during cellular differentiation and reprogramming. Here, we present selected engagement on nucleosome sequencing (SeEN-seq), a protocol designed to systematically identify potential TF-binding sites on the nucleosome. We describe steps for nucleosome library assembly, SeEN-seq assay, and cryoelectron microscopy (cryo-EM) sample preparation. This protocol facilitates the preparation of homogeneous pioneer TF-nucleosome complexes for cryo-EM structure determination using single-particle analysis.\r\nFor complete details on the use and execution of this protocol, please refer to Michael et al.1","lang":"eng"}],"article_type":"original","OA_type":"gold","main_file_link":[{"url":"https://doi.org/10.1016/j.xpro.2025.104295","open_access":"1"}],"citation":{"mla":"Kobayashi, Wataru, et al. “Protocol for Integrative Analysis of Transcription Factor-Nucleosome Interactions Using SeEN-Seq and Cryo-EM Structure Determination.” <i>STAR Protocols</i>, vol. 7, 104295, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.xpro.2025.104295\">10.1016/j.xpro.2025.104295</a>.","ieee":"W. Kobayashi, A. K. Michael, S. Ruangroengkulrith, M. Kümmecke, and K. Tachibana, “Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination,” <i>STAR Protocols</i>, vol. 7. Elsevier, 2025.","ama":"Kobayashi W, Michael AK, Ruangroengkulrith S, Kümmecke M, Tachibana K. Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination. <i>STAR Protocols</i>. 2025;7. doi:<a href=\"https://doi.org/10.1016/j.xpro.2025.104295\">10.1016/j.xpro.2025.104295</a>","chicago":"Kobayashi, Wataru, Alicia K. Michael, Siwat Ruangroengkulrith, Maximilian Kümmecke, and Kikuë Tachibana. “Protocol for Integrative Analysis of Transcription Factor-Nucleosome Interactions Using SeEN-Seq and Cryo-EM Structure Determination.” <i>STAR Protocols</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.xpro.2025.104295\">https://doi.org/10.1016/j.xpro.2025.104295</a>.","ista":"Kobayashi W, Michael AK, Ruangroengkulrith S, Kümmecke M, Tachibana K. 2025. Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination. STAR Protocols. 7, 104295.","short":"W. Kobayashi, A.K. Michael, S. Ruangroengkulrith, M. Kümmecke, K. Tachibana, STAR Protocols 7 (2025).","apa":"Kobayashi, W., Michael, A. K., Ruangroengkulrith, S., Kümmecke, M., &#38; Tachibana, K. (2025). Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2025.104295\">https://doi.org/10.1016/j.xpro.2025.104295</a>"},"pmid":1,"article_processing_charge":"Yes","oa":1,"DOAJ_listed":"1","publisher":"Elsevier","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"}}