{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T13:50:20Z","timestamp":1791381020615,"version":"4.3.3"},"reference-count":23,"publisher":"Wiley","issue":"10","license":[{"start":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T00:00:00Z","timestamp":1791331200000},"content-version":"vor","delay-in-days":6,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Current Protocols"],"published-print":{"date-parts":[[2026,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Centromeres are specialized chromosomal regions essential for faithful chromosome segregation and genome stability. Their highly repetitive DNA composition and epigenetically defined chromatin state present significant challenges for genome\u2010wide profiling approaches such as chromatin immunoprecipitation followed by sequencing (ChIP\u2010seq). Standard ChIP\u2010seq workflows often perform poorly at centromeric regions, resulting in low signal\u2010to\u2010noise ratios and limited reproducibility. This article describes a ChIP\u2010seq protocol optimized to enrich for and analyze centromeric chromatin from cell lines. The procedure builds on established ChIP\u2010seq methodologies while incorporating centromere\u2010focused modifications in nuclei isolation, chromatin fragmentation, immunoprecipitation, library preparation, and data analysis. Detailed step\u2010by\u2010step instructions, critical parameters, recommended controls, and troubleshooting guidance are provided to support reproducible implementation. When applied carefully, this protocol enables reliable profiling of centromere\u2010associated chromatin and can be integrated into broader studies of chromosome organization, centromere function, and genome stability. \u00a9 2026 The Author(s).\n                    <jats:italic>Current Protocols<\/jats:italic>\n                    published by Wiley Periodicals LLC.\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Basic Protocol 1<\/jats:bold>\n                    : Sucrose gradient\u2013based isolation of nuclei\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Support Protocol 1<\/jats:bold>\n                    : Titration of micrococcal nuclease (MNase)\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Basic Protocol 2<\/jats:bold>\n                    : MNase digestion and immunoprecipitation of CENP\u2010A chromatin\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Alternate Protocol 1<\/jats:bold>\n                    : Chromatin sonication and immunoprecipitation of CENP\u2010C chromatin complexes\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Support Protocol 2<\/jats:bold>\n                    : NET blocking and washing of Protein G Sepharose beads\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Basic Protocol 3<\/jats:bold>\n                    : DNA extraction\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Alternate Protocol 2<\/jats:bold>\n                    : Reversal of cross\u2010links and DNA purification\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Support Protocol 3<\/jats:bold>\n                    : Bead clean\u2010up\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Basic Protocol 4<\/jats:bold>\n                    : Library preparation and size selection\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Support Protocol 4<\/jats:bold>\n                    : qPCR to assess \u03b1\u2010satellite DNA enrichment\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Basic Protocol 5<\/jats:bold>\n                    : ChIP\u2010seq data processing and analysis\n                  <\/jats:p>","DOI":"10.1002\/cpz1.70471","type":"journal-article","created":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T12:51:47Z","timestamp":1791377507000},"source":"Crossref","is-referenced-by-count":0,"title":["Optimized Genome\u2010Wide Profiling of Centromeric Chromatin Complexes by ChIP\u2010seq"],"prefix":"10.1002","volume":"6","author":[{"given":"Alessia","family":"Daponte","sequence":"first","affiliation":[{"name":"Department of Biosciences, Biotechnology and Environment University of Bari  Bari Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel","family":"Schwope","sequence":"additional","affiliation":[{"name":"Istituto di Genomica Applicata  Udine Italy"},{"name":"Department of Agricultural, Food, Environmental and Animal Sciences University of Udine Udine Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caterina","family":"Manzari","sequence":"additional","affiliation":[{"name":"Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies National Research Council  Bari Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucia","family":"Trisolini","sequence":"additional","affiliation":[{"name":"Department of Biosciences, Biotechnology and Environment University of Bari  Bari Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesca","family":"Antonacci","sequence":"additional","affiliation":[{"name":"Department of Biosciences, Biotechnology and Environment University of Bari  Bari Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michele","family":"Morgante","sequence":"additional","affiliation":[{"name":"Istituto di Genomica Applicata  Udine Italy"},{"name":"Department of Agricultural, Food, Environmental and Animal Sciences University of Udine Udine Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mario","family":"Ventura","sequence":"additional","affiliation":[{"name":"Department of Biosciences, Biotechnology and Environment University of Bari  Bari Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Glennis A.","family":"Logsdon","sequence":"additional","affiliation":[{"name":"Department of Genetics, Epigenetics Institute, Perelman School of Medicine University of Pennsylvania  Philadelphia Pennsylvania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudia R.","family":"Catacchio","sequence":"additional","affiliation":[{"name":"Department of Biosciences, Biotechnology and Environment University of Bari  Bari Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,7]]},"reference":[{"key":"e_1_2_17_2_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb\u20102007\u20108\u20107\u2010r148"},{"key":"e_1_2_17_3_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abl4178"},{"key":"e_1_2_17_4_1","doi-asserted-by":"publisher","DOI":"10.1002\/9780471729259.mca02as00"},{"key":"e_1_2_17_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008"},{"key":"e_1_2_17_6_1","doi-asserted-by":"publisher","DOI":"10.64898\/2026.04.09.717302"},{"key":"e_1_2_17_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010026\u201010841\u20109"},{"key":"e_1_2_17_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb.2562"},{"key":"e_1_2_17_9_1","unstructured":"Joshi N. 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