{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T14:52:58Z","timestamp":1786978378225,"version":"build-2736575974"},"reference-count":37,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2022,3,28]],"date-time":"2022-03-28T00:00:00Z","timestamp":1648425600000},"content-version":"vor","delay-in-days":27,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Plant Direct"],"published-print":{"date-parts":[[2022,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    The eukaryotic green alga\n                    <jats:italic>Chromochloris zofingiensis<\/jats:italic>\n                    is a reference organism for studying carbon partitioning and a promising candidate for the production of biofuel precursors. Recent transcriptome profiling transformed our understanding of its biology and generally algal biology, but epigenetic regulation remains understudied and represents a fundamental gap in our understanding of algal gene expression. Chromatin immunoprecipitation followed by deep sequencing (ChIP\u2010Seq) is a powerful tool for the discovery of such mechanisms, by identifying genome\u2010wide histone modification patterns and transcription factor\u2010binding sites alike. Here, we established a ChIP\u2010Seq framework for\n                    <jats:italic>Chr.\u00a0zofingiensis<\/jats:italic>\n                    yielding over 20 million high\u2010quality reads per sample. The most critical steps in a ChIP experiment were optimized, including DNA shearing to obtain an average DNA fragment size of 250\u2009bp and assessment of the recommended formaldehyde concentration for optimal DNA\u2013protein cross\u2010linking. We used this ChIP\u2010Seq framework to generate a genome\u2010wide map of the H3K4me3 distribution pattern and to integrate these data with matching RNA\u2010Seq data. In line with observations from other organisms, H3K4me3 marks predominantly transcription start sites of genes. Our H3K4me3 ChIP\u2010Seq data will pave the way for improved genome structural annotation in the emerging reference alga\n                    <jats:italic>Chr.\u00a0zofingiensis<\/jats:italic>\n                    .\n                  <\/jats:p>","DOI":"10.1002\/pld3.392","type":"journal-article","created":{"date-parts":[[2022,3,29]],"date-time":"2022-03-29T02:19:59Z","timestamp":1648520399000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["An optimized ChIP\u2010Seq framework for profiling histone modifications in\n                    <i>Chromochloris zofingiensis<\/i>"],"prefix":"10.1002","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3420-1332","authenticated-orcid":false,"given":"Daniela","family":"Strenkert","sequence":"first","affiliation":[{"name":"California Institute for Quantitative Biosciences University of California, Berkeley  Berkeley CA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7917-1432","authenticated-orcid":false,"given":"Matthew","family":"Mingay","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute Lawrence Berkeley National Laboratory  Berkeley CA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7487-8014","authenticated-orcid":false,"given":"Stefan","family":"Schmollinger","sequence":"additional","affiliation":[{"name":"California Institute for Quantitative Biosciences University of California, Berkeley  Berkeley CA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7539-103X","authenticated-orcid":false,"given":"Cindy","family":"Chen","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute Lawrence Berkeley National Laboratory  Berkeley CA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4907-0339","authenticated-orcid":false,"given":"Ronan C.","family":"O'Malley","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute Lawrence Berkeley National Laboratory  Berkeley CA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2594-509X","authenticated-orcid":false,"given":"Sabeeha S.","family":"Merchant","sequence":"additional","affiliation":[{"name":"Department of Plant and Microbial Biology University of California, Berkeley  Berkeley CA USA"},{"name":"Department of Molecular &amp; Cell Biology University of California, Berkeley  Berkeley CA USA"},{"name":"Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory  Berkeley CA 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