{"id":988,"date":"2026-07-15T08:45:38","date_gmt":"2026-07-14T23:45:38","guid":{"rendered":"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/?post_type=information&#038;p=988"},"modified":"2026-07-22T08:55:56","modified_gmt":"2026-07-21T23:55:56","slug":"%e5%8a%a0%e8%97%a4%e5%85%ac%e5%8b%9f%e7%a0%94%e7%a9%b6%e3%81%ab%e3%82%88%e3%82%8b%e6%88%90%e6%9e%9c%e3%81%8cgene%e8%aa%8c%e3%81%ab%e6%8e%b2%e8%bc%89%e3%81%95%e3%82%8c%e3%81%be%e3%81%97%e3%81%9f","status":"publish","type":"information","link":"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/archives\/information\/%e5%8a%a0%e8%97%a4%e5%85%ac%e5%8b%9f%e7%a0%94%e7%a9%b6%e3%81%ab%e3%82%88%e3%82%8b%e6%88%90%e6%9e%9c%e3%81%8cgene%e8%aa%8c%e3%81%ab%e6%8e%b2%e8%bc%89%e3%81%95%e3%82%8c%e3%81%be%e3%81%97%e3%81%9f","title":{"rendered":"\u52a0\u85e4\u516c\u52df\u7814\u7a76\u306b\u3088\u308b\u6210\u679c\u304cGene\u8a8c\u306b\u63b2\u8f09\u3055\u308c\u307e\u3057\u305f!"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\"><strong>A low-input CUT&amp;RUN-qPCR method for histone modification profiling in Daphnia magna embryos<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Nikko Adhitama, Daffa Ramadhan Aridis, Nong Dang Quang, Pijar Religia, Yasuhiko Kato, Hajime Watanabe<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Abstract<\/strong><br>Understanding how organisms translate environmental variation into phenotypic variation is a central question in ecology and evolution. Histone modifications are key epigenetic regulators underlying phenotypic plasticity, enabling the generation of distinct phenotypes from a single genome. Cleavage Under Targets and Release Using Nuclease (CUT&amp;RUN) is a powerful method for profiling histone modifications from low amounts of starting material. Here, we adapted a low-input CUT&amp;RUN-qPCR protocol for embryos of the freshwater crustacean Daphnia magna, an emerging model for studying the molecular mechanisms of phenotypic plasticity. We established a cell dissociation protocol and applied the method to the male-determining gene doublesex1 (dsx1) locus during environmentally induced sex determination. CUT&amp;RUN-qPCR detected male-biased enrichment of the active histone mark H3K4me3 at the dsx1 transcription start sites, whereas the repressive marks H3K9me3 and H3K27me3 showed higher enrichment in females. Using a dsx1 reporter strain in which dsx1-expressing cells are labeled with mCherry, we estimated that mCherry-positive cells comprise approximately 11% of dissociated male embryonic cells. Despite this heterogeneity, sex-biased H3K4me3 enrichment at dsx1 remained detectable from cells derived from as few as 20 embryos, corresponding to on the order of a few thousand target cells per reaction. This benchmark provides a practical guideline for planning CUT&amp;RUN input requirements in heterogeneous and low-input samples. Our study establishes CUT&amp;RUN-qPCR as a practical approach for histone modification profiling in Daphnia and provides a methodological basis for future work on the epigenetic underpinnings of phenotypic plasticity.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong><em>Gene<\/em><\/strong>, 1010, 150317. doi: 10.1016\/j.gene.2026.150317. (2026)<br><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0378111926003276\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0378111926003276<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>A low-input CUT&amp;RUN-qPCR method for histone modification profiling in Daphni &#8230; <\/p>\n","protected":false},"featured_media":0,"menu_order":0,"template":"","format":"standard","meta":{"footnotes":""},"class_list":["post-988","information","type-information","status-publish","format-standard","hentry"],"_links":{"self":[{"href":"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/wp-json\/wp\/v2\/information\/988","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/wp-json\/wp\/v2\/information"}],"about":[{"href":"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/wp-json\/wp\/v2\/types\/information"}],"version-history":[{"count":1,"href":"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/wp-json\/wp\/v2\/information\/988\/revisions"}],"predecessor-version":[{"id":989,"href":"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/wp-json\/wp\/v2\/information\/988\/revisions\/989"}],"wp:attachment":[{"href":"https:\/\/www.bioreg.kyushu-u.ac.jp\/ext\/epicode\/wp-json\/wp\/v2\/media?parent=988"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}