{"id":251,"date":"2018-12-02T16:39:00","date_gmt":"2018-12-02T08:39:00","guid":{"rendered":"https:\/\/www.next-bioinfo.tw\/?p=251"},"modified":"2023-09-04T16:52:44","modified_gmt":"2023-09-04T08:52:44","slug":"%e3%80%903d-genome%e3%80%91-hi-c-%e6%9f%93%e8%89%b2%e9%ab%94%e4%b8%89%e7%b6%ad%e7%b5%90%e6%a7%8b%e5%88%86%e6%9e%90%e6%8a%80%e8%a1%93%e7%b0%a1%e4%bb%8b","status":"publish","type":"post","link":"https:\/\/www.next-bioinfo.tw\/en\/2018\/12\/%e3%80%903d-genome%e3%80%91-hi-c-%e6%9f%93%e8%89%b2%e9%ab%94%e4%b8%89%e7%b6%ad%e7%b5%90%e6%a7%8b%e5%88%86%e6%9e%90%e6%8a%80%e8%a1%93%e7%b0%a1%e4%bb%8b\/","title":{"rendered":"\u30103D Genome\u3011 Introduction to Hi-C and 3D genomics"},"content":{"rendered":"<p>This article will introduce the basic concept of Hi-C technology. Hi-C is an analysis method for 3D chromosome organization. With Hi-C, we can observe the interaction between different sites on the chromosome.<\/p>\n\n\n\n<div id=\"ez-toc-container\" class=\"ez-toc-v2_0_54_1 counter-hierarchy ez-toc-counter ez-toc-grey ez-toc-container-direction\">\n<div class=\"ez-toc-title-container\">\n<p class=\"ez-toc-title\" >Table of Contents<\/p>\n<span class=\"ez-toc-title-toggle\"><a href=\"#\" class=\"ez-toc-pull-right ez-toc-btn ez-toc-btn-xs ez-toc-btn-default ez-toc-toggle\" aria-label=\"Toggle Table of Content\" role=\"button\"><label for=\"item-6a6d40dc4ec7e\" ><span class=\"\"><span style=\"display:none;\">Toggle<\/span><span class=\"ez-toc-icon-toggle-span\"><svg style=\"fill: #999;color:#999\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" class=\"list-377408\" width=\"20px\" height=\"20px\" viewbox=\"0 0 24 24\" fill=\"none\"><path d=\"M6 6H4v2h2V6zm14 0H8v2h12V6zM4 11h2v2H4v-2zm16 0H8v2h12v-2zM4 16h2v2H4v-2zm16 0H8v2h12v-2z\" fill=\"currentColor\"><\/path><\/svg><svg style=\"fill: #999;color:#999\" class=\"arrow-unsorted-368013\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" width=\"10px\" height=\"10px\" viewbox=\"0 0 24 24\" version=\"1.2\" baseprofile=\"tiny\"><path d=\"M18.2 9.3l-6.2-6.3-6.2 6.3c-.2.2-.3.4-.3.7s.1.5.3.7c.2.2.4.3.7.3h11c.3 0 .5-.1.7-.3.2-.2.3-.5.3-.7s-.1-.5-.3-.7zM5.8 14.7l6.2 6.3 6.2-6.3c.2-.2.3-.5.3-.7s-.1-.5-.3-.7c-.2-.2-.4-.3-.7-.3h-11c-.3 0-.5.1-.7.3-.2.2-.3.5-.3.7s.1.5.3.7z\"\/><\/svg><\/span><\/span><\/label><input aria-label=\"Toggle\" type=\"checkbox\"  id=\"item-6a6d40dc4ec7e\"><\/a><\/span><\/div>\n<nav><ul class='ez-toc-list ez-toc-list-level-1' ><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-1\" href=\"https:\/\/www.next-bioinfo.tw\/en\/2018\/12\/%e3%80%903d-genome%e3%80%91-hi-c-%e6%9f%93%e8%89%b2%e9%ab%94%e4%b8%89%e7%b6%ad%e7%b5%90%e6%a7%8b%e5%88%86%e6%9e%90%e6%8a%80%e8%a1%93%e7%b0%a1%e4%bb%8b\/#%E4%BD%95%E8%AC%82Hi-C\" title=\"\u4f55\u8b02Hi-C\">\u4f55\u8b02Hi-C<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-2\" href=\"https:\/\/www.next-bioinfo.tw\/en\/2018\/12\/%e3%80%903d-genome%e3%80%91-hi-c-%e6%9f%93%e8%89%b2%e9%ab%94%e4%b8%89%e7%b6%ad%e7%b5%90%e6%a7%8b%e5%88%86%e6%9e%90%e6%8a%80%e8%a1%93%e7%b0%a1%e4%bb%8b\/#Hi-C%E7%9A%84%E5%AF%A6%E9%A9%97%E6%B5%81%E7%A8%8B\" title=\"Hi-C\u7684\u5be6\u9a57\u6d41\u7a0b\">Hi-C\u7684\u5be6\u9a57\u6d41\u7a0b<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-3\" href=\"https:\/\/www.next-bioinfo.tw\/en\/2018\/12\/%e3%80%903d-genome%e3%80%91-hi-c-%e6%9f%93%e8%89%b2%e9%ab%94%e4%b8%89%e7%b6%ad%e7%b5%90%e6%a7%8b%e5%88%86%e6%9e%90%e6%8a%80%e8%a1%93%e7%b0%a1%e4%bb%8b\/#Hi-C%E5%AF%A6%E5%8B%99%E4%B8%8A%E7%9A%84%E9%9B%A3%E8%99%95\" title=\"Hi-C\u5be6\u52d9\u4e0a\u7684\u96e3\u8655\">Hi-C\u5be6\u52d9\u4e0a\u7684\u96e3\u8655<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-4\" href=\"https:\/\/www.next-bioinfo.tw\/en\/2018\/12\/%e3%80%903d-genome%e3%80%91-hi-c-%e6%9f%93%e8%89%b2%e9%ab%94%e4%b8%89%e7%b6%ad%e7%b5%90%e6%a7%8b%e5%88%86%e6%9e%90%e6%8a%80%e8%a1%93%e7%b0%a1%e4%bb%8b\/#Hi-C%E9%AB%94%E9%A9%97\" title=\"Hi-C\u9ad4\u9a57\">Hi-C\u9ad4\u9a57<\/a><\/li><\/ul><\/nav><\/div>\n<h3 class=\"wp-block-heading has-medium-font-size\"><span class=\"ez-toc-section\" id=\"%E4%BD%95%E8%AC%82Hi-C\"><\/span>\u4f55\u8b02Hi-C<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p>Hi-C \u5168\u7a31\u70ba\u9ad8\u901a\u91cf\u67d3\u8272\u9ad4\u4e09\u7dad\u69cb\u8c61\u6355\u7372\u6280\u8853\uff08High-throughput chromosome conformation capture\uff09\u5229\u7528\u6b21\u4e16\u4ee3\u5b9a\u5e8f(Next Generation Sequencing, NGS)\u7684\u5feb\u901f\u4e14\u4fbf\u5b9c\u7684\u5927\u91cf\u5b9a\u5e8f\u80fd\u529b\uff0c\u4e26\u7d50\u5408\u5de8\u91cf\u8cc7\u6599\u8655\u7406\u4ee5\u53ca\u7d71\u8a08\u7684\u4e00\u7a2e\u7814\u8868\u89c0\u907a\u50b3\u5b78(epigenetics)\u7684\u5229\u5668\u3002\u4e3b\u8981\u80fd\u5efa\u69cb\u67d3\u8272\u9ad4\u5728\u4e09\u7dad\u7a7a\u9593\u4e2d\u7684\u4e92\u4f5c\u95dc\u4fc2\uff0c\u4e26\u642d\u914d\u5176\u4ed6\u7d44\u5b78\u5206\u6790(\u4f8b\u5982ATAC-Seq , ChIP-Seq \u7b49)\u4f86\u89c0\u5bdf\u67d3\u8272\u9ad4\u76f8\u4e92\u4f5c\u7528\u751a\u81f3\u5230\u7279\u5b9a\u57fa\u56e0\u4f4d\u9ede\u7684\u8abf\u63a7\u72c0\u614b\u3002<\/p>\n\n\n\n<p>\u67d3\u8272\u8cea\u74b0(Chromatin Loops)\u88ab\u8a8d\u70ba\u662f\u4e00\u6bb5\u57fa\u56e0\u9032\u884c\u8f49\u9304\u6642\u9700\u8981\u5efa\u7acb\u7684\u7269\u7406\u7d50\u69cb\uff0c\u67d3\u8272\u8cea\u6703\u88ab\u5851\u578b\u5143\u4ef6(\u4f8b\u5982CTCF)\u51f9\u6210\u74b0\u578b\uff0c\u800c\u9019\u5fae\u89c0\u7684\u7269\u7406\u7d50\u69cb\u80fd\u8b93\u539f\u672c\u5728\u5e8f\u5217\u4e0a\u7a7a\u9593\u4e0d\u9130\u8fd1\u7684\u4f4d\u9ede(\u6709\u53ef\u80fd\u662f\u5916\u986f\u5b50\uff0c\u4f46\u4e5f\u53ef\u80fd\u662f\u589e\u5f37\u5b50\u6216\u662f\u555f\u52d5\u5b50\u7b49\u7b49)\uff0c\u8f49\u8b8a\u6210\u5f7c\u6b64\u9130\u8fd1\u7684\u4f4d\u7f6e(\u9019\u9053\u7406\u6709\u9ede\u985e\u4f3c\u6642\u7a7a\u626d\u66f2\u6539\u8b8a\u7269\u7406\u76f4\u7dda\u8ddd\u96e2\u7684\u6982\u5ff5)\uff0c\u4e26\u53ef\u80fd\u5229\u7528\u9019\u500b\u7269\u7406\u7d50\u69cb\u4f86\u9032\u884c\u5404\u7a2e\u8f49\u9304\u5de5\u4f5c\u3002\u67d3\u8272\u8cea\u74b0\u4ee5\u53ca\u76f8\u95dc\u7684\u7d50\u69cb\u53ef\u4ee5\u900f\u904eHi-C\u6280\u8853\uff0c\u4ee5\u8cc7\u6599\u7d71\u8a08\u7684\u65b9\u5f0f\u5f97\u51fa\u3002<\/p>\n\n\n\n<figure class=\"wp-block-embed is-type-video is-provider-youtube wp-block-embed-youtube wp-embed-aspect-16-9 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<iframe title=\"MCB 182 Lecture 10.5 - Visualization of Hi-C data, bias in the Hi-C assay\" width=\"500\" height=\"281\" src=\"https:\/\/www.youtube.com\/embed\/gRNO_GlJLuU?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe>\n<\/div><\/figure>\n\n\n\n<figure class=\"wp-block-embed is-type-video is-provider-youtube wp-block-embed-youtube wp-embed-aspect-16-9 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<iframe title=\"MCB 182 Lecture 10.7 - Chromatin looping, loop extrusion model\" width=\"500\" height=\"281\" src=\"https:\/\/www.youtube.com\/embed\/VfnolfaUMNE?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe>\n<\/div><\/figure>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Hi-C%E7%9A%84%E5%AF%A6%E9%A9%97%E6%B5%81%E7%A8%8B\"><\/span>Hi-C\u7684\u5be6\u9a57\u6d41\u7a0b<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" width=\"794\" height=\"523\" src=\"https:\/\/ml4fi34j3t2e.i.optimole.com\/w:auto\/h:auto\/q:mauto\/f:avif\/https:\/\/www.next-bioinfo.tw\/wp-content\/uploads\/2023\/09\/image.png\" alt=\"\" class=\"wp-image-252\"\/><figcaption class=\"wp-element-caption\"><strong><br>Boxer, L.D. (2010). Hi-C: Genome-wide Chromosome Conformation Capture.Figure2<\/strong><\/figcaption><\/figure>\n\n\n\n<p>\u70ba\u4e86\u5efa\u7acb\u4efb\u610f\u67d3\u8272\u8cea\u4e4b\u9593\u4efb\u610f\u4f4d\u9ede\u9593\u7684\u4ea4\u4e92\u4f5c\u7528\u983b\u7387\u77e9\u9663\uff0c\u9700\u8981\u5148\u5c07\u7a7a\u9593\u4e0a\u9130\u8fd1\u7684\u67d3\u8272\u8cea\u4f5ccrosslinking\uff0c\u7528\u9650\u5236\u6027\u5167\u5207\u9176\u5207\u65b7\u67d3\u8272\u8cea\uff0c\u518d\u5c07\u9019\u4e9b\u7247\u6bb5\u6253\u788e\u7528\u5f8c\u4e26\u5b9a\u5e8f\u3002<\/p>\n\n\n\n<p>\u5b9a\u5e8f\u5f8c\u7684\u6bcf\u7b46\u8cc7\u6599\u6703\u5206\u5225\u4f86\u81ea\u5169\u500b\u4e0d\u540c\u7684\u4f4d\u7f6e\uff0c\u9808\u5c07\u9019\u4e00\u5c0d\u7684\u5169\u6bb5\u67d3\u8272\u9ad4\u5bc6\u78bc\u5206\u5225\u9032\u884c\u6bd4\u5c0d\uff0c\u4e26\u8a18\u9304\u5b83\u5011\u5206\u5225\u662f\u4f86\u81ea\u54ea\u500b\u67d3\u8272\u9ad4\u7684\u4f4d\u9ede\u3002\u518d\u900f\u904e\u6578\u91cf\u9f90\u5927\u7684\u6210\u5c0d\u7684\u8cc7\u6599\u9032\u884c\u7d71\u8a08\uff0c\u6700\u7d42\u5c31\u53ef\u4ee5\u5efa\u7acb\u6240\u6709\u67d3\u8272\u9ad4\u7684\u4efb\u610f\u4f4d)\u9ede\u5c0d\u6240\u6709\u67d3\u8272\u9ad4\u7684\u4efb\u610f\u4f4d\u9ede\u4e4b\u9593\u7684\u95dc\u806f\u983b\u7387\uff0c\u5f62\u6210\u4e00\u500b\u5de8\u5927\u7684\u77e9\u9663\uff0c\u9019\u88e1\u8209\u500b\u4f8b\u5982\u4e0b\u5716<\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized is-style-default\"><img decoding=\"async\" src=\"https:\/\/aistudio.tw\/wp-content\/uploads\/2023\/01\/\u4e0b\u8f09.png\" alt=\"\" class=\"wp-image-346\" style=\"width:576px;height:576px\" width=\"576\" height=\"576\"\/><figcaption class=\"wp-element-caption\"><strong>chr1:1-249,250,621  vs chr1:1-249,250,621<\/strong><br>Rao, S. S. P.,et.al. (2017). Cohesin Loss Eliminates All Loop Domains. Cell, 171(2), 305\u2013320.e24. https:\/\/doi.org\/10.1016\/j.cell.2017.09.026<\/figcaption><\/figure>\n\n\n\n<p>\u5982\u518d\u642d\u914d\u57fa\u56e0\u7d44\u5b78\u6280\u8853\uff0c\u4f8b\u5982\u7d93\u5178\u7684ChIP-Seq (\u67d3\u8272\u8cea\u514d\u75ab\u5171\u6c89\u6fb1\u5b9a\u5e8f)\u7b49\u65b9\u6cd5\uff0c\u5c31\u53ef\u4ee5\u5efa\u7acb\u8ffd\u8e64\u5f9e\u67d3\u8272\u9ad4\u7a7a\u9593\u4e92\u4f5c\u5230\u95dc\u806f\u7684\u86cb\u767d\u8cea\u6216\u662f\u8f49\u9304\u56e0\u5b50\u7684\u904b\u4f5c\u60c5\u6cc1\u3002<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Hi-C%E5%AF%A6%E5%8B%99%E4%B8%8A%E7%9A%84%E9%9B%A3%E8%99%95\"><\/span>Hi-C\u5be6\u52d9\u4e0a\u7684\u96e3\u8655<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p>Hi-C\u4ee5\u53ca\u76f8\u95dc\u7684\u4e09\u7dad\u5ea6\u57fa\u56e0\u7d44\u5b78\u7684\u96e3\u8655\u662f\u5b9a\u5e8f\u6602\u8cb4\u5230\u8a08\u7b97\u7684\u786c\u9ad4\u8a2d\u65bd\u5c0d\u8a18\u61b6\u9ad4\u548c\u786c\u789f\u7684\u8981\u6c42\u5de8\u5927\u800c\u4e14\u6602\u8cb4\uff0c\u4e00\u500breplicate\u6574\u5957\u8655\u7406\u4e0b\u4f86\u52d5\u8f12\u6d88\u8017\u6389\u5e7e\u767eGB\u5230TB\u7684\u5132\u5b58\u7a7a\u9593\u3002(\u901a\u5e38\u5728\u8dd1\u5b9a\u5e8f\u6df1\u5ea6\u8f03\u6df1\u7684\u6a23\u672c\u4e4b\u524d\uff0c\u6703\u8dd1\u5b9a\u5e8f\u8f03\u6dfa\u7684\u4f86\u505a\u6e2c\u8a66\uff0c\u9019\u88e1\u6307\u7684\u662f\u5b9a\u5e8f\u8f03\u6df1\u7684\u6b63\u5f0f\u6a23\u672c)\u4e0d\u904e\uff0c\u4e5f\u662f\u4ee3\u8868\u9032\u5165Hi-C\u6280\u8853\u7684\u9580\u6abb\uff0c\u5176\u4e2d\u4e00\u9805\u662f\u5c31\u662f\u540c\u6642\u719f\u6089HPC\u74b0\u5883\u548cBioinformatics\u3002<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Hi-C%E9%AB%94%E9%A9%97\"><\/span>Hi-C\u9ad4\u9a57<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p>\u00a0<a rel=\"noreferrer noopener\" href=\"https:\/\/aidenlab.org\/\" target=\"_blank\">Aiden Lab<\/a> \u6709\u958b\u767c\u4e86\u4e00\u5957\u7dda\u4e0a\u7248\u7684Hi-C\u8996\u89ba\u5316\u5de5\u5177(https:\/\/aidenlab)\uff0c\u65b9\u4fbf\u6211\u5011\u02d9\u700f\u89bd\u904e\u5f80Hi-C\u8ad6\u6587\u7684HiC\u6578\u64da\uff0c\u9019\u908a\u5c31\u76f4\u63a5\u5d4c\u9032\u4f86\u8b93\u5927\u5bb6\u9ad4\u9a57\u4e00\u4e0b\u64cd\u4f5c\uff1a<\/p>\n\n\n\n<iframe frameborder=\"0\" src=\"https:\/\/aidenlab.org\/juicebox\/\" class=\"\" allowfullscreen style=\"width:100%;max-width:100%;height:320px\"><\/iframe>\n\n\n\n<p>\u4ee5\u4e0a\u5c31\u662fHiC\u6280\u8853\u7684\u7c21\u55ae\u5206\u4eab\u3002<\/p>","protected":false},"excerpt":{"rendered":"<p>\u672c\u7bc7\u6587\u7ae0\u5c07\u7c21\u55ae\u4ecb\u7d39Hi-C\u9019\u500b\u6280\u8853\u7684\u57fa\u672c\u6982\u5ff5\uff0cHi-C\u662f\u67d3\u8272\u9ad4\u7d50\u69cb\u6355\u6349\u7684\u4e00\u500b\u5206\u652f\u3002\u900f\u904eHi-C\uff0c\u6211\u5011\u80fd\u5efa\u7acb\u67d3\u8272 [&hellip;]<\/p>","protected":false},"author":1,"featured_media":264,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_mi_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"site-container-style":"default","site-container-layout":"default","site-sidebar-layout":"default","site-transparent-header":"default","disable-article-header":"default","disable-site-header":"default","disable-site-footer":"default","disable-content-area-spacing":"default","footnotes":""},"categories":[20],"tags":[21,23,22,24],"_links":{"self":[{"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/posts\/251"}],"collection":[{"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/comments?post=251"}],"version-history":[{"count":13,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/posts\/251\/revisions"}],"predecessor-version":[{"id":266,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/posts\/251\/revisions\/266"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/media\/264"}],"wp:attachment":[{"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/media?parent=251"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/categories?post=251"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/tags?post=251"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}