{"id":1200,"date":"2020-04-03T16:43:00","date_gmt":"2020-04-03T16:43:00","guid":{"rendered":"https:\/\/www.embl.org\/groups\/zaugg\/?p=1200"},"modified":"2022-06-07T16:45:18","modified_gmt":"2022-06-07T16:45:18","slug":"our-paper-on-gene-regulatory-networks-to-understand-disease-mechanism-of-pulmonary-arterial-hypertension-pah-is-out","status":"publish","type":"post","link":"https:\/\/www.embl.org\/groups\/zaugg\/blog\/2020\/04\/our-paper-on-gene-regulatory-networks-to-understand-disease-mechanism-of-pulmonary-arterial-hypertension-pah-is-out\/","title":{"rendered":"Our paper on gene regulatory networks to understand disease mechanism of pulmonary arterial hypertension (PAH) is out!"},"content":{"rendered":"\n<p>This work results from a collaboration with 2 groups at Stanford. Check it out here: https:\/\/www.nature.com\/articles\/s41467-020-15463-x<\/p>\n\n\n\n<p>Our main take-home messages from the study:<br>1) Chromatin is more sensitive than RNA to capture a cell&#8217;s regulatory state<br>2) Chromatin changes are best interpreted in the context of a gene regulatory network<br>3) The PAH phenotype in pulmonary arterial endothelial cells involves a complex network of different processes that are reflected in epigenetic marks<\/p>\n\n\n\n<figure class=\"vf-figure wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"258\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/groups\/zaugg\/wp-content\/uploads\/2022\/06\/websummary-1024x258.png\" alt=\"\" class=\"wp-image-1156\" srcset=\"https:\/\/www.embl.org\/groups\/zaugg\/wp-content\/uploads\/2022\/06\/websummary-1024x258.png 1024w, https:\/\/www.embl.org\/groups\/zaugg\/wp-content\/uploads\/2022\/06\/websummary-300x76.png 300w, https:\/\/www.embl.org\/groups\/zaugg\/wp-content\/uploads\/2022\/06\/websummary-768x194.png 768w, https:\/\/www.embl.org\/groups\/zaugg\/wp-content\/uploads\/2022\/06\/websummary-1536x387.png 1536w, https:\/\/www.embl.org\/groups\/zaugg\/wp-content\/uploads\/2022\/06\/websummary-2048x516.png 2048w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p>A striking part of this study was that we didn&#8217;t find any detectable difference in gene expression, yet huge changes in H3K27ac marks, which recapitulated differential activity in almost all known PAH TFs (using <a href=\"https:\/\/www.zaugg.embl.de\/data-and-tools\/difftf\/\">diffTF<\/a>) and suggested a complete rewiring of the gene regulatory network. The changes in the regulatory network converge on endothelial to mesenchymal transition and response to signaling. And follow-up experiments confirmed that genes with differential H3K27ac in enhancers show a differential response to endogenous stimuli despite the no difference at baseline expression.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>This work results from a collaboration with 2 groups at Stanford. Check it out here: https:\/\/www.nature.com\/articles\/s41467-020-15463-x Our main take-home messages from the study:1) Chromatin is more sensitive than RNA to capture a cell&#8217;s regulatory state2) Chromatin changes are best&hellip;<\/p>\n","protected":false},"author":5,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[8828],"tags":[],"embl_taxonomy":[],"class_list":["post-1200","post","type-post","status-publish","format-standard","hentry","category-new-publication"],"acf":[],"embl_taxonomy_terms":[],"featured_image_src":"https:\/\/www.embl.org\/groups\/zaugg\/wp-includes\/images\/media\/default.svg","_links":{"self":[{"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/posts\/1200","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/users\/5"}],"replies":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/comments?post=1200"}],"version-history":[{"count":1,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/posts\/1200\/revisions"}],"predecessor-version":[{"id":1202,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/posts\/1200\/revisions\/1202"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/media?parent=1200"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/categories?post=1200"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/tags?post=1200"},{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/embl_taxonomy?post=1200"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}