{"id":240129,"date":"2026-07-01T23:15:46","date_gmt":"2026-07-02T04:15:46","guid":{"rendered":"https:\/\/lifeboat.com\/blog\/2026\/07\/rna-folding-energy-of-long-range-genomic-interactions-regulates-discontinuous-transcription-in-sars-cov-2"},"modified":"2026-07-01T23:15:46","modified_gmt":"2026-07-02T04:15:46","slug":"rna-folding-energy-of-long-range-genomic-interactions-regulates-discontinuous-transcription-in-sars-cov-2","status":"publish","type":"post","link":"https:\/\/lifeboat.com\/blog\/2026\/07\/rna-folding-energy-of-long-range-genomic-interactions-regulates-discontinuous-transcription-in-sars-cov-2","title":{"rendered":"RNA Folding Energy of Long-Range Genomic Interactions Regulates Discontinuous Transcription in SARS-CoV-2"},"content":{"rendered":"<p style=\"padding-right: 20px\"><a class=\"aligncenter blog-photo\" href=\"https:\/\/lifeboat.com\/blog.images\/rna-folding-energy-of-long-range-genomic-interactions-regulates-discontinuous-transcription-in-sars-cov-2.jpg\"><\/a><\/p>\n<p>Coronaviruses use discontinuous transcription to generate subgenomic RNAs (sgRNAs) that encode structural and accessory proteins. However, the factors regulating sgRNA abundance in SARS-CoV-2 remain unclear. Here, we combined strand-specific RNA sequencing, RNA\u2013RNA interaction mapping, prediction of RNA folding energies, and targeted mutagenesis to define the regulation of (\u2013) sgRNA synthesis in SARS-CoV-2 infection. We demonstrated that the relative (\u2013) sgRNA abundance across viral genes is stable throughout infection and largely correlates with corresponding (+) sgmRNA levels. Through meta-analysis of published SPLASH data, we found that the frequency of long-range interactions between the 5\u2032 genomic transcription regulatory sequence TRS-Leader and downstream TRS-Body sequences correlates with sgRNA abundance.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Coronaviruses use discontinuous transcription to generate subgenomic RNAs (sgRNAs) that encode structural and accessory proteins. However, the factors regulating sgRNA abundance in SARS-CoV-2 remain unclear. Here, we combined strand-specific RNA sequencing, RNA\u2013RNA interaction mapping, prediction of RNA folding energies, and targeted mutagenesis to define the regulation of (\u2013) sgRNA synthesis in SARS-CoV-2 infection. We demonstrated [\u2026]<\/p>\n","protected":false},"author":662,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[11,1497,1965],"tags":[],"class_list":["post-240129","post","type-post","status-publish","format-standard","hentry","category-biotech-medical","category-energy","category-mapping"],"_links":{"self":[{"href":"https:\/\/lifeboat.com\/blog\/wp-json\/wp\/v2\/posts\/240129","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/lifeboat.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/lifeboat.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/lifeboat.com\/blog\/wp-json\/wp\/v2\/users\/662"}],"replies":[{"embeddable":true,"href":"https:\/\/lifeboat.com\/blog\/wp-json\/wp\/v2\/comments?post=240129"}],"version-history":[{"count":0,"href":"https:\/\/lifeboat.com\/blog\/wp-json\/wp\/v2\/posts\/240129\/revisions"}],"wp:attachment":[{"href":"https:\/\/lifeboat.com\/blog\/wp-json\/wp\/v2\/media?parent=240129"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/lifeboat.com\/blog\/wp-json\/wp\/v2\/categories?post=240129"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/lifeboat.com\/blog\/wp-json\/wp\/v2\/tags?post=240129"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}