{"id":2787,"date":"2023-06-13T01:08:24","date_gmt":"2023-06-13T00:08:24","guid":{"rendered":"https:\/\/archive.belbi.bg.ac.rs\/2023\/?post_type=abstract&p=2787"},"modified":"2023-06-14T18:37:23","modified_gmt":"2023-06-14T17:37:23","slug":"alternative-splicing-impacts-microrna-regulation-within-coding-regions","status":"publish","type":"abstract","link":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/alternative-splicing-impacts-microrna-regulation-within-coding-regions\/","title":{"rendered":"Alternative splicing impacts microRNA regulation within coding regions"},"content":{"rendered":"\n

Lena Maria Hackl1*<\/sup>, Amit Fenn1,2<\/sup>, Zakaria Louadi1,2<\/sup>, Jan Baumbach1,3<\/sup>, Tim Kacprowski4,5<\/sup>, Markus List2<\/sup> and Olga Tsoy1<\/sup><\/p>\n\n\n\n

1<\/sup>Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany<\/p>\n\n\n\n

2<\/sup>Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Arcisstra\u00dfe 21, 80333 Munich, Germany<\/p>\n\n\n\n

3<\/sup>Computational BioMedicine Lab, University of Southern Denmark, Campusvej 50, 5230 Odense, Denmark<\/p>\n\n\n\n

4<\/sup>Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Rebenring 56, 38106 Braunschweig, Germany<\/p>\n\n\n\n

5<\/sup>Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Rebenring 56, 38106 Braunschweig, Germany<\/p>\n\n\n\n

olga.tsoy [at] uni-hamburg.de<\/p>\n\n\n\n

Abstract<\/strong><\/p>\n\n\n\n

MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate post-transcriptional gene expression by binding to specific target sites. Approximately 95% of human multi-exon genes can be spliced alternatively, which enables the production of functionally diverse transcripts and proteins from a single gene. In complex diseases, such as cancer, gene but also miRNA dysregulation plays a significant role. According to most studies miRNAs preferably bind to 3\u2019-untranslated regions of mRNA. However, through alternative splicing, transcripts might lose exons harboring miRNA target sites and, hence, become unresponsive to miRNA regulation. <\/p>\n\n\n\n

To check this hypothesis, we studied the role of miRNA target sites in both coding and noncoding regions using six cancer data sets from The Cancer Genome Atlas (TCGA). First, we predicted miRNA target sites on mRNAs from their sequence using TarPmiR. For our analysis, we focused on miRNAs whose expression was negatively correlated with gene expression (as evidence for active regulation) as well as genes that were at least moderately expressed and showed evidence of alternative splicing. We chose different subsets of transcripts to differentiate the effects of target sites in different gene regions. To check whether alternative splicing interferes with miRNA regulation, we trained linear regression models to predict miRNA expression from transcript expression. Using nested models, we compared the predictive power of transcripts with miRNA target sites to that of transcripts without target sites in the investigated gene region. For all six cancer data sets and all subsets, models containing transcripts with target sites predicted miRNA abundance signi\ufb01cantly better. <\/p>\n\n\n\n

We conclude that alternative splicing does interfere with miRNA regulation by skipping exons with miRNA target sites within the coding region.<\/p>\n\n\n\n

Keywords:<\/strong> alternative splicing, miRNA, machine learning, nested models, cancer<\/p>\n","protected":false},"excerpt":{"rendered":"

Lena Maria Hackl1*<\/sup>, Amit Fenn1,2<\/sup>, Zakaria Louadi1,2<\/sup>, Jan Baumbach1,3<\/sup>, Tim Kacprowski4,5<\/sup>, Markus List2<\/sup> and Olga Tsoy1<\/sup><\/p>\n

1<\/sup>Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany<\/p>\n

2<\/sup>Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Arcisstra\u00dfe 21, 80333 Munich, Germany<\/p>\n

3<\/sup>Computational BioMedicine Lab, University of Southern Denmark, Campusvej 50, 5230 Odense, Denmark<\/p>\n

4<\/sup>Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Rebenring 56, 38106 Braunschweig, Germany<\/p>\n

5<\/sup>Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Rebenring 56, 38106 Braunschweig, Germany<\/p>\n

Continue reading<\/span><\/i><\/a> <\/p>\n","protected":false},"author":162,"featured_media":0,"template":"","categories":[18],"tags":[],"yoast_head":"\nAlternative splicing impacts microRNA regulation within coding regions - BelBi 2023<\/title>\n<meta name=\"robots\" content=\"noindex, follow\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Alternative splicing impacts microRNA regulation within coding regions - BelBi 2023\" \/>\n<meta property=\"og:description\" content=\"Lena Maria Hackl1*, Amit Fenn1,2, Zakaria Louadi1,2, Jan Baumbach1,3, Tim Kacprowski4,5, Markus List2 and Olga Tsoy11Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany2Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Arcisstra\u00dfe 21, 80333 Munich, Germany3Computational BioMedicine Lab, University of Southern Denmark, Campusvej 50, 5230 Odense, Denmark4Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Rebenring 56, 38106 Braunschweig, Germany5Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Rebenring 56, 38106 Braunschweig, Germany Continue reading\" \/>\n<meta property=\"og:url\" content=\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/alternative-splicing-impacts-microrna-regulation-within-coding-regions\/\" \/>\n<meta property=\"og:site_name\" content=\"BelBi 2023\" \/>\n<meta property=\"article:modified_time\" content=\"2023-06-14T17:37:23+00:00\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"2 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/alternative-splicing-impacts-microrna-regulation-within-coding-regions\/\",\"url\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/alternative-splicing-impacts-microrna-regulation-within-coding-regions\/\",\"name\":\"Alternative splicing impacts microRNA regulation within coding regions - BelBi 2023\",\"isPartOf\":{\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#website\"},\"datePublished\":\"2023-06-13T00:08:24+00:00\",\"dateModified\":\"2023-06-14T17:37:23+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/alternative-splicing-impacts-microrna-regulation-within-coding-regions\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/alternative-splicing-impacts-microrna-regulation-within-coding-regions\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/alternative-splicing-impacts-microrna-regulation-within-coding-regions\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Alternative splicing impacts microRNA regulation within coding regions\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#website\",\"url\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/\",\"name\":\"BelBi 2023\",\"description\":\"\",\"publisher\":{\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#organization\"},\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/?s={search_term_string}\"},\"query-input\":\"required name=search_term_string\"}],\"inLanguage\":\"en-US\"},{\"@type\":\"Organization\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#organization\",\"name\":\"Belgrade Bioinformatics Conference\",\"url\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/\",\"logo\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#\/schema\/logo\/image\/\",\"url\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-content\/uploads\/2023\/02\/145_97_171.png\",\"contentUrl\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-content\/uploads\/2023\/02\/145_97_171.png\",\"width\":278,\"height\":500,\"caption\":\"Belgrade Bioinformatics Conference\"},\"image\":{\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#\/schema\/logo\/image\/\"}}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Alternative splicing impacts microRNA regulation within coding regions - BelBi 2023","robots":{"index":"noindex","follow":"follow"},"og_locale":"en_US","og_type":"article","og_title":"Alternative splicing impacts microRNA regulation within coding regions - BelBi 2023","og_description":"Lena Maria Hackl1*, Amit Fenn1,2, Zakaria Louadi1,2, Jan Baumbach1,3, Tim Kacprowski4,5, Markus List2 and Olga Tsoy11Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany2Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Arcisstra\u00dfe 21, 80333 Munich, Germany3Computational BioMedicine Lab, University of Southern Denmark, Campusvej 50, 5230 Odense, Denmark4Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Rebenring 56, 38106 Braunschweig, Germany5Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Rebenring 56, 38106 Braunschweig, Germany Continue reading","og_url":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/alternative-splicing-impacts-microrna-regulation-within-coding-regions\/","og_site_name":"BelBi 2023","article_modified_time":"2023-06-14T17:37:23+00:00","twitter_card":"summary_large_image","twitter_misc":{"Est. reading time":"2 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/alternative-splicing-impacts-microrna-regulation-within-coding-regions\/","url":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/alternative-splicing-impacts-microrna-regulation-within-coding-regions\/","name":"Alternative splicing impacts microRNA regulation within coding regions - BelBi 2023","isPartOf":{"@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/#website"},"datePublished":"2023-06-13T00:08:24+00:00","dateModified":"2023-06-14T17:37:23+00:00","breadcrumb":{"@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/alternative-splicing-impacts-microrna-regulation-within-coding-regions\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/alternative-splicing-impacts-microrna-regulation-within-coding-regions\/"]}]},{"@type":"BreadcrumbList","@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/alternative-splicing-impacts-microrna-regulation-within-coding-regions\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/archive.belbi.bg.ac.rs\/2023\/"},{"@type":"ListItem","position":2,"name":"Alternative splicing impacts microRNA regulation within coding regions"}]},{"@type":"WebSite","@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/#website","url":"https:\/\/archive.belbi.bg.ac.rs\/2023\/","name":"BelBi 2023","description":"","publisher":{"@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/#organization"},"potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/archive.belbi.bg.ac.rs\/2023\/?s={search_term_string}"},"query-input":"required name=search_term_string"}],"inLanguage":"en-US"},{"@type":"Organization","@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/#organization","name":"Belgrade Bioinformatics Conference","url":"https:\/\/archive.belbi.bg.ac.rs\/2023\/","logo":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/#\/schema\/logo\/image\/","url":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-content\/uploads\/2023\/02\/145_97_171.png","contentUrl":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-content\/uploads\/2023\/02\/145_97_171.png","width":278,"height":500,"caption":"Belgrade Bioinformatics Conference"},"image":{"@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/#\/schema\/logo\/image\/"}}]}},"_links":{"self":[{"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/abstract\/2787"}],"collection":[{"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/abstract"}],"about":[{"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/types\/abstract"}],"author":[{"embeddable":true,"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/users\/162"}],"wp:attachment":[{"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/media?parent=2787"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/categories?post=2787"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/tags?post=2787"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}