{"id":6303,"date":"2024-03-02T10:31:11","date_gmt":"2024-03-02T09:31:11","guid":{"rendered":"https:\/\/www.bordeaux-population-health.center\/?p=6303"},"modified":"2024-04-08T11:37:34","modified_gmt":"2024-04-08T09:37:34","slug":"seminaire-scientifiqueconference-par-hagen-tilgnerde-weill-cornell-school-of-medical-sciencesamphi-louis-isped","status":"publish","type":"post","link":"https:\/\/www.bordeaux-population-health.center\/fr\/seminaire-scientifiqueconference-par-hagen-tilgnerde-weill-cornell-school-of-medical-sciencesamphi-louis-isped\/","title":{"rendered":"S\u00c9MINAIRE SCIENTIFIQUE<br \/>Conf\u00e9rence par Hagen Tilgner<br \/>de Weill Cornell School of Medical Sciences<br \/><span style=\"color: #13a500;\">Amphi Louis &#8211; Isped<\/span>"},"content":{"rendered":"<div style=\"font-family: arial; font-size: 1.1em;\">\n<p><img decoding=\"async\" class=\"size-medium wp-image-2266 alignright\" style=\"margin-left: 10%; width: 80%;\" src=\"https:\/\/www.bordeaux-population-health.center\/wp-content\/uploads\/2024\/04\/Shiva_Scientific-Seminar_Hagen-Tilgner_bandeau.jpg\" alt=\"\" \/><\/p>\n<p><strong style=\"display: block; text-align: center; font-size: 1.2em;\">S\u00c9MINAIRE SCIENTIFIQUE<\/strong><br \/>\n<strong style=\"display: block; text-align: center; font-size: 1.4em; margin-bottom: 1em;\">Understanding splicing and isoform regulation across cell types,<br \/>brain regions, postnatal development and species<br \/>-or- single-cell isoforms in time and space<\/strong><\/p>\n<div style=\"display: block; text-align: center; margin-bottom: 2em;\">12h<br \/>\nAmphi Louis &#8211; Isped<br \/>\nCampus Carreire &#8211; Universit\u00e9 de Bordeaux<\/div>\n<div style=\"margin-left: 10%; width: 80%; margin-top: 5em;\">\n<p>Ouvert \u00e0 tout le monde, en pr\u00e9sentiel &#038; videoconference<\/p>\n<div style=\"color: #ee9900; font-weight: bold; display: block; margin-top: 2em;\">Intervenant :<\/div>\n<p><span style=\"font-size: 1.2em; font-weight: bold;\">Hagen Tilgner<\/span>, PhD<br \/>\nAssociate Professor<br \/>\nThe Feil Family Brain and Mind Research Institute<br \/>\nWeill Cornell Medicine Graduate School of Medical Sciences<br \/>\nNew York, NY<\/p>\n<div style=\"color: #ee9900; font-weight: bold; display: block; margin-top: 2em;\">Abstract :<\/div>\n<p>Most mammalian genes encode multiple distinct RNA isoforms and the brain harbors especially diverse isoforms. Complex tissue includes diverse cell types, which employ distinct isoforms. To untangle cell-type specific brain isoform profiles, we developed the first single-cell long-read technology for >>1,000 cells and fresh tissues (Single-cell isoform RNA sequencing &#8211; ScISOr-Seq)<span style=\"font-variant-position: super;\">1<\/span> as well as for frozen tissues (Single-nuclei isoform RNA sequencing &#8211; SnISOr-Seq<span style=\"font-variant-position: super;\">2<\/span>). To add spatial resolution, we developed Slide-isoform sequencing (Sl-ISO-Seq)<span style=\"font-variant-position: super;\">3<\/span>. Collectively, these long-read approaches reveal a striking difference between coordinated pairs of exons with in-between exons (\u201cDistant coordinated exons\u201d) and without in-between exons (\u201cAdjacent coordinated exons\u201d): The former show strong enrichment for cell-type specific usage of exons, whereas the latter do not in mouse<span style=\"font-variant-position: super;\">1<\/span> and human brain<span style=\"font-variant-position: super;\">2<\/span>. Of note, coordinated TSS-exon pairs and exon-polyA-site pairs follow the same trend as distant coordinated exon pairs<span style=\"font-variant-position: super;\">2<\/span>. Simultaneously, autism-associated exons are among the most highly variably used exons across cell types<span style=\"font-variant-position: super;\">2<\/span>. Spatially barcoded isoform sequencing revealed that often region-specific isoform differences correlate with precise boundaries of brain structures (e.g., from the choroid plexus to the hippocampus). However, genes including Snap25 go against this trend, using a steady gradient of exon inclusion as one traverses the brain<span style=\"font-variant-position: super;\">3<\/span>. Moreover, choroid plexus epithelial cells show a dramatically distinct isoform profile, which originates from distinct exon and poly(A) site usage, but most strongly from distinct TSS usage<span style=\"font-variant-position: super;\">3<\/span>. For the NIH Brain Initiative, we have mapped single-cell isoform expression across development, brain regions and species. Neurotransmitter release and reuptake as well as synapse turnover genes harbor variability in the same cell type across anatomical regions but the same cell type traced across development shows more isoform variability than across adult anatomical regions. Moreover, most cell-type specific exons in adult mouse hippocampus behave similarly in human hippocampi. However, human brains have evolved additional cell-type specificity in splicing, suggesting gain-of-function isoforms<span style=\"font-variant-position: super;\">4<\/span>. Most recently, we have made advances in understanding the error sources of Pacific Biosciences and Oxford Nanopore long-read sequencing technologies<span style=\"font-variant-position: super;\">5<\/span> and have implemented highly accurate long-read interpretation software<span style=\"font-variant-position: super;\">6<\/span>. Finally, I will comment on further, yet unpublished, technologies of the lab. <\/p>\n<p style=\"font-size: 0.8em; font-style: italic;\">1.Gupta*, Collier* et al, Nature Biotechnology, 2018; 2.Hardwick*, Hu*, Joglekar* et al, Nature Biotechnology, 2022; 3.Joglekar et al, Nature Communications, 2021; 4. Joglekar et al, Nature Neuroscience, in press; 5. Mikheenko*, Prjibelski* et al, Genome Research, 2022 ; 6. Prjibelski*, Mikheenko* et al, Nature Biotechnology, 2023<\/p>\n<div style=\"color: #ee9900; font-weight: bold; display: block; margin-top: 2em;\">Bio :<\/div>\n<p>Hagen Tilgner studied computer science in Germany and France, and after a brief stint at the Sanger Institute (UK), did his PhD with Roderic Guig\u00f3 at the Centre for Genomic Regulation in Barcelona. There he focused on RNA and the co-transcriptionality of splicing (see Tilgner et al, Genome Res, 2012 for example). His postdoctoral work at Stanford with Michael Snyder focused on technology development, specifically for long-read transcriptomics (see for example Sharon*, Tilgner*, Grubert, Snyder, Nature Biotechnology\u201913, Tilgner*, Sharon*, Grubert*, Snyder, PNAS\u201914 or Tilgner*, Jahanbani* et al, Nature Biotechnology\u201915). He started his lab at Weill Cornell in New York City in 2016 focusing on technologies to decipher the actions of RNA isoforms in the brain. The lab is a multi-disciplinary lab, including wet-lab technology development (see for example single-cell isoform RNA sequencing, ScISOr-Seq, Gupta et al, Nature Biotechnology\u201918 or SnISOr-Seq, Hardwick et al, Nature Biotechnology\u201922) and dry-lab approaches (see for example Joglekar et al, Nature Communications\u201921 or Prjibelski et al, Nature Biotechnology\u201923) as well as combined large-scale efforts centered on the brain (for example, Joglekar et al, Nature Neuroscience, in press) where Maths\/CS, molecular biology and neuroscience backgrounds interact to further our understanding of isoforms in healthy and diseased brain of humans and model organisms.<\/p>\n<div style=\"color: #ee9900; font-weight: bold; display: block; margin-top: 2em;\">Lien Zoom :<\/div>\n<p><a href=\"https:\/\/u-bordeaux-fr.zoom.us\/j\/83444497870?pwd=MHdBQmlIOEI2VUc3cGdXNHRpeDkxZz09\" rel=\"noopener\" target=\"_blank\">https:\/\/u-bordeaux-fr.zoom.us\/j\/83444497870?pwd=MHdBQmlIOEI2VUc3cGdXNHRpeDkxZz09<\/a><\/p>\n<p>&nbsp;<\/p>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>S\u00c9MINAIRE SCIENTIFIQUE Understanding splicing and isoform regulation across cell types,brain regions, postnatal development and species-or- single-cell isoforms in time and space 12h Amphi Louis &#8211; Isped Campus Carreire &#8211; Universit\u00e9 de Bordeaux Ouvert \u00e0 tout le monde, en pr\u00e9sentiel &#038; videoconference Intervenant : Hagen Tilgner, PhD Associate Professor The Feil Family Brain and Mind Research [&hellip;]<\/p>\n","protected":false},"author":613,"featured_media":6298,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[26],"tags":[],"class_list":["post-6303","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-seminaires"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.4 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>S\u00c9MINAIRE SCIENTIFIQUEConf\u00e9rence par Hagen Tilgnerde Weill Cornell School of Medical SciencesAmphi Louis - Isped | Bordeaux population health<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.bordeaux-population-health.center\/fr\/seminaire-scientifiqueconference-par-hagen-tilgnerde-weill-cornell-school-of-medical-sciencesamphi-louis-isped\/\" \/>\n<meta property=\"og:locale\" content=\"fr_FR\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"S\u00c9MINAIRE SCIENTIFIQUEConf\u00e9rence par Hagen Tilgnerde Weill Cornell School of Medical SciencesAmphi Louis - Isped | Bordeaux population health\" \/>\n<meta property=\"og:description\" content=\"S\u00c9MINAIRE SCIENTIFIQUE Understanding splicing and isoform regulation across cell types,brain regions, postnatal development and species-or- single-cell isoforms in time and space 12h Amphi Louis &#8211; 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