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DTSTART;TZID=America/Detroit:20220912T160000
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DTSTAMP:20260501T081249
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SUMMARY:RNA Innovation Seminar: Zhipeng Lu\, USC
DESCRIPTION:“RNA Structures\, Interactions and Modifications”\nZhipeng Lu (鲁志鹏)\, Ph.D.\nAssistant Professor\nPharmacology and Pharmaceutical Sciences\nUniversity of Southern California \n  \nFlyer in PDF \nIn-person: BSRB\, ABC seminar rooms / hybrid link \nAbstract: RNA in living cells are in constant motion\, form dynamic structures\, and interact with many molecules\, including other RNAs. Direct determination of RNA structures and interactions in vivo is essential to understanding their functions\, but has been challenging in the past. We developed a number of novel chemical and computational tools to capture the 2D and 3D RNA structurome and interactome in cells\, providing a comprehensive view of RNA conformations that underlie their roles in gene regulation and human diseases. Applications of these methods revealed new mechanisms in lncRNA functions\, RNA modifications and splicing regulation.
URL:https://rna.umich.edu/events/zhipeng-lu/
CATEGORIES:Seminar
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DTSTART;TZID=America/Detroit:20220926T160000
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LAST-MODIFIED:20220906T131746Z
UID:10554-1664208000-1664211600@rna.umich.edu
SUMMARY:RNA Innovation Seminar: David Shechner\, University of Washington
DESCRIPTION:“Meet the neighbors: A universal technology for probing RNA-interactions and RNA-scaffolded subcellular compartments in situ”\nDavid Shechner Ph.D.\nAssistant Professor of Pharmacology\nUniversity of Washington \n  \nFlyer in PDF \nIn-person: BSRB\, ABC seminar rooms / hybrid link \nKeywords: RNA\, proximity-biotinylation\, subcellular architecture\, nuclear architecture\, spatial biology\, biomolecular condensates\, interactomics\, nucleolus\, Xist. \n  \nAbstract: In the context of the living cell\, very little RNA is naked. RNA molecules form complex\, dynamic networks of molecular interactions that underlie a host of biochemical functions\, and which are central to organizing subcellular compartmentalization. In humans\, for example\, RNAs are key determinants of chromatin folding\, and they nucleate and scaffold a host of biomolecular condensates that collectively control cellular metabolic\, epigenetic\, and stress-signaling pathways. But\, characterizing these structures—identifying the biomolecules within an RNA’s subcellular microenvironment—remains technically cumbersome. \nTo address this challenge\, I introduce oligonucleotide-mediated proximity-interactome mapping (O-MAP)\, a straightforward and flexible method for identifying the proteins\, RNAs\, and genomic loci near a target RNA\, within its native cellular context. O-MAP uses programmable oligonucleotide probes to deliver proximity-biotinylating enzymes to a target RNA. These enzymes then pervasively label all nearby (~20 nm) molecules\, enabling their enrichment by streptavidin pulldown. O-MAP induces exceptionally precise RNA-targeted biotinylation\, and its modular design enables straightforward validation of probe pools and real-space optimization of the biotinylation radius\, thus overcoming key technical challenges for the field. Moreover\, O-MAP can be readily ported across different target RNAs and specimen types\, including patient-derived organoids and tissue samples. And\, O-MAP achieves this without complex cell-line engineering\, using only off-the-shelf parts and standard manipulations. \nUsing a small cohort of model RNAs\, we have developed a robust O-MAP toolkit for proteomic (O-MAP-MS)\, transcriptomic (O-MAP-Seq) and genome interaction (O-MAP-ChIP) discovery. O-MAP of the 47S-pre-rRNA—the long noncoding RNA that scaffolds the nucleolus—enabled a comprehensive “multi-omic” analysis of this subnuclear structure\, and revealed hundreds of novel nucleolar protein-\, RNA-\, and chromatin interactions. O-MAP of XIST—the master regulator of X-chromosome inactivation—revealed novel RNAs that may play a role in this process\, and unanticipated interactions between XIST and other chromatin-regulatory RNAs. Finally\, targeting O-MAP to introns within a key cardiac developmental gene enabled unprecedented molecular dissection of a subnuclear compartment that would be impossible to purify biochemically. \nGiven these results\, we believe that O-MAP will be a powerful tool for elucidating the mechanisms by which RNA molecules drive subcellular compartmentalization in time and space\, with particular impact on our understanding of nuclear architecture. Moreover\, with O-MAP’s precision\, flexibility\, and ease\, we anticipate its broad use in studying countless other RNA phenomena throughout biology\, and as a clinical diagnostic- and discovery tool.
URL:https://rna.umich.edu/events/david-shechner/
CATEGORIES:Seminar
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