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- W2950337819 abstract "not only shuttles information between DNA andproteins but also carries out many other essential cellularfunctions. Nearly all steps of an RNA's life cycle are controlledby approximately one thousand binding proteins (RBPs) thatdirect splicing, cleavage and polyadenylation, localization,translation, and degradation. Despite the central role of RBPs inRNA processing and gene expression, they have been less wellstudied than DNA binding proteins, in part due to the historicaldearth of technologies to probe RBP binding and activity in ahigh-throughput, comprehensive manner. In this thesis, I describethe affinity landscapes of the largest set of human RBPs to dateelucidated through a highthroughput version of Bind-N-Seq(RBNS), an unbiased in vitro assay that determines the primarysequence, secondary structure, and contextual preferences of anRBP. The 78 RBPs bound an unexpectedly low diversity of motifs,implying convergence of binding specificity toward a small set ofRNA motifs characterized by low compositional complexity.Offsetting the low diversity of sequence motifs, extensivepreferences for contextual features beyond short linear motifs wereobserved, including bipartite motifs, flanking nucleotide content,and preference for or against structure. These features likelyrefine which motif occurrences are selected in cells, enabling RBPsthat bind the same linear motif to act on distinct subsets oftranscripts. Additionally, RBNS data is integrated withcomplementary in vivo binding sites from enhanced crosslinking andimmunoprecipitation (eCLIP) and functional (RNAi/RNA-seq) dataproduced through collaborative efforts with the ENCODE consortium.These data enable creation of RNA maps of RBP activity inpre-mRNA splicing and gene expression levels, either with (eCLIP)or without (RBNS) crosslinking-based assays. The mapping andcharacterization of elements recognized by over 200 human RBPsis also presented in two human cell lines, K562 and HepG2 cells.Together, these novel data augment the catalog of functionalelements encoded in the human genome to include those that act atthe level and provide a basis for how RBPs select their RNAtargets, a fundamental requirement in more fully understanding RNAprocessing mechanisms and outcomes." @default.
- W2950337819 created "2019-06-27" @default.
- W2950337819 creator A5005384908 @default.
- W2950337819 date "2018-01-01" @default.
- W2950337819 modified "2023-09-23" @default.
- W2950337819 title "Biochemical and functional characterization of humanRNA binding proteins" @default.
- W2950337819 hasPublicationYear "2018" @default.
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