RIP-PEN-seq identifies a class of kink-turn RNAs as splicing regulators
, Genome-browser plot of RIP-PEN-seq for representative forward K-turn RNAs in the introns of GAS5., Computational workflow for analysis of the RIP-PEN-seq sequencing data and identification of candidate transcripts., KturnSeeker core algorithm workflow. KturnSeeker was developed to identify and quantify forward and backward ktRNAs from RIP-PEN-seq data. KturnSeeker can screen bktRNAs as well as fktRNAs by reverse searching the K-turn structure.
Extended Data Fig. 3 The backward K-turn sequence composition, predicted functions and tissue-specific expression profile of bktRNAs., The secondary structure of consensus forward K-turn RNA and backward K-turn RNA . The nucleotide positions in the K-turn structure are named according to the nomenclature rules for the forward K-turn structure., Matrix plot showing the number of human bktRNAs with the indicated nucleotide in the 3b:3n sequences.
, Matrix plot showing the number of mouse bktRNAs with the indicated nucleotide in the 3b:3n sequences.f, Number of bktRNAs with or without m, Enrichment analysis of the bktRNA host protein-coding genes by Metascape software., Tissue-specific expression profiles of bktRNAs. The expression levels of bktRNAs are displayed in the rows and the tissues are shown in the columns. The rows and columns are sorted based on k-means clustering of bktRNA genes.
Extended Data Fig. 4 Genomic characterization, expression, conservation, and secondary structure of bktRNA1., Genome-browser plot of RIP-PEN-seq for bktRNA1, as well as the evolutionary conservation across 100 vertebrates ., Secondary structure of bktRNA1 in the human genome was predicted by R-scape software. The SHAPE reactivities for each nucleotide were mapped to secondary structures using R2R software.
Extended Data Fig. 5 Secondary structures and subcellular localization of bktRNA1 and its interacting partner U12 snRNA., Predicted conserved RNA structure of bktRNA1 determined by measuring pairwise covariations with R-scape software. The H/ACA domain is indicated with a black dashed box. The functional region paired with U12 snRNA is indicated with a blue dashed box., In situ co-localization of bktRNA1 with 15.
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