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Expression profiling of circular RNAs during differentiation of human pluripotent stem cells into vascular endothelial and smooth muscle cells

ABSTRACT: To identify novel circular RNAs (circRNAs) and to investigate their expression levels during human pluripotent stem cells (hiPSC) differentation, we have converted these cells to vascular endothelial cells (ECs) and smooth muscle cells (SMCs). Circular RNAs were de novo identified using RNase R treated samples and quantified in total RNA samples at 13 timepoints per differentiation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE210361 | GEO | 2025/04/01

REPOSITORIES: GEO

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Project description:The pervasive expression of circular RNA from protein coding loci is a recently discovered feature of many eukaryotic gene expression programs. Computational methods to discover and quantify circular RNA are essential to the study of the mechanisms of circular RNA biogenesis and potential functional roles they may play. In this paper, we present a new statistical algorithm that increases the sensitivity and specificity of circular RNA detection.by discovering and quantifying circular and linear RNA splicing events at both annotated exon boundaries and in un-annotated regions of the genome Unlike previous approaches which rely on heuristics like read count and homology between exons predicted to be circularized to determine confidence in prediction of circular RNA expression, our algorithm is a statistical approach. We have used this algorithm to discover general induction of circular RNAs in many tissues during human fetal development. We find that some regions of the brain show marked enrichment for genes where circular RNA is the dominant isoform. Beyond this global trend, specific circular RNAs are tissue specifically induced during fetal development, including a circular isoform of NCX1 in the developing fetal heart that, by 20 weeks, is more highly expressed than the linear isoform as well as beta-actin. In addition, while the vast majority of circular RNA production occurs at canonical U2 (major spliceosome) splice sites, we find the first examples of developmentally induced circular RNAs processed by the U12 (minor) spliceosome, and an enriched propensity of U12 donors to splice into circular RNA at un-annotated, rather than annotated, exons. Together, our algorithm and its results suggest a potentially significant role for circular RNA in human development. 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold sample prep kit.

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Expression profiling of circular RNAs during differentiation of human pluripotent stem cells into vascular endothelial and smooth muscle cells

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