Cell-Type Specific Features of Circular RNA Expression

By Julia Salzman, Raymond E. Chen, M. Olsen, Peter L Wang, Patrick O. Brown. PLoS Genetics, 2013

1,693 citations recorded by the source corpus.

Thousands of loci in the human and mouse genomes give rise to circular RNA transcripts; at many of these loci, the predominant RNA isoform is a circle. Using an improved computational approach for circular RNA identification, we found widespread circular RNA expression in Drosophila melanogaster and estimate that in humans, circular RNA may account for 1% as many molecules as poly(A) RNA. Analysis of data from the ENCODE consortium revealed that the repertoire of genes expressing circular RNA, the ratio of circular to linear transcripts for each gene, and even the pattern of splice isoforms of circular RNAs from each gene were cell-type specific. These results suggest that biogenesis of circular RNA is an integral, conserved, and regulated feature of the gene expression program.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/26cdfe5f289d1a785c4b0a63a602b3bf79aff169

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Citations in the corpus

Expanded identification and characterization of mammalian circular RNAs (2014, methodology): “When circRNAs are experimentally enriched by either poly(A)-depletion [15] or RNase R digestion [14], tens of thousands of more circRNAs are found, even when limiting the search to only those that use annotated splice sites.”
Circular RNA: A new star of noncoding RNAs. (2015, background): “However, with the development of highthroughput sequencing technology and computational analysis, thousands of circRNAs across species from Archaea to humans have been discovered [10–16,38].”
Diverse alternative back-splicing and alternative splicing landscape of circular RNAs (2016, positive): “…of being covalently closed without open ends, circRNAs are largely missed by polyadenylated transcriptome profiling but can be captured by RNA deep-sequencing (RNA-seq) from nonpolyadenylated RNAs (Yang et al. 2011; Jeck et al. 2013; Memczak et al. 2013; Salzman et al. 2013; Zhang et al. 2014).”
circRNA biogenesis competes with pre-mRNA splicing. (2014, background): “In agreement with a previous report (Salzman et al., 2013), we found thousands of circRNA candidates expressed in fly heads (Figure 1A, blue dots; Table S1 available online).”
Circular RNAs: diversity of form and function (2014, background): “As such, backsplicing will be subject to all of the same regulatory inputs as alternative splicing, which may provide an explanation for the celltype expression of different circRNAs (Salzman et al. 2013).”
CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs (2016, background): “In eukaryotes, circRNAs arise most often through backsplicing, a process in which the 5' and 3' ends of a spliced RNA are covalently linked to form a closed RNA molecule that contains exon and/or intron sequences.(1-3) Although a few examples of circRNAs have been known for several decades, only wit”
Circular RNA-protein interactions: functions, mechanisms, and identification (2020, background): “Numerous circRNAs exhibit specificity to certain tissues and developmental periods [5, 31, 32].”