Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types
TLDR
By deep sequencing of RNA from a variety of normal and malignant human cells, this work suggests that a non-canonical mode of RNA splicing, resulting in a circular RNA isoform, is a general feature of the gene expression program in human cells.Abstract:
Most human pre-mRNAs are spliced into linear molecules that retain the exon order defined by the genomic sequence. By deep sequencing of RNA from a variety of normal and malignant human cells, we found RNA transcripts from many human genes in which the exons were arranged in a non-canonical order. Statistical estimates and biochemical assays provided strong evidence that a substantial fraction of the spliced transcripts from hundreds of genes are circular RNAs. Our results suggest that a non-canonical mode of RNA splicing, resulting in a circular RNA isoform, is a general feature of the gene expression program in human cells.read more
Citations
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Predicting disease-associated circular RNAs using deep forests combined with positive-unlabeled learning methods.
TL;DR: This study proposes the use of deep forests combined with positive-unlabeled learning methods to predict potential disease-related circRNAs and provided a new framework to investigate the associations between circRNA and disease and might improve the understanding of its functions.
Journal ArticleDOI
Biogenesis of circular RNAs and their roles in cardiovascular development and pathology
TL;DR: The latest research on the biogenesis and functions of circRNAs with emphasis on the regulatory roles of circ RNAs in the development and pathologies of the cardiovascular system is summarized.
Journal ArticleDOI
Noncoding RNA in Oncogenesis: A New Era of Identifying Key Players
Guorui Deng,Guangchao Sui +1 more
TL;DR: The function and regulation of miRNAs are discussed, especially focusing on the interplay between mi RNAs and several key cancer genes, including p53, PTEN and c-Myc, and the research of long ncRNAs (lncRNAs) in cancers is summarized.
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NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision
TL;DR: A new NCL-transcript-detecting method (‘NCLscan’) was developed, which utilized a stepwise alignment strategy to almost completely eliminate false calls without sacrificing true positives, enabling NCLscan to outperform 18 other publicly-available tools in terms of sensitivity and precision.
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Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency
Chan-Shuo Wu,Chun-Ying Yu,Ching-Yu Chuang,Michael Hsiao,Cheng-Fu Kao,Hung-Chih Kuo,Trees-Juen Chuang +6 more
TL;DR: A new computational pipeline, TSscan, is developed, which integrates different types of high-throughput long-/short-read transcriptome sequencing of different human embryonic stem cell (hESC) lines to effectively minimize false positives while detecting trans-splicing.
References
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TL;DR: To the knowledge, this is the first case of circular transcripts being processed from nuclear pre‐mRNA in eukaryotes, and might represent a novel aspect of gene expression and hold some interesting clues about the splicing mechanism.
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Expression of Linear and Novel Circular Forms of an INK4/ARF-Associated Non-Coding RNA Correlates with Atherosclerosis Risk
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