What happens at or after transcription: Insights into circRNA biogenesis and function

Huang, Chuan; Ge, Shengfang

doi:10.1080/21541264.2015.1071301

Cited by 102 publications

(90 citation statements)

References 37 publications

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“…GO and KEGG pathway analyses revealed that the parent genes are involved in certain pathways associated with cancer, such as the PPAR signaling pathway (related circRNAs and genes: chr19:4511523-4511918− and PLIN4; chr10:97154758-97170534− and SORBS1) and adherens junction (related circRNAs and genes: chr7:116339125-116340338+ and MET; chr10:97154758-97170534− and SORBS1). Previous studies have suggested that the PPAR signaling pathway contributes to thyroid cancer [30][31][32], and MET is a well-known proto-oncogene associated with multiple [4,36], which enables them to sequester miRNAs and act as sponges of miRNA that regulate expression of target miRNAs [37,38]. For example, the circRNA CiRS-7 contains more than 70 binding sites for miR-7 and can function as a sponge of this miRNA [5,39].…”

Section: Discussionmentioning

confidence: 99%

The Landscape of Circular RNA Expression Profiles in Papillary Thyroid Carcinoma Based on RNA Sequencing

Lan

Chen

et al. 2018

Cell Physiol Biochem

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Background/Aims: Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. However, the molecular mechanisms responsible for its tumorigenesis and progression remain largely unknown. Circular RNA (circRNA) is a novel type of noncoding RNA that can serve as an ideal biomarker due to its stability. Recent evidence suggests that circRNAs play important roles in tumorigenesis. This study aims to investigate circRNA expression profiles and their potential biological functions in PTC. Methods: High-throughput RNA sequencing was used to assess circRNA expression profiles in PTC, and quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate dysregulated circRNAs. Receiver operating characteristic (ROC) curves were generated to evaluate the diagnostic value of circRNAs for PTC. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were employed to determine the biological functions of differentially expressed circRNAs. Bioinformatic analyses were applied to predict interactions between circRNAs and microRNAs (miRNAs), and a circRNA-miRNA-mRNA network was constructed using Cytoscape software. Results: We identified a number of differentially expressed circRNAs in PTC tissues compared with paired normal thyroid tissues, with chr5: 160757890-160763776–, chr12: 40696591-40697936+, chr7: 22330794-22357656-, and chr21: 16386665-16415895– being upregulated, and chr7: 91924203-91957214+, chr2: 179514891-179516047–, chr9: 16435553-16437522–, and chr22: 36006931-36007153– being downregulated. These findings were confirmed by qRT-PCR, and ROC curves indicated that they can serve as potential biomarkers for PTC. GO and KEGG pathway analyses showed that some of these circRNAs are related to cancers. Additionally, bioinformatic analyses revealed a potential competing-endogenous-RNA-regulating network among circRNAs, miRNAs, and mRNAs. Conclusions: Our study results depict the landscape of circRNA expression profiles in PTC and also provide potential biomarkers for PTC. Further functional and mechanistic studies of these circRNAs may improve our understanding of PTC tumorigenesis.

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Section: Discussionmentioning

confidence: 99%

The Landscape of Circular RNA Expression Profiles in Papillary Thyroid Carcinoma Based on RNA Sequencing

Lan

Chen

et al. 2018

Cell Physiol Biochem

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“…Precise gene expression in a spatiotemporal manner that is correlated with tissue-specific events is important in animal metabolism and development (Lee et al , 2017; Huang and Shan, 2015). CircRNA is predominantly produced by back-splicing reactions and confirmed to serve as a transcription regulator, significantly increasing the complexity of regulation.…”

Section: Discussionmentioning

confidence: 99%

Comprehensive circular RNA expression profiles in intermuscular fat from lean and obese pigs

Miao

Zhang

Wang

et al. 2019

Preprint

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The paper explored the expression profile of circRNAs in intermuscular fat from Landrace and Jinhua pigs at the fattening period, to provide insights into circRNAregulation in animal adipose metabolism. AbstractCircular RNA (circRNA) plays an important regulatory role in development and differentiation. Intermuscular fat in pork affects the tenderness and juiciness of the meat. In this study, we investigated the performances of Landrace (lean) and Jinhua (obese) pigs at the fattening period and explored the expression profile of circRNAs in intermuscular fat from the two breeds by Illumina high-throughput sequencing. we identified 5 548 circRNAs, specifically 2 651 (47.78%) in the Jinhua pigs, and 2 897 (52.22%) in the Landrace pigs. A totale of 809 differentially expressed circRNAs were observed between the the Jinhua and Landrace pigs, but only 29 of these circRNAs showed significant difference (19 upregulated and 10 downregulated). All 1 306 unigenes and 27 differentially expressed unigenesinvolved in lipid transport and metabolism; replication, recombination and repair; and signaling pathway were annotated. A total of 550 target miRNAs were perfect seed matches and 20 522 target genes were foundBy RNAhybrid and miRanda software prediction. Results from real-time quantitative PCR also confirmed the differential expression of 13 mRNAs between the two pig breeds. This study provides comprehensive expression profiles of circRNAs in Sus scrofa adipose metabolism and development, which can be used to clarify their functions.

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“…Recent studies have now connected circRNAs to brain function, highlighting the potential importance of circRNAs in neurological disorders and other human pathology [21]. Nevertheless, like many other non-coding RNAs (ncRNAs), circRNAs probably have various important roles in many biological events, but their functions are largely yet to be defined [22].…”

Section: Biogenesis and Functions Of Circrnasmentioning

confidence: 99%

The nuclear export of circular RNAs is primarily defined by their length

Kearse

Huang

2018

RNA Biology

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Although it was long assumed that eukaryotic pre-mRNAs are almost always spliced to generate linear mRNAs, it is now clear that thousands of protein-coding genes can be non-canonically spliced using backsplicing to produce circular RNAs (circRNAs). Most mature circRNAs accumulate in the cytoplasm; however, little is known about how circRNAs are exported from the nucleus to the cytoplasm as they lack many of the common signals used for mRNA export. In this point-of-view article, we will discuss our recently identified circRNA nuclear export pathway and address important open questions in the field. ARTICLE HISTORY

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What happens at or after transcription: Insights into circRNA biogenesis and function

Cited by 102 publications

References 37 publications

The Landscape of Circular RNA Expression Profiles in Papillary Thyroid Carcinoma Based on RNA Sequencing

The Landscape of Circular RNA Expression Profiles in Papillary Thyroid Carcinoma Based on RNA Sequencing

Comprehensive circular RNA expression profiles in intermuscular fat from lean and obese pigs

The nuclear export of circular RNAs is primarily defined by their length

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