Interior circular RNA

Liu, Xiaoxin; Hu, Zhangfeng; Zhou, Jian; Tian, Cheng; Tian, Guangmei; He, Miao; Gao, Lifen; Li, Tiantian; Peng, Hai; Zhang, Weixiong

doi:10.1080/15476286.2019.1669391

Cited by 28 publications

(37 citation statements)

References 62 publications

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“…We characterized sub-exonic circRNA produced by nc genes in porcine species but the interest of this study goes beyond the pig genome. We note that the production of circRNA by the mono-exonic gene RNase_MRP was also reported in humans by Liu et al [44]. Using a similar method to the one we used in the present study, these authors identified a group of interior circRNAs.…”

Section: Discussionsupporting

confidence: 82%

In-Depth Analysis Reveals Production of Circular RNAs from Non-Coding Sequences

Robic

Demars

Kühn

2020

Cells

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The sequencing of total RNA depleted for ribosomal sequences remains the method of choice for the study of circRNAs. Our objective was to characterize non-canonical circRNAs, namely not originating from back splicing and circRNA produced by non-coding genes. To this end, we analyzed a dataset from porcine testis known to contain about 100 intron-derived circRNAs. Labelling reads containing a circular junction and originating from back splicing provided information on the very small contribution of long non-coding genes to the production of canonical circRNAs. Analyses of the other reads revealed two origins for non-canonical circRNAs: (1) Intronic sequences for lariat-derived intronic circRNAs and intron circles, (2) Mono-exonic genes (mostly non-coding) for either a new type of circRNA (including only part of the exon: sub-exonic circRNAs) or, even more rarely, mono-exonic canonical circRNAs. The most complex set of sub-exonic circRNAs was produced by RNase_MRP (ribozyme RNA). We specifically investigated the intronic circRNA of ATXN2L, which is probably an independently transcribed sisRNA (stable intronic sequence RNA). We may be witnessing the emergence of a new non-coding gene in the porcine genome. Our results are evidence that most non-canonical circRNAs originate from non-coding sequences.

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Section: Discussionsupporting

confidence: 82%

In-Depth Analysis Reveals Production of Circular RNAs from Non-Coding Sequences

Robic

Demars

Kühn

2020

Cells

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“…Even though we know that a few snoRNAs [ 20 , 29 ] are able to produce classical exonic circRNA, we did not detect any mono-exonic gene capable of producing exonic and sub-exonic circRNAs. We would like to underline the fact that also in humans, the production of a set of circRNAs by the mono-exonic gene RMRP (orthologous gene of porcine RNase_MRP ) was highlighted by Liu et al [ 42 ].…”

Section: Non-canonical Circrnas Are Even More Poorly Known Than Lamentioning

confidence: 99%

Beyond Back Splicing, a Still Poorly Explored World: Non-Canonical Circular RNAs

Robic

Kühn

2020

Genes

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Most of the circRNAs reported to date originate from back splicing of a pre-mRNA, and these exonic circRNAs are termed canonical circRNAs. Our objective was to provide an overview of all other (non-canonical) circRNAs that do not originate from the junction of two exons and to characterize their common properties. Those generated through a failure of intron lariat debranching are the best known, even though studies on them are rare. These circRNAs retain the 2′–5′ bond derived from the intron lariat, and this feature probably explains the difficulties in obtaining efficient reverse transcription through the circular junction. Here, we provide an unprecedented overview of non-canonical circRNAs (lariat-derived intronic circRNAs, sub-exonic circRNAs, intron circles, tricRNAs), which all derive from non-coding sequences. As there are few data suggesting their involvement in cellular regulatory processes, we believe that it is early to propose a general function for circRNAs, even for lariat-derived circRNAs. We suggest that their small size and probably strong secondary structures could be major obstacles to their reliable detection. Nevertheless, we believe there are still several possible ways to advance our knowledge of this class of non-coding RNA.

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“…Further, due to circRNAs being highly conserved in many species, such as humans, nematodes, zebrafish, and mice ( Salzman et al, 2012 ; Li X. et al, 2019 ), only a small number of them can evolve and change rapidly ( Zhang et al, 2013 , 2014 ). Some studies point out that the number of circRNAs found in eukaryotic cells has been as high as more than 20,000 ( Cocquerelle et al, 1993 ; Westholm et al, 2014 ); a few are formed by direct cyclization of introns, and most of them come from exons ( Liu et al, 2020a ). In addition, as a kind of non-coding RNA, circRNA can only regulate the formation of proteins at the transcriptional or post-transcriptional level ( Westholm et al, 2014 ), and only a few of them can regulate life activities by encoding proteins ( Pamudurti et al, 2017 ; Yang et al, 2018 ).…”

Section: Overview Of Circrnasmentioning

confidence: 99%

The Roles of CircRNAs in Regulating Muscle Development of Livestock Animals

Yang

Chen

2021

Front. Cell Dev. Biol.

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The muscle growth and development of livestock animals is a complex, multistage process, which is regulated by many factors, especially the genes related to muscle development. In recent years, it has been reported frequently that circular RNAs (circRNAs) are involved widely in cell proliferation, cell differentiation, and body development (including muscle development). However, the research on circRNAs in muscle growth and development of livestock animals is still in its infancy. In this paper, we briefly introduce the discovery, classification, biogenesis, biological function, and degradation of circRNAs and focus on the molecular mechanism and mode of action of circRNAs as competitive endogenous RNAs in the muscle development of livestock and poultry. In addition, we also discuss the regulatory mechanism of circRNAs on muscle development in livestock in terms of transcription, translation, and mRNAs. The purpose of this article is to discuss the multiple regulatory roles of circRNAs in the process of muscle development in livestock, to provide new ideas for the development of a new co-expression regulation network, and to lay a foundation for enriching livestock breeding and improving livestock economic traits.

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Interior circular RNA

Cited by 28 publications

References 62 publications

In-Depth Analysis Reveals Production of Circular RNAs from Non-Coding Sequences

In-Depth Analysis Reveals Production of Circular RNAs from Non-Coding Sequences

Beyond Back Splicing, a Still Poorly Explored World: Non-Canonical Circular RNAs

The Roles of CircRNAs in Regulating Muscle Development of Livestock Animals

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