JMIR Publications

ABSTRACT

Background:

Next generation sequencing (NGS) has detected numerous circular RNAs (cirRNAs) in the past two decades. For example, a recent analysis of many full-length RNA-sequencing datasets identifies 139,643 human and 214,747 mouse circRNAs. Why before the NGS era few ciRNAs had been identified using Sanger sequencing thus becomes a question. Moreover, few, if any, of the numerous cirRNAs found in human cells have been shown for the procedural and mechanistic details of their formations.

Objective:

This essay aims to analyze whether human cells really express numerous cirRNAs and, if yes, what are the procedures and mechanisms of their formations.

Methods:

We rummaged through the whole Pubmed for procedural and mechanistic details of how cirRNAs were produced in human cells. We also reviewed the history of the first cirRNAs found in human and mouse cells and analyzed the genomic organizations of the genes that expressed these cirRNAs. In addition, we summarized the difficulties and pitfalls of the techniques used to identify and verify cirRNAs described in the literature.

Results:

CirRNAs are thought to be derived from transsplicing or poorly-defined backsplicing, recursive splicing (RS) or intron-lariat splicing (ILS). However, procedural and mechanistic niceties of how they are formed in human cells have never been shown for any single cirRNA. For example, it remains unknown whether a spliceosome is involved and, if yes, which small nuclear RNAs recruit which nucleoproteins to form the spliceosome that executes the formation of a particular cirRNA. Most reported human cirRNAs were previously missed by Sanger sequencing, which in our opinion has three possibilities that need to be tested: 1. Most of human cirRNAs are technical artifacts, which may be related to the reversely complementary regions of the pre-RNAs that form a hybrid, such as the stem of a hairpin structure. 2. Some cirRNAs may be intermediate products of a spliceosome-mediated RS or ILS with unknown details. 3. Some others may be attributed to the ribozyme of the pre-RNAs that self-ligates their two ends, which may actually be the mechanism of the so-called backsplicing that may also be related to the reversely complementary regions of the pre-RNAs.

Conclusions:

Until procedural and mechanistic niceties of how cirRNAs are formed have been articulated for some human cirRNAs as examples, such as whether small nuclear RNAs and spliceosomes are involved, the notion that “human cells express numerous cirRNAs” remains hypothetical. However, continuing researches on the effects of cirRNAs and the mechanisms underlying these effects are warranted, because many man-made cirRNAs may be promising medicines or tools in biomedical researches or industries.