Abstract
During pre-mRNA splicing, exons in the primary transcript are precisely connected to generate an mRNA. Intron lariat RNAs are formed as by-products of this process. In addition, some exonic circular RNAs (circRNAs) may also result from exon skipping as by-products. Lariat RNAs and circRNAs are both RNase R resistant RNAs. RNase R is a strong 3' to 5' exoribonuclease, which efficiently degrades linear RNAs, such as mRNAs and rRNAs; therefore, the circular parts of lariat RNAs and the circRNAs can be segregated from eukaryotic total RNAs by their RNase R resistance. Thus, RNase R resistant RNAs could provide unexplored splicing information not available from mRNAs. Analyses of these RNAs identified repeating splicing phenomena, such as re-splicing of mature mRNAs and nested splicing. Moreover, circRNA might function as microRNA sponges. There is an enormous variety of endogenous circRNAs, which are generally synthesized in cells and tissues.
Highlights
RNA Digestion by RNase R TreatmentRNase R, originally identified in Escherichia coli [1,2], has two cold shock domains, an RNase catalytic domain, an S1 domain and a basic domain [3]
We showed that RNase R could not digest the circular part of an intron lariat
In addition to circRNA and lariat RNAs, Danan et al showed that other types of circular RNAs, generated from permuted tRNAs, rRNA processing intermediates, or C/D box RNAs, were present in Archaea and were resistant to RNase R treatment [32]
Summary
RNase R, originally identified in Escherichia coli [1,2], has two cold shock domains, an RNase catalytic domain, an S1 domain and a basic domain [3]. Key recognitions of substrate RNAs have been analyzed and the structural model of RNase R active site suggests that the 2'-hydroxyl group of the 3rd nucleobase towards the 5' from the scissile phosphate is recognized by the 463th glutamic acid of RNase R (of Mycoplasma genitalium) [9]. It is important for recognition of the substrate RNA, and modification of 2'-hydroxyl may affect the degradation of RNA. RNase R efficiently degrades linear mRNAs from their unprotected 3' ends
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