Human Survival Motor Neuron genes generate a vast repertoire of circular RNAs.

Eric W Ottesen,Natalia N Singh,Ravindra N Singh,Diou Luo,Joonbae Seo

doi:10.1093/nar/gkz034

Abstract

Circular RNAs (circRNAs) perform diverse functions, including the regulation of transcription, translation, peptide synthesis, macromolecular sequestration and trafficking. Inverted Alu repeats capable of forming RNA:RNA duplexes that bring splice sites together for backsplicing are known to facilitate circRNA generation. However, higher limits of circRNAs produced by a single Alu-rich gene are currently not predictable due to limitations of amplification and analyses. Here, using a tailored approach, we report a surprising diversity of exon-containing circRNAs generated by the Alu-rich Survival Motor Neuron (SMN) genes that code for SMN, an essential multifunctional protein in humans. We show that expression of the vast repertoire of SMN circRNAs is universal. Several of the identified circRNAs harbor novel exons derived from both intronic and intergenic sequences. A comparison with mouse Smn circRNAs underscored a clear impact of primate-specific Alu elements on shaping the overall repertoire of human SMN circRNAs. We show the role of DHX9, an RNA helicase, in splicing regulation of several SMN exons that are preferentially incorporated into circRNAs. Our results suggest self- and cross-regulation of biogenesis of various SMN circRNAs. These findings bring a novel perspective towards a better understanding of SMN gene function.

Highlights

Circular RNAs are a widely expressed class of non-colinear RNAs (NCRs) generated in a diverse set of eukaryotic organisms, including animals, plants, yeasts and protists [1,2,3]
Using a tailored approach, we report a surprising diversity of exon-containing circRNAs generated by the Alu-rich Survival Motor Neuron (SMN) genes that code for SMN, an essential multifunctional protein in humans
To capture cell-specific differences in the repertoire of SMN circRNAs, we conducted these experiments in four cell lines: HeLa, human embryonic kidney-derived (HEK-293), spinal muscular atrophy (SMA) patient fibroblasts (GM03813) and neuronal SH-SY5Y

Summary

Introduction

Circular RNAs (circRNAs) are a widely expressed class of non-colinear RNAs (NCRs) generated in a diverse set of eukaryotic organisms, including animals, plants, yeasts and protists [1,2,3]. Due to their lack of 5 and 3 termini, circRNAs are extremely stable. In the absence of backsplicing, lariat intermediates can directly produce circRNAs by degradation of the linear 3 sequence of the lariat [9] The latter mechanism is predominantly used for producing intron-only-containing circRNAs. There is evidence to suggest that tissuespecific factors independently regulate biogenesis of circRNAs [10,11,12]. The current number of circRNAs known to be generated by the human genome in all probability represents an underestimate

Objectives

Methods

Results

Conclusion