Identification and Analysis of Micro-Exon Genes in the Rice Genome.

Qi Song,Ling-Ling Chen,Fang Lv,Huan Li,Feng Xing,Muhammad Tahir Ul Qamar,Run Zhou

doi:10.3390/ijms20112685

Qi Song, Ling-Ling Chen + Show 5 more

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https://doi.org/10.3390/ijms20112685

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Abstract

Micro-exons are a kind of exons with lengths no more than 51 nucleotides. They are generally ignored in genome annotation due to the short length, whereas recent studies indicate that they have special splicing properties and important functions. Considering that there has been no genome-wide study of micro-exons in plants up to now, we screened and analyzed genes containing micro-exons in two indica rice varieties in this study. According to the annotation of Zhenshan 97 (ZS97) and Minghui 63 (MH63), ~23% of genes possess micro-exons. We then identified micro-exons from RNA-seq data and found that >65% micro-exons had been annotated and most of novel micro-exons were located in gene regions. About 60% micro-exons were constitutively spliced, and the others were alternatively spliced in different tissues. Besides, we observed that approximately 54% of genes harboring micro-exons tended to be ancient genes, and 13% were Oryza genus-specific. Micro-exon genes were highly conserved in Oryza genus with consistent domains. In particular, the predicted protein structures showed that alternative splicing of in-frame micro-exons led to a local structural recombination, which might affect some core structure of domains, and alternative splicing of frame-shifting micro-exons usually resulted in premature termination of translation by introducing a stop codon or missing functional domains. Overall, our study provided the genome-wide distribution, evolutionary conservation, and potential functions of micro-exons in rice.

Highlights

Micro-exons are a set of small exons with lengths no more than 51 nucleotides
There were 16,508 and 17,517 micro-exons in the genome annotation of Zhenshan 97 (ZS97) and Minghui 63 (MH63), respectively, which accounted for ~6.3% of all the annotated exons
Among these annotated micro-exons, more than half (8816 in ZS97 and 9399 in MH63) were internal micro-exons, and the first or last micro-exons tended to be shorter than internal micro-exons (Figure 1A)

Summary

Introduction

Micro-exons are a set of small exons with lengths no more than 51 nucleotides. Several studies have revealed that the level of micro-exon splicing is related to physiological disease in human; for example, mis-regulation of alternative splicing for neural micro-exons mediated by nSR100 is associated with autism [1,9]. Some studies have revealed there are sets of regulatory sequences in micro-exons and flanking introns, which are called exonic and intronic splicing enhancers (ESE and ISE). These motifs are recognized and bound by RNA-binding proteins (RBP) and contribute to splicing efficiency, consistent with the fact that most micro-exons are included in transcripts [5,10,11]

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