Splicing and alternative splicing in rice and humans

Abstract

Rice is a monocot gramineous crop, and one of the most important staple foods. Rice is considered a model species for most gramineous crops. Extensive research on rice has provided critical guidance for other crops, such as maize and wheat. In recent years, climate change and exacerbated soil degradation have resulted in a variety of abiotic stresses, such as greenhouse effects, lower temperatures, drought, floods, soil salinization and heavy metal pollution. As such, there is an extremely high demand for additional research, in order to address these negative factors. Studies have shown that the alternative splicing of many genes in rice is affected by stress conditions, suggesting that manipulation of the alternative splicing of specific genes may be an effective approach for rice to adapt to abiotic stress. With the advancement of microarrays, and more recently, next generation sequencing technology, several studies have shown that more than half of the genes in the rice genome undergo alternative splicing. This mini-review summarizes the latest progress in the research of splicing and alternative splicing in rice, compared to splicing in humans. Furthermore, we discuss how additional studies may change the landscape of investigation of rice functional genomics and genetically improved rice. [BMB Reports 2013; 46(9): 439-447]

Identification and analysis of alternative splicing events in Phaseolus vulgaris and Glycine max

“…The least frequent AS event reported for both plants is ASS (Additional file 1 ). Again, these results are not consistent with the AS profiles reported for other plants where IR the most common AS event, followed by AA and AD, and ES being the least common [ 7 , 8 , 36 , 37 ]. These results suggest that the current annotation lacks a comprehensive identification of AS isoforms in these two legume species.…”

“…Serine/arginine-rich (SR) proteins facilitate the splicing of the intron while heterogeneous nuclear ribonucleoproteins inhibit the recognition of splicing sites [ 5 ]. The intron motifs as well as splicing enhancers and inhibitors are commonly found at different sites within the intron and these juxtaposed signals can give rise to variation in splicing an intron from the pre-mRNA; this phenomenon is known as alterative splicing (AS) [ 6 – 8 ].…”

“…AS is a post-transcriptional regulatory process that affects the fate of the mRNA; it has been found in several tissues, stress conditions and developmental stages of eukaryotic organisms [ 9 ]. AS can affect the localization of the mature mRNA and their translation efficiency [ 8 ]. Also, AS may produce alternative stop codons due to frame shifts in the mature mRNA sequence, thus regulating mRNA abundance by nonsense-mediated decay (NMD) [ 10 ].…”

Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation

“…In plants, isoforms are not as prevalent as in mammals, yet they still play important roles in protein diversity. Previous studies in rice indicate that the majority of alternative splice forms result from the retention of individual introns (Campbell et al 2006; E et al 2013; Wang and Brendel 2006). Among the 16,809 isoforms annotated in MSU Release 7, 8164 isoform pairs were SI vs. RI, referring to isoforms of genes with spliced introns and retained introns, respectively (Campbell et al 2006).…”

CoSREM: a graph mining algorithm for the discovery of combinatorial splicing regulatory elements

“…In AS, genes generate different mRNA isoforms from the same primary transcript [ 5 , 6 ]. Recent studies show that AS occurs in more than 95 % of human genes [ 4 , 6 , 7 ].…”