Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis

By Yamile Marquez, John W. S. Brown, C. Simpson, Andrea Barta, M. Kalyna. Genome Research, 2012

762 citations recorded by the source corpus.

Alternative splicing (AS) is a key regulatory mechanism that contributes to transcriptome and proteome diversity. As very few genome-wide studies analyzing AS in plants are available, we have performed high-throughput sequencing of a normalized cDNA library which resulted in a high coverage transcriptome map of Arabidopsis. We detect ∼150,000 splice junctions derived mostly from typical plant introns, including an eightfold increase in the number of U12 introns (2069). Around 61% of multiexonic genes are alternatively spliced under normal growth conditions. Moreover, we provide experimental validation of 540 AS transcripts (from 256 genes coding for important regulatory factors) using high-resolution RT-PCR and Sanger sequencing. Intron retention (IR) is the most frequent AS event (∼40%), but many IRs have relatively low read coverage and are less well-represented in assembled transcripts. Additionally, ∼51% of Arabidopsis genes produce AS transcripts which do not involve IR. Therefore, the significance of IR in generating transcript diversity was generally overestimated in previous assessments. IR analysis allowed the identification of a large set of cryptic introns inside annotated coding exons. Importantly, a significant fraction of these cryptic introns are spliced out in frame, indicating a role in protein diversity. Furthermore, we show extensive AS coupled to nonsense-mediated decay in AFC2, encoding a highly conserved LAMMER kinase which phosphorylates splicing factors, thus establishing a complex loop in AS regulation. We provide the most comprehensive analysis of AS to date which will serve as a valuable resource for the plant community to study transcriptome complexity and gene regulation.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f2b10d22644d273020bbf8960a3b982af8fa632d

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Citations in the corpus

Genomics of Cold Hardiness in Woody Plants (2014, background): “So far, a cold-induced alternatively spliced transcript involving intron retention (Marquez et al. 2012) has been reported for the Dehydrin 1 gene of Vitis (Xiao and Nassuth, 2006).”
Araport11: a complete reannotation of the Arabidopsis thaliana reference genome (2016, methodology): “Analysis of the exitrons identified in this work overlapped 209 of those previously reported (Marquez et al. 2012).”
Complexity of the Alternative Splicing Landscape in Plants[C][W][OPEN] (2013, methodology): “Analysis of different AS events inArabidopsis and several other plants indicated that IR is the predominant mode of AS in land plants (Ner-Gaon et al., 2004;Wang andBrendel, 2006; Baek et al., 2008; Filichkin et al., 2010; Marquez et al., 2012; Syed et al., 2012).”
Widespread intron retention in mammals functionally tunes transcriptomes (2014, background): “…transcripts, is thought to represent the least prevalent form of AS in animals (Galante et al. 2004; Sakabe and de Souza 2007;Wang et al. 2008), whereas it is the most frequent form in plants, fungi, and unicellular eukaryotes (Ner-Gaon et al. 2004;Marquez et al. 2012; Seb e-Pedr os et al. 2013).”
Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses[OPEN] (2013, background): “…it has allowed the identification of previously unknown transcript isoforms and assessment of dynamic changes in the full complement of transcript isoforms during development or in response to environmental cues (Weber et al., 2007; Filichkin et al., 2010; Marquez et al., 2012; Reddy et al., 2013).”