Analysis of Alternatively Spliced Rice Transcripts Using Microarray Data

Abstract

Alternative splicing creates a diversity of gene products in higher eukaryotes. Twenty-five percent (1,583/ 6,371) of predicted alternatively spliced transcripts can be detected using the NSF45K rice whole-genome oligonucleotide array. We used the NSF45K array to assess differential expression patterns of 507 loci showing at least a twofold change in expression between light-and darkgrown seedlings. At least 42% of these loci show evidence of alternative splicing in aerial seedling tissue of Oryza sativa ssp. japonica cv. Nipponbare. Most alternative splice forms display the same pattern of regulation as the primary, or most highly expressed, transcript; however, splice forms for ten loci, represented by 35 oligos, display opposite expression patterns in the light vs. dark. We found similar evidence of alternative splicing events in Affymetrix microarray data for Nipponbare rice treated with the causative agent of fungal rice blast, Magnaporthe grisea. This strategy for analyzing alternative splicing in microarray data will enable delineation of the diversity of splicing in rice.

Phytochrome controls alternative splicing to mediate light responses in Arabidopsis

“…Light-regulated AS has been reported not only in different species in higher plants (16)(17)(18) but also in a chlorophyte Chlamydomonas (33). Moreover, recently, phytochrome was suggested to be involved in R-dependent AS alterations in the moss Physcomitrella (34).…”

“…Accumulating evidence suggests that light regulates not only transcription but also other aspects of gene expression, such as chromatin reorganization (12), translation (13,14), posttranslational modification (11,15), and pre-mRNA splicing (16)(17)(18). Pre-mRNA splicing is a posttranscriptional event that is carried out by a macromolecular complex called the spliceosome.…”

“…Therefore, the regulation of AS depends on the expression level and posttranslational modification of SR proteins and other splicing factors (20). It has been reported that light affects the AS of several genes in plants (16)(17)(18). However, the physiological significance of this finding and the identity of the photoreceptors that mediate light-regulated AS remain unclear.…”

Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis

“…(pumpkin), and high-light-modulated AS for homologs of the family of serine/arginine-rich (SR) splicing factors from A. thaliana (Tanabe et al, 2007). Comparisons of AS profiles for light-versus dark-grown rice seedlings using microarrays (Jung et al, 2009) and for A. thaliana seedlings with a high-resolution reverse transcription polymerase chain reaction (RT-PCR) panel (Simpson et al, 2008) indicated that light-mediated changes in AS patterns might affect the expression of numerous genes. This notion was further supported by recent studies using RNA sequencing (RNA-seq) to deduce light-regulated AS patterns in a transcriptome-wide manner in the moss Physcomitrella patens (Wu et al, 2014), etiolated A. thaliana seedlings (Shikata et al, 2014), and light-grown A. thaliana plants (Mancini et al, 2016).…”

A vacuolar antiporter is differentially regulated in leaves and roots of the halophytic wild rice Porteresia coarctata (Roxb.) Tateoka

“…PcNHX1 expression in leaves of P. coarctata was investigated further by real time PCR and found to be diurnally expressed with an early morning maxima and minima at night in the absence of NaCl. Jung et al [35] have reported two alternatively spliced transcripts for Os07g47100 (OsNHX1), that show opposite differential expression in response to light. Os07g47100.2 is highly induced in the dark and does not splice out an intron that is present in the 5 0 UTR of Os07g47100.1, the latter being highly expressed in light.…”