GSE49408
GSE49408: Widespread alternative splicing contributes to the gene regulation, translation diversity and Arabidopsis photomorphogenesis [seq]
Summary: Light is a pivotal signal for plants’ growth and survival.  The promptly responses are required and achieving by sophisticated transcriptomic adjustments, the promptly translation enhancement, and effective protein surveillance.  However, the global role of alternative splicing regulations in response to the light is unknown.  Through global surveys of alternative splicing profile and frequency calculation for individual events normalized to transcriptomic changes, we identify nearly half of transcript present at this stage are alternatively spliced.  Through the unbiased event comparison in D and L4h mRNA, we reveal a clear impact of splicing control on 2,961 genes during early photomorphogenesis.  Intron retention is the most frequently event under controls of light as discovered in other developmental tissues and stages of Arabidopsis.  Cryptic exon is the most abundant event preserved only in the dark-grown Arabidopsis.  Genes underlying the splicing and transcriptional control mostly not overlapped indicate the distinct impacts of two regulatory mechanisms.  Through confirmation with a homemade microarray for their responsiveness of light, we conclude 1,792 genes as biological validated candidates.  Through functional study for genes underlying light-mediated splicing controls, we explore new light-signaling components which mainly responsive in isoform abundance but steady state mRNA.  Among examination both positive (RPR39, KH-RBP, RRM and RRC1) and negative (PIF4, AMI1, DNAJ, UKL3, TF-IIs-like, and ubknown-Golgi protein) factors are controlled by splicing.  Through predictions for example isoform structures, PIF4-IR4, AMI1-IR7-IR8, and DNAJ-IR1 both possess PTC and possibly produce truncated coding protein.  PIF4-IR4 becomes best illustration for the dysfunction for the negative regulator by light.  Above PTC+ isoforms together with one third of retained introns translate that evident for NMD-insensitive retained introns and supplements for protein levels.  The event identities and cis-motif signatures associated with light regulations confirm a given uniqueness for the gene expression regulation during Arabidopsis photomorphogenesis. Overall Design: mRNA and polysome-associated mRNA of 4 days old Arabidopsis seedling grown under the dark or with 4 h light-treatment were isolated and the transcriptome and splicing events profiles were surveyed by mRNAseq.  Independent 3 biological replicates of dark and L4h mRNA were applied for two-color-microarray using custom designed alternative-splicing array from Agilent Technologies.