Project description:Ouyang2014 - photomorphogenic UV-B signalling network This model is described in the article: Coordinated photomorphogenic UV-B signaling network captured by mathematical modeling. Ouyang X, Huang X, Jin X, Chen Z, Yang P, Ge H, Li S, Deng XW. Proc. Natl. Acad. Sci. U.S.A. 2014 Aug; 111(31): 11539-11544 Abstract: Long-wavelength and low-fluence UV-B light is an informational signal known to induce photomorphogenic development in plants. Using the model plant Arabidopsis thaliana, a variety of factors involved in UV-B-specific signaling have been experimentally characterized over the past decade, including the UV-B light receptor UV resistance locus 8; the positive regulators constitutive photomorphogenesis 1 and elongated hypocotyl 5; and the negative regulators cullin4, repressor of UV-B photomorphogenesis 1 (RUP1), and RUP2. Individual genetic and molecular studies have revealed that these proteins function in either positive or negative regulatory capacities for the sufficient and balanced transduction of photomorphogenic UV-B signal. Less is known, however, regarding how these signaling events are systematically linked. In our study, we use a systems biology approach to investigate the dynamic behaviors and correlations of multiple signaling components involved in Arabidopsis UV-B-induced photomorphogenesis. We define a mathematical representation of photomorphogenic UV-B signaling at a temporal scale. Supplemented with experimental validation, our computational modeling demonstrates the functional interaction that occurs among different protein complexes in early and prolonged response to photomorphogenic UV-B. This model is hosted on BioModels Database and identified by: BIOMD0000000545. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Project description: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.

Project description: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. 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.

Dataset Information

Expression profiling of Photomorphogenic Arabidopsis seedlings

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets