Dataset Information

Non-uniform distribution pattern for differentially expressed genes of transgenic rice Huahui 1 at different developmental stages and environments.

ABSTRACT: DNA microarray analysis is an effective method to detect unintended effects by detecting differentially expressed genes (DEG) in safety assessment of genetically modified (GM) crops. With the aim to reveal the distribution of DEG of GM crops under different conditions, we performed DNA microarray analysis using transgenic rice Huahui 1 (HH1) and its non-transgenic parent Minghui 63 (MH63) at different developmental stages and environmental conditions. Considerable DEG were selected in each group of HH1 under different conditions. For each group of HH1, the number of DEG was different; however, considerable common DEG were shared between different groups of HH1. These findings suggested that both DEG and common DEG were adequate for investigation of unintended effects. Furthermore, a number of significantly changed pathways were found in all groups of HH1, indicating genetic modification caused everlasting changes to plants. To our knowledge, our study for the first time provided the non-uniformly distributed pattern for DEG of GM crops at different developmental stages and environments. Our result also suggested that DEG selected in GM plants at specific developmental stage and environment could act as useful clues for further evaluation of unintended effects of GM plants.

SUBMITTER: Liu Z

PROVIDER: S-EPMC3350509 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Non-uniform distribution pattern for differentially expressed genes of transgenic rice Huahui 1 at different developmental stages and environments.

Liu Zhi Z Zhao Jie J Li Yunhe Y Zhang Wenwei W Jian Guiliang G Peng Yufa Y Qi Fangjun F

PloS one 20120511 5

DNA microarray analysis is an effective method to detect unintended effects by detecting differentially expressed genes (DEG) in safety assessment of genetically modified (GM) crops. With the aim to reveal the distribution of DEG of GM crops under different conditions, we performed DNA microarray analysis using transgenic rice Huahui 1 (HH1) and its non-transgenic parent Minghui 63 (MH63) at different developmental stages and environmental conditions. Considerable DEG were selected in each group ...[more]

PMID: 22606331

Similar Datasets

Project description:Osteoarthritis (OA), also known as degenerative arthritis, affects millions of people all over the world. OA occurs when the cartilage wears down over time, which is a worldwide complaint. The aim of this study was to screen and verify hub genes involved in developmental chondrogenesis as well as to explore potential molecular mechanisms.The expression profiles of GSE51812 were downloaded from the Gene Expression Omnibus (GEO) database, which contained 9 samples, including 6-week pre-chondrocytes (PC, 6 independent specimens) and 17-week fetal periarticular resting chondrocytes (RC, 3 independent specimens). The raw data were integrated to obtain differentially expressed genes (DEGs) and were further analyzed with bioinformatics analysis. The Gene Ontology (GO) and pathway enrichment of DEGs were conducted via Database for Annotation, Visualization, and Integrated Discovery (DAVID). The protein-protein interaction (PPI) networks of the DEGs were constructed based on data from the search tool for the retrieval of interacting genes (STRING) database. An intersection figure was provided to show the relationship between the DEGs identified in this study and genes from any existed related studies.A total of 9486 DEGs, including 4821 upregulated genes and 4665 downregulated genes were observed. The top 30 developmental chondrogenesis associated genes were identified, including matrix metalloproteinase (MMP)1, MMP3, MMP13, prostaglandin-endoperoxide synthase 2 (PTGS2), and so on. The majority of DEGs, including PTGS2, CCL20, CHI3L1, LIF, CXCL8, and CXCL12 were intensively enriched in immune-associated biological process terms, including inflammatory, and immune responses. Additionally, the majority of DEGs were mainly enriched in NF-kappa β (NF-kβ) signaling pathway and tumor necrosis factor (TNF) signaling pathway. The hub genes identified in STRING and Cytoscape databases included MMP1, MMP3, MMP13, PTGS2 and so on. Among the top 30 upregulated and downregulated DEGs, there were 15 genes have been reported to be associated with OA or developmental chondrogenesis.This large scale gene expression study observed genes associated with human developmental chondrogenesis and their relative GO function, which may offer opportunities for the research for cartilage tissue engineering and novel insights into the prevention of OA in the near future.

Project description:In plants, arsenic (As) stress modulates metabolic cascades at various developmental stages by influencing the pattern of gene expressions mediated by small non-coding RNAs, especially Micro-RNAs, involved in the moderation of a myriad of cellular processes needed for plant adaptation upon oxidative stress. miR156j of miR156 gene family, involved mainly in the regulation of growth and development in plants. This study was designed to find out the role of arsenic toxicity on Osa-miR156j expression in all physiological growth stages. To better understand the functional role of Osa-miR156j in rice, we observed the expression in different developmental stages (seedlings, tillering and flowering) and various tissues of leaf, stem and root tissues (at 0, 24, 48, and 72 h) under 25 ?M arsenite [As (III)] exposure. Additionally, using bioinformatic tools to target genes of Osa-miR156j and the potential co-expressed genes were explored at different development stages in the various tissues of rice under stress conditions. The expression of Osa-miR156j showed its temporal downregulation in various tissues in different developmental stages. Of note, the downregulation was more pronounced in root tissues at seedlings, tillering, and flowering stages during 0-72 h under arsenite exposure as compared to other tissues. Overall, the As stress altered the gene expression more prominently at seedlings developmental stage followed by flowering and tillering. Additionally, through the In silico approach, the target functions and presence of oxidative stress-responsive cis-acting regulatory elements/motifs also confirmed Osa-miR156j involvement in the regulation of arsenic stress in rice. The findings of this study demonstrate the prominent role of Osa-miR156j in rice under arsenite stress, which was found to modulate the metabolic activities in rice plants at different developmental stages, and thus it might be useful for the development of arsenic tolerant varieties.

Dataset Information

Non-uniform distribution pattern for differentially expressed genes of transgenic rice Huahui 1 at different developmental stages and environments.

Publications

Non-uniform distribution pattern for differentially expressed genes of transgenic rice Huahui 1 at different developmental stages and environments.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets