Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Evidence for Antisense Transcription Associated with microRNAs in Arabidopsis

ABSTRACT: Exploring miRNA-related antisense transcription in Arabidopsis through RNA transcript profiling of smRNA pathway-defective mutants on a custom high-resolution oligonucleotide array. Two custom arrays were designed with 15,000 oligonucleotide (25-mer and 36-mer) probes in each array. The probes were selected tiling 200 base upstream and downstream (3 n.t. resolution) of miRNA target sites in Arabidopsis thaliana. The arrays were fabricated by Agilent Technologies, Santa Clara, CA. The 22 target genes on the arrays were chosen based on the abundance of associated smRNAs that mapped to the loci, the amplitude of the antisense transcription signals in published whole genome tiling microarray experiments and a representative cross section of miRNA families. For 15k arrays with 24 selected miRNA targets, a dye swap loop experiment design was utilized with 12 blocks for 7 genotypes on two chip arrays. The details of the experimental design are in Supplemental Table V of the manuscript. For the hen1-1 versus Ler-0 experiment, a dye swap with two versus three biological replicates and four array blocks was performed.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Manoj Samanta

PROVIDER: E-GEOD-15199 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Evidence for antisense transcription associated with microRNA target mRNAs in Arabidopsis.

Luo Qing-Jun QJ Samanta Manoj P MP Köksal Fatih F Janda Jaroslav J Galbraith David W DW Richardson Casey R CR Ou-Yang Fangqian F Rock Christopher D CD

PLoS genetics 20090417 4

Antisense transcription is a pervasive phenomenon, but its source and functional significance is largely unknown. We took an expression-based approach to explore microRNA (miRNA)-related antisense transcription by computational analyses of published whole-genome tiling microarray transcriptome and deep sequencing small RNA (smRNA) data. Statistical support for greater abundance of antisense transcription signatures and smRNAs was observed for miRNA targets than for paralogous genes with no miRNA ...[more]

PMID: 19381263

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Project description:Porcine cytomegalovirus (PCMV) is a member of the genus Cytomegalovirus, subfamily Betaherpesvirinae, and family Herpesvirus. PCMV is a major immunosuppressive virus that mainly suppress the immune function of T lymphocytes and macrophages. PCMV is widely distributed all over the world, but there are not significantly different serotypes found. Moreover, the molecular mechanisms of host anti-PCMV infection and the molecular immunosuppressive mechanisms of PCMV is still not well charaterized. To understand the PCMV potential impact on the function of immune organs, we performed microarray assay to analyze the transcriptome of porcine immune organs after PCMV infection. We identified 5582 differential expression genes by PCMV infection in microarray. There are 2161 upregulated genes and 3421 down-regulated by PCMV infection genes compare to the uninfected control group. We confirmed 13 differentially expressed immune-related genes by quantitative real-time RT-PCR (qPCR). Gene ontology, gene interaction networks and KEGG pathway analysis uncovered the differentially expressed genes interaction regulatory network. These findings indicated that PCMV regulates multiple functional pathways, including immune system process, cellular process, metabolic process, networks of cytokine-cytokine receptor interaction, TGF-beta signaling pathway, lymphocytes receptor signaling pathway and TNF signaling pathway. Our study is the first comprehensive attempt to explore the host transcriptional response to PCMV infection in porcine immune systems. It provided new insights into the immunosuppressive molecular mechanisms and pathogenesis of PCMV. This previously unrecognized endogenous antiviral mechanism has implications for development of host-directed strategies to the prevention and treatment of immunosuppressive viral diseases. 2 samples were analysed. PCMV infected porcine immune organs; control porcine organs. piglets were divided into two groups of five pigs each, and maintained under controlled temperature and humidity. Each pig in the first group was inoculated with 5 ml of 109 PFU/ml PCMV SC strain by intramuscular and intranasal injection, and the other five pigs were injected with 5 ml of RPMI-1640 nutrient solution (Thermo Fisher Scientific, Waltham, UK) as the control. The sera, lymph nodes, spleens, and thymuses of the infected and control pigs were collected at 14 dpi

Dataset Information

Evidence for Antisense Transcription Associated with microRNAs in Arabidopsis

Publications

Evidence for antisense transcription associated with microRNA target mRNAs in Arabidopsis.

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