Unknown,Transcriptomics,Genomics,Proteomics

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MicroRNA regulate immune pathways in T-cells in multiple sclerosis (MS) mRNA

ABSTRACT: MicroRNAs are small noncoding RNA molecules that are involved in the control of gene expression. To investigate the role of microRNA in multiple sclerosis (MS), we performed global microarray analyses of mRNA and microRNA in peripheral blood T-cells from relapsing-remitting MS patients and controls. We identified 2,452 regulated genes and 21 regulated microRNA that differed between MS patients and controls. By Kolmogorov-Smirnov test, 20 of 21 regulated microRNA were shown to affect the expression of their target genes, many of which are involved in the immune system. LIGHT (TNFSF14) was a microRNA target gene significantly decreased in MS. The down-regulation of mir-494 and predicted mRNA-target LIGHT was verified by real-time PCR and we could demonstrate decreased serum levels of LIGHT in MS. Thus, regulated microRNA were significantly associated with both gene and protein expression of a molecule in immunological pathways. These findings indicate that microRNA may be important regulatory molecules in T-cells in MS. Microarray expression analysis of mRNA and miRNA in peripheral blood T-cell of control andMS patients

ORGANISM(S): Homo sapiens

SUBMITTER: Intawat Nookaew

PROVIDER: E-GEOD-43591 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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MicroRNA regulate immune pathways in T-cells in multiple sclerosis (MS).

Jernås Margareta M Malmeström Clas C Axelsson Markus M Nookaew Intawat I Wadenvik Hans H Lycke Jan J Olsson Bob B

BMC immunology 20130729

<h4>Background</h4>MicroRNA are small noncoding RNA molecules that are involved in the control of gene expression. To investigate the role of microRNA in multiple sclerosis (MS), we performed genome-wide expression analyses of mRNA and microRNA in T-cells from MS patients and controls.<h4>Methods</h4>Heparin-anticoagulated peripheral blood was collected from MS-patients and healthy controls followed by isolation of T-cells. MicroRNA and RNA from T-cells was prepared and hybridized to Affymetrix ...[more]

PMID: 23895517

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Project description:To study the genes regulated by transcription factor SQUAMOSA PROMOTER BINDING PROTEIN-LIKE7 (SPL7) in Arabidopsis thaliana, we conducted chromatin immunoprecipitation-based sequencing (ChIP-seq) in 35S:FALG-SPL7 transgenic plant and spl7 mutant, and genome-wide sequencing-based transcript profiling of Arabidopsis thaliana wild-type plants and of spl7 mutant under MS medium and MS supplement with 5µM CuSO4. These experiments led to the identification of genes that are direct target of SPL7 and genes differentially expressed in an SPL7-dependent or Cu-dependent manner. This study provides a framework for the identification of SPL7 regulated genes towards characterization of SPL7 in copper homeostasis. ChIP-Seq: Chromatin isolation was performed with 7-day-old whole seedlings of spl7 mutant (negative control) and 35S:FALG-SPL7 transgene (sample) grown on standard MS medium under continuous white light according to Bowler et al. (2004). The resuspended chromatin pellet was sonicated at 4°C with a Diagenode Bioruptor set at high intensity for 10 min (30 s on, 30 s off intervals). The DNA was sheared to an average size of approximately 500 bp. Chromatin was immunoprecipitated with FLAG antibody (Sigma) according to the Affymetrix Chromatin Immunoprecipitation Assay Protocol Rev.3. Reverse cross-linked DNA was purified and used for sequencing libraries construction following the manufacture’s protocol (Illumina). RNA-Seq: DNase I-treated total RNA was prepared from 7-day-old whole seedlings of wild type (Col-0) and spl7 mutant grown on standard MS medium and MS supplement with 5µM CuSO4 under continuous white light (WL). First- and second-strand cDNA were generated using SuperScript II and random hexamer primers. Double-stranded cDNA was fragmented by nebulization and used for mRNA library construction following the manufacturer’s protocol (Illumina). Tophat was used to map the sequence reads to the Arabidopsis genome and only uniquely mapped reads were used in subsequent analyses. mRNA profiles of 7-day-old whole seedlings of wild type (Col-0) or spl7 mutant grown on standard MS medium and MS supplement with 5µM CuSO4 under continuous white light (WL) were generated by deep sequencing using illumine HiSeq2000.

Dataset Information

MicroRNA regulate immune pathways in T-cells in multiple sclerosis (MS) mRNA

Publications

MicroRNA regulate immune pathways in T-cells in multiple sclerosis (MS).

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