Transcription profiling of mouse smooth muscle cells in atherosclerosis-prone and resistant regions of aorta
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ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Joke Allemeersch
PROVIDER: E-GEOD-13865 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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2009-05-27 | E-GEOD-13836 | biostudies-arrayexpress
Project description:Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization between complementary nucleic acid strands, inciting us to create a collection of gene-specific sequence tags (GSTs) representing at least 21,500 Arabidopsis genes and which are compatible with both approaches. The GSTs were carefully selected to ensure that each of them shared no significant similarity with any other region in the Arabidopsis genome. They were synthesized by PCR amplification from genomic DNA. Spotted microarrays fabricated from the GSTs show good dynamic range, specificity and sensitivity in transcript profiling experiments. The GSTs have also been transferred to bacterial plasmid vectors via recombinational cloning protocols. These cloned GSTs constitute the ideal starting point for a variety of functional approaches, including reverse genetics. We have subcloned GSTs on a large scale into vectors designed for gene silencing in plant cells. We show that in planta expression of GST hairpin RNA results in the expected phenotypes in silenced Arabidopsis lines. These versatile GST resources provide novel and powerful tools for functional genomics. Supplemental material is available online at www.genome.org. The sequence data have been submitted to GenBank under accession number XXXXX. The GST sequence information is accessible via the CATMA database (www.catma.org) and other Arabidopsis databases, the corresponding CATMA array, or corresponding CATMA-based transcript profiling service, are available from multiple genomics facilities and the GST clone repertoire will be distributed by the Nottingham Arabidopsis Stock Centre (nasc.nott.ac.uk).
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Project description:Stomatal guard-cells modulate gas exchange between the plant and the atmosphere.<br><br>Regulation of transcription is emerging as an important mechanism in<br><br>controlling guard cells activity. The Arabidopsis transcription factor<br><br>AtMYB60, is specifically expressed in guard cells and controls stomatal<br><br>movements. Opening of stomatal pores is constitutively reduced in the<br><br>atmyb60-1 null allele, and water loss during drought is diminished in<br><br>the mutant compared to wild type. To address the effect of the AtMYB60<br><br>disruption on global gene expression, total mRNAs, derived from<br><br>atmyb60-1 and WT rosette leaves, grown in standard conditions, were hybridized to a cDNA microarray.
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Project description:One of the major primary features of the neurocutaneous genetic disorder Neurofibromatosis type 1 are the hyperpigmentary café-au-lait macules where dysregulation of melanocyte development, proliferation and differentiation is considered to play a key etiopathogenic role. To gain better insight in the possible role of the tumor suppressor gene NF1, a transcriptomic microarray analysis was performed on human NF1 heterozygous (NF1+/-) melanocytes of a Neurofibromatosis type 1 patient and NF1 wild type (NF1+/+) melanocytes of a healthy control patient, both cultured from normally pigmented and hyperpigmented lesional café-au-lait skin. Out of 13,850 unique genes, a total of 137 had a significant twofold or more up- (72) or down-regulated (65) expression in NF1+/- melanocytes compared to NF1+/+ melanocytes (genotype effect). Considering possible intrinsic genetic variation in lesional skin, melanocytes showed a total of 51 genes having a significant twofold or more up- (37) or down-regulated (14) expression when they were cultured from hyperpigmentary café-au-lait skin compared to normally pigmented skin (lesional skin type effect). NF1+/- café-au-lait skin melanocytes showed 468 genes with a significant two-fold or more up- (183) or down-regulated (285) expression going beyond the sum of the separate main effects (interaction). Detailed analysis enabled the identification of several modulated genes in NF1+/- (café-au-lait skin) melanocytes, mainly involved in controlling cell proliferation and cell maintenance, in cell adhesion and, surprisingly, in the immune response. An interesting finding was that a high number of transcription factor genes were differentially modulated, among which a specific subset - important in melanocyte-lineage development - showed downregulation in a transcriptional cis-regulatory network governing the activation of the melanocyte-specific dopachrome tautomerase (DCT) gene.
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Project description:Insights into mechanisms involved during intra-medullary myeloma progression could be helpful in the better understanding of this disease and in the development of new therapeutical strategies. Herein gene expression profile of multiple myeloma (MM) cells during intra-medullary progression was investigated using the 5T2MM murine model. MM-cells from 3 subsequent disease stages, quiescent, intermediate and end stage were analyzed using microarrays containing 21,492 Unigene cDNA sequences. ~ 3000 calls of differentially expressed genes were obtained. Most of these genes were silenced during tumor progression. In the early stage the MM-cells had up-regulated genes involved in bone marrow (BM) homing (CCR2, CCR5), motility (tetraspanins, 67kD laminin receptor, paxillin, zyxin, prolactin receptor), invasion (annexin II, cathepsins), adhesion (integrins, ALCAM) and cell adhesion mediated drug resistance (fibronectin). Genes involved in apoptosis (Mcl-1), plasma cell differentiation (XBP-1), angiogenesis (neuropilin-2, angiopoietin-like 4), hypoxia (HIF-1a, carbonic anhydrase 9) and in retention (CXCR4/CXCL12) and anchoring of MM-cells (laminin, collgens) in the BM were up-regulated during progressive stages. Quantative RT-PCR confirmed the trend of expression. These data provide a framework of mechanisms involved in intra-medullary myeloma progression; several genes known to be important in MM-biology are highlighted and novel candidate genes are illuminated as potentially more effective therapeutical targets.
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Project description:Large-scale screening studies carried out to date to elucidate the causal mechanism of an allelic imbalance are generally limited to descriptions of allele-specific differences in expression detected in vivo and to linking them to differences in cis- and trans-regulatory changes. Although such gene surveys for regulatory variation leave the underlying mechanisms unexplored, they are a first step in identifying the specific nucleotide changes that govern gene expression differences. We describe a quantitative genetics approach to distinguish between cis- and trans-regulatory changes at a genome-wide scale and, hence, to detect cis-regulatory variation. For this purpose, we took advantage of diallel designs that are often used in plant breeding programs in which the goal is the estimation of general combining abilities (GCAs) of specific inbred lines and the identification of high yielding hybrid combinations of parents based on their specific combining abilities (SCAs). We show that in a context of gene expression, empirical estimates of GCA and SCA are valid parameters to distinguish between cis- and trans-regulatory changes and, hence, to detect cis-regulatory variation. By using this approach, we identified a considerable number of genes that showed evidence of cis-regulated allele-specific expression in a total of 10 diploid Arabidopsis hybrids. The method can also be used to explore naturally occurring cis-regulatory variation among inbred lines for laboratory animals, such as mouse and rat. This experiment covers data from 10 pairs of reciprocal hybrid samples, referred to as Hx.y where x=1...10 and y=1,2; The related data from 20 Recombinant Inline Line samples is submitted as experiment : - VIB Plant Systems Biology "RIL")
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