Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Differential gene expression profiling in the presence and absence of cohesin in Drosophila salivary glands (gene expression data)

ABSTRACT: Analysis of differential gene expression in third instar Drosophila salivary glands in the absence versus presence of cohesin. ABSTRACT: Developmental abnormalities observed in Cornelia de Lange Syndrome (CdLS) have been genetically linked to mutations in the cohesin machinery. These findings raise the possibility that cohesin, in addition to its canonical function of mediating sister chromatid cohesion, might also be involved in regulating gene expression. We report that cleavage of cohesinM-CM-^Us kleisin subunit in post-mitotic Drosophila salivary glands induces major changes (both up and down) in the transcript levels of many genes. Kinetic analyses of changes in transcript levels upon cohesin cleavage reveal that a subset of genes responds to cohesin cleavage within a few hours. In addition, cohesin binds to most of these loci, suggesting that cohesin is directly regulating their expression. Amongst these genes are several that are regulated by the steroid hormone Ecdysone. Transcripts at EcR and Eip74EF, which encode an Ecdysone Receptor and an Ecdysone-regulated transcription factor, respectively, decline ten-fold within four hours of cohesin cleavage. Cytological visualization of transcription at selected Ecdysone-responsive genes reveals that puffing at Eip74EF ceases within an hour or two of cohesin cleavage, long before any decline in EcR associated with this locus. We conclude that cohesin regulates expression of a distinct set of genes, including those mediating the Ecdysone response. A heat-inducible transgene (hs-TEV) was used to induce TEV in terminally differentiated third instar Drosophila salivary glands expressing either wild type (+ cohesin) or TEV-cleavable myc10-tagged Rad21 protein (Rad21TEV, - cohesin). Total RNA was isolated from + and - cohesin salivary glands 10-12 hours after heat shock induction of TEV (7 independent biological samples each). RNA samples were converted to cDNA, labeled with Cy3 and Cy5 respectively (3x) and vice versa (4x; dye swaps), and hybridized to INDAC FL003 arrays. Analysis of seven arrays, each hybridized to an independently generated sample-pair revealed major differences in transcript levels between + and - cohesin samples.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Andrea Pauli

PROVIDER: E-GEOD-21844 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A direct role for cohesin in gene regulation and ecdysone response in Drosophila salivary glands.

Pauli Andrea A van Bemmel Joke G JG Oliveira Raquel A RA Itoh Takehiko T Shirahige Katsuhiko K van Steensel Bas B Nasmyth Kim K

Current biology : CB 20101007 20

<h4>Background</h4>Developmental abnormalities observed in Cornelia de Lange syndrome have been genetically linked to mutations in the cohesin machinery. These and other recent experimental findings have led to the suggestion that cohesin, in addition to its canonical function of mediating sister chromatid cohesion, might also be involved in regulating gene expression.<h4>Results</h4>We report that cleavage of cohesin's kleisin subunit in postmitotic Drosophila salivary glands induces major chan ...[more]

PMID: 20933422

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Project description:It is now well established that mature mammalian spermatozoa carry a population of mRNA molecules, at least some of which are transferred to the oocyte at fertilisation. However, the function of the sperm transcriptome remains largely unclear. To shed light on the evolutionary conservation of this feature of sperm biology, we analysed highly purified populations of mature sperm from the fruitfly, Drosophila melanogaster. As with mammalian sperm, we found a consistently enriched population of mRNA molecules that are not likely to be derived from contaminating somatic cells or immature sperm. Using tagged transcripts for three of the spermatozoal mRNAs, we demonstrate that they are transferred to the oocyte at fertilisation and can be detected at least until the onset of zygotic gene expression. We find a remarkable conservation in the functional annotations associated with fly and human spermatozoal mRNAs, in particular a highly significant enrichment for transcripts encoding Ribosomal Proteins. The identification of a conserved set of spermatozoal transcripts opens the possibility of using the power of Drosophila genetics to address the function of this enigmatic class of molecules. RNA extracted from three biological replicates of purified sperm (Sperm rep1, Sperm rep2 and Sperm rep3) was used as a template for oligo-dT-primed reverse transcription, amplification, labelling of dye swapped technical replicates and hybridisation to long oligonucleotides microarrays. As a control, RNA from two biological replicates of dissected adult testis plus accessory glands (Testis_rep1, Testis_rep2) was amplified, labelled (dye-swap technical replicate) and hybridised to similar arrays. To help with the spot-finding of the arrays genomic DNA was co-hybridised in some cases (this genomic DNA data was excluded from further analysis). Genes with an intensity level below 200 in at least one channel across the Sperm or Testis set were removed (5579 transcripts present in all three sperm replicates, 5358 transcripts from the testis/accessory gland samples and 4295 transcripts common to both data sets). Then the quantile normalisation was independently applied to the Sperm replicate samples and Testis replicates.

Dataset Information

Differential gene expression profiling in the presence and absence of cohesin in Drosophila salivary glands (gene expression data)

Publications

A direct role for cohesin in gene regulation and ecdysone response in Drosophila salivary glands.

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