Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of human fibroblast cells transfected with a MDB-VP16 fusion to identify possible target genes for MBD1

ABSTRACT: We compared cells transfected with a MBD-VP16 fusion, with cells transfected with a control construct.
The purpose was to turn a repressor protein (MBD1) into an activator, and use differences in transcription to identify possible gene promoter targets.
A common reference was employed for all comparisons within each cell line: cDNA from the untransfected cell line.

ORGANISM(S): Homo sapiens

SUBMITTER: Jose de las Heras

PROVIDER: E-MTAB-103 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Recruitment of MBD1 to target genes requires sequence-specific interaction of the MBD domain with methylated DNA.

Clouaire Thomas T de Las Heras Jose Ignacio JI Merusi Cara C Stancheva Irina I

Nucleic acids research 20100408 14

MBD1, a member of the methyl-CpG-binding domain family of proteins, has been reported to repress transcription of methylated and unmethylated promoters. As some MBD1 isoforms contain two DNA-binding domains-an MBD, which recognizes methylated DNA; and a CXXC3 zinc finger, which binds unmethylated CpG-it is unclear whether these two domains function independently of each other or if they cooperate in facilitating recruitment of MBD1 to particular genomic loci. In this report we investigate DNA-bi ...[more]

PMID: 20378711

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Project description:Phenotypic plasticity, the ability of one genotype to express different phenotypes in response to changing environmental conditions, is one of the most common phenomena characterising the living world and is not only relevant for the ecology but also for the evolution of species. Daphnia, the waterflea, is a textbook example for predator induced phenotypic plastic defences including changes in life-history, behaviour and morphology. However, the analysis of molecular mechanisms underlying these inducible defences is still in its early stages. We exposed Daphnia magna to chemical cues of the predator Triops cancriformis to identify key processes underlying plastic defensive trait formation. D. magna is known to develop an array of morphological changes in the presence of T. cancriformis including changes of carapace morphology and cuticle hardening. To get a more comprehensive idea of this phenomenon, we studied four different genotypes originating from habitats with different predation history, reaching from predator-free to temporary habitats containing T. cancriformis. We analysed the morphologies as well as proteomes of predator-exposed and control animals. Three genotypes showed morphological changes when the predator was present. Using a high-throughput proteomics approach, we found 294 proteins which were significantly altered in their abundance after predator exposure in a general or genotype dependant manner. Proteins connected to genotype dependant responses were related to the cuticle, protein synthesis and calcium binding whereas the yolk protein vitellogenin increased in abundance in all genotypes, indicating their involvement in a more general response. Furthermore, genotype dependant responses at the proteome level correlated well with local adaptation to Triops predation. Altogether, our study provides new insights concerning genotype dependant and general molecular processes involved in predator-induced phenotypic plasticity in D. magna.

Dataset Information

Transcription profiling of human fibroblast cells transfected with a MDB-VP16 fusion to identify possible target genes for MBD1

Publications

Recruitment of MBD1 to target genes requires sequence-specific interaction of the MBD domain with methylated DNA.

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