E-GEOD-44362 - Transcription landscape at the HoxD locus in developing caeca

Status
Released on 23 October 2013, last updated on 3 May 2014
Organism
Mus musculus
Samples (16)
Array (1)
Protocols (5)
Description
Hox genes are required for the development of the intestinal caecum, a major organ of species eating plants. We have analysed the transcriptional regulation of Hoxd genes in caecal buds and show that they are controlled by a series of enhancers located in a gene desert telomeric to the HoxD cluster. The start site of two neighboring and opposite long non-coding RNAs, Hotdog and Twin of Hotdog, specifically transcribed in the caecum, contacts the expressed Hoxd genes in the framework of a topological domain, a large domain of interactions, which ensures a robust transcription of these genes during caecum budding. We show that hedgehogs have kept this regulatory potential despite the absence of caecum, suggesting that these enhancers are used in other developmental situations. In this context, we discuss some striking similarities between the caecum and the limb buds, suggesting the implementation of a common budding tool-kit. Transcriptional activity at the HoxD locus in developing caeca at E13.5, Array data were quantile normalized within cDNA/genomic DNA replicate groups and scaled to medial feature intensity of 100 using TAS software (Affymetrix). For each genomic position, a data set was generated consisting of all (PM-MM) pairs mapping within a sliding window of 80 bp. For each tissue, two independent RNA extractions, cDNA synthesis and array hybridizations were performed, except for del(1-4i) and del(9-11) mutant caeca.
Experiment type
transcription profiling by tiling array 
Contacts
Marion LELEU <geo@ncbi.nlm.nih.gov>, D Duboule, S Delpretti
Citation
Multiple Enhancers Regulate Hoxd Genes and the Hotdog LncRNA during Cecum Budding. Delpretti S, Montavon T, Leleu M, Joye E, Tzika A, Milinkovitch M, Duboule D. , Europe PMC 24075990
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-44362.idf.txt
Sample and data relationshipE-GEOD-44362.sdrf.txt
Raw data (1)E-GEOD-44362.raw.1.zip
Array designA-GEOD-14183.adf.txt
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