| Experiment Id | GSE31656 | Name | Transcription landscape at the HoxD locus in developing limbs and brain |
| Experiment Type | transcription profiling by array | Study Type | Baseline |
| Source | GEO | Curation Date | 2022-10-31 |
| description | The emergence and evolution of digits was an essential step in the success of the tetrapod lineage. Amongst the key players, Hoxd genes were functionally co-opted in the developing digital plate, where they help organize growth and patterns. To understand both the evolutionary recruitment and transcriptional regulation of this genomic locus, we analyzed its architecture and chromatin status in developing digits, combined with a deletion approach in vivo. We show that the active and inactive parts of the gene cluster adopt opposite spatial configurations, corresponding to different chromatin domains. Active genes are contacted by several regulatory islands, located within a neighboring gene desert, which contribute quantitatively or qualitatively to the global transcriptional readout. We refer to this novel type of control as a 'regulatory archipelago' and discuss the value of this concept to understand both the morphological flexibility of tetrapod digits and the robustness of the underlying developmental process. Transcriptional activity at the Hoxd locus in developing limbs and brain at E12.5 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. |
