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Chromatin architecture and cis-regulatory landscape of the DACT2-SMOC2 locus in the developing synovial joint.

ABSTRACT: We report the 3D chromatin organization of the 3.4Mb DACT2-SMOC2 locus generated for interphalangeal interzone and phalange, tissues collected during synovial joint formation. The interzone and phalange samples have been dissected from developing hindlimb digits of the chicken embryo at Hamilton Hamburger stage 32 (HH32). Collected material has been processed using the Targeted Chromatin Capture protocol optimized for the 1mln cell. Generation of the T2C-interaction maps has revealed the 3D chromatin architecture of the DACT2-SMOC2 locus in the interzone and phalange tissues as well as identified potential candidate enhancers located in spatial proximity of DACT2 and SMOC2 gene promoters. We report the ChIPseq derived Candidate Enhancer (CE) atlas generated for interphalangeal interzone and phalange, tissues collected during synovial joint formation. Three replicates for interzone and three replicated for phalange were immunoprecipitated (IP) with the H3K27ac antibodies. Also, two replicates for interzone and two replicates for phalange were immunoprecipitated with H3K4me1 antibodies. The IP samples for both histone marks were sequenced and used for annotation of CEs. Further, the CEs were functionally annotated. In parallel, the total RNA for three interzone and three phalange replicates was isolated and mRNA sequencing libraries were constructed. Next the identification of differentially expressed genes (DEGs) and integrative analysis of DEGs and CEs was performed.

ORGANISM(S): Gallus gallus

PROVIDER: GSE210108 | GEO | 2024/07/01

REPOSITORIES: GEO

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