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Nat Commun 2021 Feb 19;121:1157. doi: 10.1038/s41467-021-21426-7.
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Characterising open chromatin in chick embryos identifies cis-regulatory elements important for paraxial mesoderm formation and axis extension.

Mok GF , Folkes L , Weldon SA , Maniou E , Martinez-Heredia V , Godden AM , Williams RM , Sauka-Spengler T , Wheeler GN , Moxon S , Münsterberg AE .

Somites arising from paraxial mesoderm are a hallmark of the segmented vertebrate body plan. They form sequentially during axis extension and generate musculoskeletal cell lineages. How paraxial mesoderm becomes regionalised along the axis and how this correlates with dynamic changes of chromatin accessibility and the transcriptome remains unknown. Here, we report a spatiotemporal series of ATAC-seq and RNA-seq along the chick embryonic axis. Footprint analysis shows differential coverage of binding sites for several key transcription factors, including CDX2, LEF1 and members of HOX clusters. Associating accessible chromatin with nearby expressed genes identifies cis-regulatory elements (CRE) for TCF15 and MEOX1. We determine their spatiotemporal activity and evolutionary conservation in Xenopus and human. Epigenome silencing of endogenous CREs disrupts TCF15 and MEOX1 gene expression and recapitulates phenotypic abnormalities of anterior-posterior axis extension. Our integrated approach allows dissection of paraxial mesoderm regulatory circuits in vivo and has implications for investigating gene regulatory networks.

PubMed ID: 33608545
PMC ID: PMC7895974
Article link: Nat Commun
Grant support: [+]

Species referenced: Xenopus laevis
Genes referenced: cdx2 ddc foxo1 homer1 hoxa11 hoxa2 hoxa5 lef1 rara sall4 spry1 tcf15 zic3

Article Images: [+] show captions
References [+] :
Abou-Elhamd, Klhl31 attenuates β-catenin dependent Wnt signaling and regulates embryo myogenesis. 2015, Pubmed, Xenbase