Characterising open chromatin in chick embryos identifies cis-regulatory elements important for paraxial mesoderm formation and axis extension

Gi Fay Mok, Leighton Folkes, Shannon A. Weldon, Eirini Maniou, Victor Martinez-Heredia, Alice M. Godden, Ruth M. Williams, Tatjana Sauka-Spengler, Grant N. Wheeler, Simon Moxon and Andrea E. Münsterberg ()
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Gi Fay Mok: University of East Anglia, Norwich Research Park
Leighton Folkes: University of East Anglia, Norwich Research Park
Shannon A. Weldon: University of East Anglia, Norwich Research Park
Eirini Maniou: University of East Anglia, Norwich Research Park
Victor Martinez-Heredia: University of East Anglia, Norwich Research Park
Alice M. Godden: University of East Anglia, Norwich Research Park
Ruth M. Williams: University of Oxford
Tatjana Sauka-Spengler: University of Oxford
Grant N. Wheeler: University of East Anglia, Norwich Research Park
Simon Moxon: University of East Anglia, Norwich Research Park
Andrea E. Münsterberg: University of East Anglia, Norwich Research Park

Nature Communications, 2021, vol. 12, issue 1, 1-15

Abstract: Abstract 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.

Date: 2021
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-21426-7

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DOI: 10.1038/s41467-021-21426-7

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