A transcriptional and regulatory map of mouse somite maturation

Ximena Ibarra-Soria, Elodie Thierion, Gi Fay Mok, Andrea E. Münsterberg, Duncan T. Odom, John C. Marioni

Research output: Contribution to journalArticlepeer-review


The mammalian body plan is shaped by rhythmic segmentation of mesoderm into somites, which are transient embryonic structures that form down each side of the neural tube. We have analyzed the genome-wide transcriptional and chromatin dynamics occurring within nascent somites, from early inception of somitogenesis to the latest stages of body plan establishment. We created matched gene expression and open chromatin maps for the three leading pairs of somites at six time points during mouse embryonic development. We show that the rate of somite differentiation accelerates as development progresses. We identified a conserved maturation program followed by all somites, but somites from more developed embryos concomitantly switch on differentiation programs from derivative cell lineages soon after segmentation. Integrated analysis of the somitic transcriptional and chromatin activities identified opposing regulatory modules controlling the onset of differentiation. Our results provide a powerful, high-resolution view of the molecular genetics underlying somitic development in mammals.

Original languageEnglish
Pages (from-to)1983-1995.e7
Number of pages9
JournalDevelopmental Cell
Issue number19
Early online date26 Jul 2023
Publication statusPublished - 9 Oct 2023


  • ATAC-seq
  • chromatin
  • gene regulation
  • mouse development
  • RNA-seq
  • somite maturation
  • somites
  • transcription

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