The Gastrula Transition Reorganizes Replication-Origin Selection in Caenorhabditis Elegans

Nat Struct Mol Biol. 2017 Mar;24(3):290-299. doi: 10.1038/nsmb.3363. Epub 2017 Jan 23.


Although some features underlying replication-origin activation in metazoan cells have been determined, little is known about their regulation during metazoan development. Using the nascent-strand purification method, here we identified replication origins throughout Caenorhabditis elegans embryonic development and found that the origin repertoire is thoroughly reorganized after gastrulation onset. During the pluripotent embryonic stages (pregastrula), potential cruciform structures and open chromatin are determining factors that establish replication origins. The observed enrichment of replication origins in transcription factor-binding sites and their presence in promoters of highly transcribed genes, particularly operons, suggest that transcriptional activity contributes to replication initiation before gastrulation. After the gastrula transition, when embryonic differentiation programs are set, new origins are selected at enhancers, close to CpG-island-like sequences, and at noncoding genes. Our findings suggest that origin selection coordinates replication initiation with transcriptional programs during metazoan development.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Caenorhabditis elegans / embryology*
  • Caenorhabditis elegans / metabolism*
  • Chromatin / metabolism
  • Chromosomes / metabolism
  • CpG Islands / genetics
  • DNA Replication / genetics
  • Embryo, Nonmammalian / metabolism
  • Embryonic Development / genetics
  • Enhancer Elements, Genetic / genetics
  • Gastrula / metabolism*
  • Histones / metabolism
  • Inverted Repeat Sequences / genetics
  • Operon / genetics
  • Replication Origin / genetics*
  • Transcription, Genetic


  • Chromatin
  • Histones