Genomic cis-regulatory architecture and trans-acting regulators of a single interneuron-specific gene battery in C. elegans

Dev Cell. 2004 Jun;6(6):757-70. doi: 10.1016/j.devcel.2004.05.004.


Gene batteries are sets of coregulated genes with common cis-regulatory elements that define the differentiated state of a cell. The nature of gene batteries for individual neuronal cellular subtypes and their linked cis-regulatory elements is poorly defined. Through molecular dissection of the highly modular cis-regulatory architecture of individual neuronally expressed genes, we have defined a conserved 16 bp cis-regulatory motif that drives gene expression in a single interneuron subtype, termed AIY, in the nematode Caenorhabditis elegans. This motif is bound and activated by the Paired- and LIM-type homeodomain proteins CEH-10 and TTX-3. Using genome-wide phylogenetic footprinting, we delineated the location, distribution, and evolution of AIY-specific cis-regulatory elements throughout the genome and thereby defined a large battery of AIY-expressed genes, all of which represent direct Paired/LIM homeodomain target genes. The identity of these homeodomain targets provides novel insights into the biology of the AIY interneuron.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Motifs / genetics
  • Animals
  • Base Sequence / genetics
  • Caenorhabditis elegans / cytology
  • Caenorhabditis elegans / genetics*
  • Caenorhabditis elegans Proteins / genetics
  • Cell Differentiation / genetics*
  • Cell Lineage / genetics
  • Gene Expression Regulation, Developmental / genetics*
  • Genome Components / genetics
  • Homeodomain Proteins / genetics
  • Interneurons / cytology
  • Interneurons / metabolism*
  • Molecular Sequence Data
  • Multigene Family / genetics*
  • Nervous System / cytology
  • Nervous System / growth & development
  • Nervous System / metabolism
  • Neuropeptides / genetics
  • Regulatory Sequences, Nucleic Acid / genetics


  • Caenorhabditis elegans Proteins
  • Homeodomain Proteins
  • Neuropeptides
  • TTX-3 protein, C elegans
  • ceh-10 protein, C elegans