Genomic cis-regulatory architecture and trans-acting regulators of a single interneuron-specific gene battery in C. elegans.
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.
Wenick
Adam S
AS
Department of Biochemistry and Molecular Biophysics, Center for Neurobiology and Behavior, Columbia University Medical Center, 701 West 168th Street, New York, NY 10032, USA.
Hobert
Oliver
O
D020816:Amino Acid Motifs / Q000235:genetics; D000818:Animals; D001483:Base Sequence / Q000235:genetics; D017173:Caenorhabditis elegans / Q000166:cytology / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000235:genetics; D002454:Cell Differentiation / Q000235:genetics*; D019070:Cell Lineage / Q000235:genetics; D018507:Gene Expression Regulation, Developmental / Q000235:genetics*; D040481:Genome Components / Q000235:genetics; D018398:Homeodomain Proteins / Q000235:genetics; D007395:Interneurons / Q000166:cytology / Q000378:metabolism*; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics*; D009420:Nervous System / Q000166:cytology / Q000254:growth & development / Q000378:metabolism; D009479:Neuropeptides / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics
D029742:Caenorhabditis elegans Proteins; D018398:Homeodomain Proteins; D009479:Neuropeptides; C108368:TTX-3 protein, C elegans; C094292:ceh-10 protein, C elegans