title: cis-regulatory analysis of the Drosophila pdm locus reveals a diversity of neural enhancers.
abstract: BACKGROUND
  One of the major challenges in developmental biology is to understand the regulatory events that generate neuronal diversity. During Drosophila embryonic neural lineage development, cellular temporal identity is established in part by a transcription factor (TF) regulatory network that mediates a cascade of cellular identity decisions. Two of the regulators essential to this network are the POU-domain TFs Nubbin and Pdm-2, encoded by adjacent genes collectively known as pdm. The focus of this study is the discovery and characterization of cis-regulatory DNA that governs their expression.
  
  
  RESULTS
  Phylogenetic footprinting analysis of a 125 kb genomic region that spans the pdm locus identified 116 conserved sequence clusters. To determine which of these regions function as cis-regulatory enhancers that regulate the dynamics of pdm gene expression, we tested each for in vivo enhancer activity during embryonic development and postembryonic neurogenesis. Our screen revealed 77 unique enhancers positioned throughout the noncoding region of the pdm locus. Many of these activated neural-specific gene expression during different developmental stages and many drove expression in overlapping patterns. Sequence comparisons of functionally related enhancers that activate overlapping expression patterns revealed that they share conserved elements that can be predictive of enhancer behavior. To facilitate data accessibility, the results of our analysis are catalogued in cisPatterns, an online database of the structure and function of these and other Drosophila enhancers.
  
  
  CONCLUSIONS
  These studies reveal a diversity of modular enhancers that most likely regulate pdm gene expression during embryonic and adult development, highlighting a high level of temporal and spatial expression specificity. In addition, we discovered clusters of functionally related enhancers throughout the pdm locus. A subset of these enhancers share conserved elements including sequences that correspond to known TF DNA binding sites. Although comparative analysis of the nubbin and pdm-2 encoding sequences indicate that these two genes most likely arose from a duplication event, we found only partial evidence of sequence duplication between their enhancers, suggesting that after the putative duplication their cis-regulatory DNA diverged at a higher rate than their coding sequences.
authors.affiliation: The Neural Cell-Fate Determinants Section, NINDS, NIH, Bethesda, MD, USA. rossje@ninds.nih.gov.
authors.forename: Jermaine
authors.initials: J
authors.lastname: Ross
authors.affiliation: The Neural Cell-Fate Determinants Section, NINDS, NIH, Bethesda, MD, USA. kuzina@ninds.nih.gov.
authors.forename: Alexander
authors.initials: A
authors.lastname: Kuzin
authors.affiliation: The Neural Cell-Fate Determinants Section, NINDS, NIH, Bethesda, MD, USA. brodyt@ninds.nih.gov.
authors.forename: Thomas
authors.initials: T
authors.lastname: Brody
authors.affiliation: The Neural Cell-Fate Determinants Section, NINDS, NIH, Bethesda, MD, USA. odenwaldw@ninds.nih.gov.
authors.forename: Ward F
authors.initials: WF
authors.lastname: Odenwald
mesh_terms: D000818:Animals; D001483:Base Sequence; D001921:Brain / Q000378:metabolism; D016000:Cluster Analysis; D017124:Conserved Sequence; D004330:Drosophila / Q000235:genetics*; D029721:Drosophila Proteins / Q000737:chemistry / Q000235:genetics*; D004742:Enhancer Elements, Genetic; D005786:Gene Expression Regulation; D018507:Gene Expression Regulation, Developmental; D023061:Gene Order; D017930:Genes, Reporter; D056426:Genetic Loci; D018398:Homeodomain Proteins / Q000737:chemistry / Q000235:genetics*; D008969:Molecular Sequence Data; D055495:Neurogenesis / Q000235:genetics*; D009928:Organ Specificity / Q000235:genetics; D050809:POU Domain Factors / Q000737:chemistry / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D019076:Transgenes
chemical_list: D029721:Drosophila Proteins; D018398:Homeodomain Proteins; D050809:POU Domain Factors; C104121:nub protein, Drosophila