title: Position and sequence conservation in Amniota of polymorphic enhancer HS1.2 within the palindrome of IgH 3'Regulatory Region.
abstract: BACKGROUND
  The Immunoglobulin heavy chain (IgH) 3' Regulatory Region (3'RR), located at the 3' of the constant alpha gene, plays a crucial role in immunoglobulin production. In humans, there are 2 copies of the 3'RR, each composed of 4 main elements: 3 enhancers and a 20 bp tandem repeat. The single mouse 3'RR differs from the two human ones for the presence of 4 more regulative elements with the double copy of one enhancer at the border of a palindromic region.
  
  
  RESULTS
  We compared the 3'RR organization in genomes of vertebrates to depict the evolutionary history of the region and highlight its shared features. We found that in the 8 species in which the whole region was included in a fully assembled contig (mouse, rat, dog, rabbit, panda, orangutan, chimpanzee, and human), the shared elements showed synteny and a highly conserved sequence, thus suggesting a strong evolutionary constraint. In these species, the wide 3'RR (~30 kb in human) bears a large palindromic sequence, consisting in two ~3 kb complementary branches spaced by a ~3 kb sequence always including the HS1.2 enhancer. In mouse and rat, HS3 is involved by the palindrome so that one copy of the enhancer is present on each side. A second relevant feature of our present work concerns human polymorphism of the HS1.2 enhancer, associated to immune diseases in our species. We detected a similar polymorphism in all the studied Catarrhini (a primate parvorder). The polymorphism consists of multiple copies of a 40 bp element up to 12 in chimpanzees, 8 in baboons, 6 in macaque, 5 in gibbons, 4 in humans and orangutan, separated by stretches of Cytosine. We show specific binding of this element to nuclear factors.
  
  
  CONCLUSIONS
  The nucleotide sequence of the palindrome is not conserved among evolutionary distant species, suggesting pressures for the maintenance of two self-matching regions driving a three-dimensional structure despite of the inter-specific divergence at sequence level. The information about the conservation of the palindromic structure and the settling in primates of the polymorphic feature of HS1.2 show the relevance of these structures in the control and modulation of the Ig production through the formation of possible three-dimensional structures.
authors.affiliation: Department of Genetics and Microbiology, University of Bari, Italy.
authors.forename: Pietro
authors.initials: P
authors.lastname: D'Addabbo
authors.forename: Moira
authors.initials: M
authors.lastname: Scascitelli
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Giambra
authors.forename: Mariano
authors.initials: M
authors.lastname: Rocchi
authors.forename: Domenico
authors.initials: D
authors.lastname: Frezza
mesh_terms: D000818:Animals; D001665:Binding Sites; D017124:Conserved Sequence; D004742:Enhancer Elements, Genetic; D006801:Humans; D007143:Immunoglobulin Heavy Chains / Q000235:genetics*; D055029:Inverted Repeat Sequences; D008322:Mammals / Q000235:genetics*; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D026801:Synteny
chemical_list: D007143:Immunoglobulin Heavy Chains