title: Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage.
abstract: BACKGROUND
  All vertebrates share a remarkable degree of similarity in their development as well as in the basic functions of their cells. Despite this, attempts at unearthing genome-wide regulatory elements conserved throughout the vertebrate lineage using BLAST-like approaches have thus far detected noncoding conservation in only a few hundred genes, mostly associated with regulation of transcription and development.
  
  
  RESULTS
  We used a unique combination of tools to obtain regional global-local alignments of orthologous loci. This approach takes into account shuffling of regulatory regions that are likely to occur over evolutionary distances greater than those separating mammalian genomes. This approach revealed one order of magnitude more vertebrate conserved elements than was previously reported in over 2,000 genes, including a high number of genes found in the membrane and extracellular regions. Our analysis revealed that 72% of the elements identified have undergone shuffling. We tested the ability of the elements identified to enhance transcription in zebrafish embryos and compared their activity with a set of control fragments. We found that more than 80% of the elements tested were able to enhance transcription significantly, prevalently in a tissue-restricted manner corresponding to the expression domain of the neighboring gene.
  
  
  CONCLUSIONS
  Our work elucidates the importance of shuffling in the detection of cis-regulatory elements. It also elucidates how similarities across the vertebrate lineage, which go well beyond development, can be explained not only within the realm of coding genes but also in that of the sequences that ultimately govern their expression.
authors.affiliation: Telethon Institute of Genetics and Medicine, Via P, Castellino, 80131 Napoli, Italy.
authors.forename: Remo
authors.initials: R
authors.lastname: Sanges
authors.forename: Eva
authors.initials: E
authors.lastname: Kalmar
authors.forename: Pamela
authors.initials: P
authors.lastname: Claudiani
authors.forename: Maria
authors.initials: M
authors.lastname: D'Amato
authors.forename: Ferenc
authors.initials: F
authors.lastname: Muller
authors.forename: Elia
authors.initials: E
authors.lastname: Stupka
mesh_terms: D000465:Algorithms; D000818:Animals; D004742:Enhancer Elements, Genetic; D019143:Evolution, Molecular; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid; D012854:Sister Chromatid Exchange; D014714:Vertebrates / Q000235:genetics*; D015027:Zebrafish / Q000196:embryology / Q000235:genetics