Regulatory elements retained during chordate evolution: coming across tunicates.
Understanding the role of conserved noncoding elements (CNEs) throughout the genome is taking advantage of the improved efficiency of genome-sequencing techniques and bioinformatics tools. Tunicates diverged before the vertebrate whole genome duplications and, therefore, represent an optimal model system to study the evolution of complex regulatory networks. Here, we review the current knowledge on the characterization of CNEs during embryonic development, focusing on the evolutionary similarity and divergence between tunicates and other chordates. Many vertebrate specific CNEs that regulate developmental processes were identified based on high level of sequence conservation, but only few of them have been recognized in tunicates or other invertebrates because of genomic sequences divergence. We discuss recent studies demonstrating that a combination of different methodologies, based not only on high sequence identity, can collectively be used to identify CNEs with regulatory activity in phylogenetically distant species. Here, a low sequence constraints approach was successfully used to search orthologous chordate gene regions for cross-species conserved regulatory elements that control developmental genes.
Cellular and Developmental Biology Laboratory, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.
Quirino Attilio
QA
Vassalli
Evgeniya
E
Anishchenko
Luigi
L
Caputi
Paolo
P
Sordino
Salvatore
S
D'Aniello
Annamaria
A
Locascio
D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D043344:Chordata / Q000235:genetics*; D017124:Conserved Sequence; D053263:Gene Regulatory Networks; D016678:Genome; D023281:Genomics; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D012045:Regulatory Sequences, Nucleic Acid; D014561:Urochordata / Q000235:genetics*
gene clusters; homeobox-containing genes; non-coding elements; phylogenetic footprinting; transcription factors