Regulatory elements retained during chordate evolution: Coming across tunicates

Abstract

Summary: Understanding the role of conserved noncoding elements (CNEs) throughout the genome is taking advantage of the improved efficiency of genomesequencing 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 crossspecies conserved regulatory elements that control developmental genes. genesis 53:66-81, 2015. V C 2014Wiley Periodicals, Inc.

Segmental arithmetic: summing up the Hox gene regulatory network for hindbrain development in chordates

“…Transgenesis is technically challenging in amphioxus, being more readily achieved in ascidian tunicates such as Ciona . Only a modest number of regulatory elements are identifiable by sequence conservation between tunicates and vertebrates (reviewed in), but comprehensive regulatory surveys of Ciona Hox loci have uncovered a number of enhancer sequences . For example, two enhancers proximal to ci‐Hox1 have been implicated in its neural and ectodermal expression, which contain RAREs that may be homologues of those in amphioxus and vertebrate Hox clusters.…”

Novel Insights on Nitric Oxide Synthase and NO Signaling in Ascidian Metamorphosis

“…The DNA fragments were amplified by PCR from C. robusta genomic DNA and were cloned as reported by Caccavale et al [ 32 ]. The LacZ expression construct was made by using the pBluScript II KS containing the human beta-globin basal promoter upstream to the LacZ reporter gene and the SV40 polyA sequence [ 107 ]. Similarly, the GFP expression construct was prepared by using the pSP72 vector (Promega, Madison, Wisconsin, USA) containing the GFP gene and SV40 polyA, as described by Zeller et al [ 108 ], to which we added the human beta-globin basal promoter.…”

Non‐coding regulatory elements: Potential roles in disease and the case of epilepsy

“…Comparative genomics tools may be used to identify in silico conserved non‐coding sequences, which may correspond to functional regions according to the evolutionary conservation principle [74]. The hypothesis is that vertebrates use the same regulatory sequences across phylogeny to control gene expression and, assuming that mutations in such sequences are deleterious or disadvantageous to the organism, these regions are likely to have remained stable and unmutated throughout evolution [75, 76]. However, non‐coding sequences are known to have a higher evolutionary turnover than protein‐coding sequences, such that conservation per se is not a strong indicator of functional relevance but may be useful if combined with other types of data.…”

“…Comparative genomics tools may be used to identify in silico conserved non-coding sequences, which may correspond to functional regions according to the evolutionary conservation principle [74]. The hypothesis is that vertebrates use the same regulatory sequences across phylogeny to control gene expression and, assuming that mutations in such sequences are deleterious or disadvantageous to the organism, these regions are likely to have remained stable and unmutated throughout evolution [75,76]…”