Genomic organization of the rDNA cistron of the teleost fish Cyprinus carpio

Abstract

The seasonal adaptation of the teleost Cyprinus carpio to the cyclical changes of its habitat demands physiological compensatory responses. The process involves profound nucleolar adjustments and remarkable changes in rRNA synthesis, which affects ribosomal biosynthesis. In this context, we have demonstrated that the synthesis of several proteins involved in ribosomal biogenesis as protein kinase CK2, ribosomal protein L41 and nucleolin, as well as U3 snoRNP, are differentially regulated in summer-acclimatized carp compared to the cold-season adapted fish. To understand the mechanisms involved in the seasonal regulation of rRNA gene transcription, we have been studying the carp rDNA cistron structure. Because the cis-elements that regulate the expression of the tandem organized ribosomal genes are located in the non-transcribed intergenic spacer (IGS), we analyzed the primary structure of the carp rDNA gene IGS. The gene organization is similar to that described from other vertebrate species, including numerous repetitive sequences, the transcription start site, and some potential cis-elements such as ribosomal enhancers, proximal terminator and transcriptional terminators. Ribosomal DNA is a remarkable case of gene duplication and has been used as a model to test the concerted evolution theory. We performed sequence comparison analyses of 18S rRNA coding sequences from carp with different species, data with which an unrooted phylogram was constructed.

Maintenance of multiple lineages of R1 and R2 retrotransposable elements in the ribosomal RNA gene loci of Nasonia

“…The rDNA spacer region (IGS) of Nasonia adhered to the general pattern found in animals of being a repetitive, tandem structure ( Fig. 1B) (Collins & Cunningham, 2000;Grozdanov et al, 2003;Vera et al, 2003). In N. vitripennis, starting from the 3′ end of the 28S gene, there is a 336 bp non-repetitive sequence followed by a series of 47 bp repeats, a series of 84 bp repeats, a 265 bp nonrepetitive sequence, and finally a series of 21 bp repeats.…”

Epigenetic regulation of the ribosomal cistron seasonally modulates enrichment of H2A.Z and H2A.Zub in response to different environmental inputs in carp (Cyprinus carpio)

“…In this context, we have reported the hypermethylated state of ribosomal gene promoter in winter-acclimatized carp, as well the histone H2A replacement by variant subtypes of macroH2A, help the seasonal transcriptional activity of ribosomal genes [32,33]. In addition to trans-acting factors, we also reported on the genomic organization of the carp ribosomal cistron [34], when cis-acting elements located in the intergenic spacer (IGS), named T 0 ´ and T 0 , and core promoter (CP), can contribute to the modulation of rRNA synthesis.…”

First cytogenetic characterization of the sub-arctic marine fish Mallotus villosus (Müller, 1776), Osmeriformes, Osmeridae

“…Vera et al, 2003;Hatanaka and Galetti, 2004;Kavalco et al, 2004;Mantovani et al, 2005) and, to a lesser degree, for marine species (Jankun et al, 2001;Pardo et al, 2001;Sola et al, 2003;Vitturi et al, 2005;Galetti et al, 2006), including polar fishes (Mazzei et al, 2004). The chromosomal patterns of rRNA genes have been investigated in model and domestic fishes such as Tetraodon nigroviridis (Fischer et al, 2000), Oreochromis niloticus (Martins et al, 2000), Danio rerio Sola and Gornung, 2001), Xiphophorus maculatus (Ocalewicz, 2004), Oncorhynchus mykiss, and O. kisutch (Iturra et al, 2001).…”