Molecular characterization and chromosomal mapping of the 5S rRNA gene in <i>Solea senegalensis</i>: a new linkage to the U1, U2, and U5 small nuclear RNA genes

Manchado, Manuel; Zuasti, Eugenia; Cross, Ismael; Merlo, Alejandro Serani; Infante, Carlos; Rebordinos, Laureana

doi:10.1139/g05-068

Cited by 53 publications

(57 citation statements)

References 34 publications

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“…In several species, linkeage of snRNAs with 5S rRNA has been observed [42,40,16,63,11,46]. We found only one further example of this type: in Daphnia pulex 5S and U5 snRNA are separated by only 308bp.…”

Section: Clusters Of Snrna Genesmentioning

confidence: 59%

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

2008

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While studies of the evolutionary histories of protein families are common place, little is known on noncoding RNAs beyond microRNAs and some snoRNAs. Here we investigate in detail the evolutionary history of the 9 spliceosomal snRNA families (U1, U2, U4, U5, U6, U11, U12, U4atac, and U6atac) across the completely or partially sequenced genomes of metazoan animals. Representatives of the five major spliceosomal snRNAs were found in all genomes. None of the minor splicesomal snRNAs was detected in Nematodes and in the shotgun traces of Oikopleura dioica, while in all other animal genomes at most one of them is missing. Although snRNAs are present in multiple copies in most genomes, distinguishable paralog groups are not stable over long evolutionary times, although they appear independently in several clades. In general, animal snRNA secondary structures are highly conserved, albeit in particular U11 and U12 in insects exhibit dramatic variations. An analysis of genomic context of snRNAs reveals that they behave like mobile elements, exhibiting very little syntenic conservation.

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Section: Clusters Of Snrna Genesmentioning

confidence: 59%

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

2008

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“…The linkage between 5S rDNA and U1 snDNA has only been reported in one crustacean (Pelliccia et al, 2001) and in one fish (Manchado et al, 2006). In this survey, we report linked units of 5S rDNA and U1 snDNA in 10 razor shell species (Mollusca: Bivalvia: Pharidae) from four different genera.…”

Section: Introductionmentioning

confidence: 70%

“…U1 snDNA, transcribed by RNA polymerase II, is a multigene family with a variable number of repeats in each genome (around tens of repeats in the metazoan species studied by Marz et al, 2008). Although not much information is available about the organisation of U1 snDNA, it was found to be linked to other multigene families, such as 5S rDNA (Pelliccia et al, 2001), other spliceosomal snDNA families (Marz et al, 2008) and organised in the same array together with 5S rDNA repeats and other spliceosomal snDNA (Manchado et al, 2006). In general, however, clustered copies of distinct or the same small nuclear RNA coding genes are not common in metazoan genomes (Marz et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

The linked units of 5S rDNA and U1 snDNA of razor shells (Mollusca: Bivalvia: Pharidae)

et al. 2011

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The linkage between 5S ribosomal DNA and other multigene families has been detected in many eukaryote lineages, but whether it provides any selective advantage remains unclear. In this work, we report the occurrence of linked units of 5S ribosomal DNA (5S rDNA) and U1 small nuclear DNA (U1 snDNA) in 10 razor shell species (Mollusca: Bivalvia: Pharidae) from four different genera. We obtained several clones containing partial or complete repeats of both multigene families in which both types of genes displayed the same orientation. We provide a comprehensive collection of razor shell 5S rDNA clones, both with linked and nonlinked organisation, and the first bivalve U1 snDNA sequences. We predicted the secondary structures and characterised the upstream and downstream conserved elements, including a region at À25 nucleotides from both 5S rDNA and U1 snDNA transcription start sites. The analysis of 5S rDNA showed that some nontranscribed spacers (NTSs) are more closely related to NTSs from other species (and genera) than to NTSs from the species they were retrieved from, suggesting birth-and-death evolution and ancestral polymorphism. Nucleotide conservation within the functional regions suggests the involvement of purifying selection, unequal crossing-overs and gene conversions. Taking into account this and other studies, we discuss the possible mechanisms by which both multigene families could have become linked in the Pharidae lineage. The reason why 5S rDNA is often found linked to other multigene families seems to be the result of stochastic processes within genomes in which its high copy number is determinant.

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“…For each of the ncRNAs, we provide a number of mixture model plots on the Supplemental Page. Genomic linkage of 5S rDNA to major spliceosomal RNA genes has been reported for nematodes (Vahidi et al, 1988), crustaceans (U1, U5 (Pelliccia et al, 2001;Marz et al, 2008)), molluscs (U1, U2, (Cross and Rebordinos, 2005;Vierna et al, 2011)) and fishes (U1, U2, U5 (Manchado et al, 2006)). In this work, we detected a weak correlation to U1, U4 and U5 snRNA genes, and a slightly more evolutionary consistent linkage to U2.…”

Section: S Rrna and Protein Interactionsmentioning

confidence: 98%

“…These repeats can occur in tandem forming long arrays in some species, whereas in other cases they are dispersed throughout the genome. In some organisms, 5S rDNA repeats have been found linked to other noncoding RNA (ncRNA) gene families, such as small nuclear RNAs (snRNAs) (Vahidi et al, 1988;Nilsen et al, 1989;Zeng et al, 1990;Keller et al, 1992;Pelliccia et al, 2001;Cross and Rebordinos, 2005;Manchado et al, 2006;Marz et al, 2008;Freire et al, 2010;Vierna et al, 2011;Vizoso et al, 2011) or to protein-coding genes such as histones (Eirin-Lopez et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

Systematic analysis and evolution of 5S ribosomal DNA in metazoans

et al. 2013

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Several studies on 5S ribosomal DNA (5S rDNA) have been focused on a subset of the following features in mostly one organism: number of copies, pseudogenes, secondary structure, promoter and terminator characteristics, genomic arrangements, types of non-transcribed spacers and evolution. In this work, we systematically analyzed 5S rDNA sequence diversity in available metazoan genomes, and showed organism-specific and evolutionary-conserved features. Putatively functional sequences (12 766) from 97 organisms allowed us to identify general features of this multigene family in animals. Interestingly, we show that each mammal species has a highly conserved (housekeeping) 5S rRNA type and many variable ones. The genomic organization of 5S rDNA is still under debate. Here, we report the occurrence of several paralog 5S rRNA sequences in 58 of the examined species, and a flexible genome organization of 5S rDNA in animals. We found heterogeneous 5S rDNA clusters in several species, supporting the hypothesis of an exchange of 5S rDNA from one locus to another. A rather high degree of variation of upstream, internal and downstream putative regulatory regions appears to characterize metazoan 5S rDNA. We systematically studied the internal promoters and described three different types of termination signals, as well as variable distances between the coding region and the typical termination signal. Finally, we present a statistical method for detection of linkage among noncoding RNA (ncRNA) gene families. This method showed no evolutionary-conserved linkage among 5S rDNAs and any other ncRNA genes within Metazoa, even though we found 5S rDNA to be linked to various ncRNAs in several clades.

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Molecular characterization and chromosomal mapping of the 5S rRNA gene in Solea senegalensis: a new linkage to the U1, U2, and U5 small nuclear RNA genes

Cited by 53 publications

References 34 publications

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

The linked units of 5S rDNA and U1 snDNA of razor shells (Mollusca: Bivalvia: Pharidae)

Systematic analysis and evolution of 5S ribosomal DNA in metazoans

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