A U3 RNA pseudogene in mouse: sequence and organization in genomic DNA

Ferrer, P.; Qu, Liang; Bouche, Gérard; Bachellerie, Jean‐Pierre

doi:10.1016/0014-5793(86)80834-1

Cited by 3 publications

(3 citation statements)

References 24 publications

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“…4 [presence of a 88-bp stretch, containing a (GT),, motif, about 80 bp upstream from the U3-coding sequence], in mouse y3B.9 (over the approximately 100-bp 5'-and 3'-flanking sequences) and also in mouse y3B.15 (starting about 160 bp downstream from the U3-coding sequence). This observation also applies to the two previously reported specimens of rodent U3 retrogenes which are flanked by a direct repetition; a large number of purine stretches are present over the 200 bp which flank the U3-coding sequence of mouse y3B.PI [19], together with several short tandem repeats, also found around the rat 3.1 pseudogene [22]. Outside the U3-coding region, no extended similarity among the mouse retrogenes was detected by 'homology' matrixes.…”

Section: Resultsmentioning

confidence: 61%

“…The mouse genome contains 20-25 copies of sequences homologous to U3 RNA [19], among which only a minor fraction corresponds to functional genes [18]. The four nonfunctional U3-coding regions studied so far in mouse, this work and [19], all correspond to retrogenes.…”

Section: Discussionmentioning

confidence: 99%

“…The four nonfunctional U3-coding regions studied so far in mouse, this work and [19], all correspond to retrogenes.…”

Section: Discussionmentioning

confidence: 99%

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Mouse U3‐RNA‐processed pseudogenes are nonrandomly integrated into genomic DNA

Mazan

Michot

Bachellerie

1989

European Journal of Biochemistry

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We have characterized three mouse U3-RNA-processed pseudogenes. Together with previous analyses of mouse functional genes and of rat genes and pseudogenes, these data provide some insights into the processes of U3 retrogene formation during the evolution of rodents. All the mouse retrogenes correspond to a full-length U3B-coding sequence with a 3'-poly(A) tail and are precisely flanked by a pair of direct repeats, in agreement with formation through an RNA intermediate followed by insertion at staggered nicks in the genome. All the rodents U3 retrogenes identified so far are produced from a U3B-RNA form, with two of them (one for each rodent) formed from a 3'-elongated U3-RNA precursor, pointing to the particular susceptibility of RNA precursors forms to serve as templates for retrogene formation. Rodent full-length U3 retrogenes are not inserted randomly in the genome but are systematically found in a context of simple sequences, prone to slipped-strand mispairings and likely to favour the appearance of single-stranded DNA. Moreover their flanking repeats share not only the same size (15 bp) but also common sequence features (which extend to vicinal upstream nucleotides) suggesting that common mechanisms, specific to this class of retrogenes, have been involved in their formation. For the first time, a model accounting for the generation of full-length cDNA copies from nonpolyadenylated RNA templates is proposed. Rodent U3 retrogenes appear to be of rather recent origin (posterior to the mouse/ rat divergence) and some of them could have undergone subsequent genetic exchanges with the functional genes.The reverse flow of genetic information from RNA into DNA has played a substantial part in the evolution of eukaryotic genomes, particularly in mammals [l, 21. The generation of the transposed information through reverse transcription appears to apply either to proretroviral-like or to nonviral elements [I -41. Members of the first class of retroposons have been identified in a variety of eukaryotes [5 -81. As for the nonviral family, it comprises three major groups: the processed genes, corresponding to cDNA copies of mRNAs, the 'Alu-like' families of dispersed repeats and a subset of the small-nuclear RNA pseudogenes [3, 41. These nonviral retrogenes share characteristic structural features, i.e. sequence boundaries precisely congruent with an RNA species (with possible truncations, mostly at the 3' side), presence of a repetitive poly(A)-rich 3' tail and of a pair of direct repeats (usually of 8 -19 bp) which flank the homologous poly(A)-tailed RNA sequence. The biological processes involved in creation of these remain speculative. However, the potential role of retroviral intermediates has been recently suggested: mutant retroviruses defective in their ability to encapsulate viral genomic RNA can indeed package and reverse transcribe cellular RNAs devoid to retroviral cis-acting sequences and can integrate the newly formed cDNAs into the cellular genome [9 -121. The molecular mechanisms inCorrespondence to J. ...

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Section: Resultsmentioning

confidence: 61%

Section: Discussionmentioning

confidence: 99%

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Mouse U3‐RNA‐processed pseudogenes are nonrandomly integrated into genomic DNA

Mazan

Michot

Bachellerie

1989

European Journal of Biochemistry

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Structure and organization of mouse U3B RNA functional genes.

Mazan

Bachellerie

1988

Journal of Biological Chemistry

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Structure of the differentially expressed mouse U3A gene

Mazan

Gulli

Joseph

et al. 1992

European Journal of Biochemistry

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Two markedly different forms of U3 RNA are present in mouse, the relative abundance of which largely depends upon the tissues. In all cases studied so far, the more abundant form is U3B, encoded by four previously characterized genes. We report here the isolation and analysis of the unique gene encoding the U3A variant, which completes the characterization of the mouse U3 multigene family. Comparisons with rat U3 genes indicate that the diversification of the A and B forms has predated the mouse/rat separation. The two forms of U3 RNA are submitted to similar, but not identical, primary and secondary structure constraints. As for the sequences flanking the RNA coding region, similar observations emerge for both types of genes: for each type, the 5' flanks are strongly conserved between mouse and rat, over at least the proximal 500 bp, whereas only about 30 bp of proximal 3' flanks are preserved, which include a signal for the formation of vertebrate U small nRNA 3' end.By constrast the 5' flanks of the two types of genes diverge extensively from each other, either in mouse or in rat, and could be involved in the differential expression of the two forms. Even over the few conserved motifs thought to be involved in the basic transcriptional control of vertebrate U small nRNA genes, the A and B forms of U3 genes exhibit specific differences maintained in the two rodent species.In several species, variant forms of several spliceosomal U small nRNAs (snRNAs) have been detected but their biological significance remains unclear. Some of them are expressed in a developmental stage-or tissue-specific manner [l -71, suggesting that they could be involved in the regulation of alternative splicing mechanisms [8]. However, in no cases have the structural bases for the differential expression of U snRNA variants been elucidated.U3 RNA is an abundant nucleolar U snRNA which appears to participate in ribosomal RNA processing in eucaryotes [9, lo], but the molecular mechanisms underlying this function remain unknown so far. Like the spliceosomal U snRNAs, U3 RNA is present under different molecular forms in several eukaryotic species. In Succhuromyces cerevisiae, two genes encoding two variant forms of U3 RNA, termed snR17A and snR17B, have been characterized [ll], which both contain an intron at an identical position [12]. While the deletion of both copies is lethal to the cell, the disruption of either of the two genes shows no phenotypic effect. One of them appears dosage-compensated in the absence of the other, suggesting some common feature of regulation. Outside the RNA coding region, which exhibits a 8% sequence divergence, the two yeast gene copies diverge extensively except for the gene-upstream proximal 50 bp. The presCorrespondence ro J.-P. Bachellerie, Centre de Recherche de Biochimie et de Gknetique Cellulaires du CNRS, Universitk PaulSabatier. 118 route de Narbonne, F-31062, Toulouse Cedex France Abbreviatiuns. DSE, distal sequence element; PSE, proximal sequence elemenl; snRNA, small nuclear RNA.Nore. The novel nu...

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A U3 RNA pseudogene in mouse: sequence and organization in genomic DNA

Cited by 3 publications

References 24 publications

Mouse U3‐RNA‐processed pseudogenes are nonrandomly integrated into genomic DNA

Mouse U3‐RNA‐processed pseudogenes are nonrandomly integrated into genomic DNA

Structure and organization of mouse U3B RNA functional genes.

Structure of the differentially expressed mouse U3A gene

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