Direct repeats flank three small nuclear RNA pseudogenes in the human genome

Arsdell, S W Van; Denison, R A; Bernstein, L B; Weiner, Alan M.; Manser, Tim; Gesteland, Raymond F.

doi:10.1016/0092-8674(81)90028-3

Cited by 308 publications

(181 citation statements)

References 37 publications

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“…Thus, horizontal transmission of the retrovirus itself could explain weak similarities in the tRNA-unrelated regions of SINEs that arose independently in distantly related species (9). In contrast, the close relationships between the various Salmonidae Hpa I subfamilies, distinguished solely by afew diagnostic nucleotides (Table 4), are more consistent with horizontal transmission of the SINE itself as an RNA intermediate sequestered within a retroviral capsid like tRNAs and 7SL RNA (35). The horizontal transmission model and the transposon model, however, are not mutually exclusive, and it is possible that these two models together provide the explanation of the phylogenetic distribution of the Hpa I SINEs.…”

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confidence: 74%

Species-specific amplification of tRNA-derived short interspersed repetitive elements (SINEs) by retroposition: a process of parasitization of entire genomes during the evolution of salmonids.

Takasaki

Murata²,

Saitoh³

et al. 1994

Proc. Natl. Acad. Sci. U.S.A.

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Fourteen members ofthe Hpa I subfilies of tRNA-derived SINEs in particular salmonid species were isolated from genomic libraries of chum salmon, koknee, coho salmon, masu salmon, and s e. Ali t of the sequences of these 14 members, together with those of4 members already published, 3 of which were previously d sted to have been amplied speificaly in certain lineages, revealed the presence of five sbfali with particular disc nucleotides. The amplification of members of the same subfamily in different salmonid lineages and the amplification of members of different subfamilies in the same saAmonid lineage suggest that multiple dispersed loci were responsible for amplification or, alternatively, that SINEs were transmitted horizontally between species. These two possibilities are not mutually exclusive. Our results also indicate that the Hpa I SINEs in salmonids behave like parasites. The amplifiation of these

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mentioning

confidence: 74%

Species-specific amplification of tRNA-derived short interspersed repetitive elements (SINEs) by retroposition: a process of parasitization of entire genomes during the evolution of salmonids.

Takasaki

Murata²,

Saitoh³

et al. 1994

Proc. Natl. Acad. Sci. U.S.A.

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“…The processed genes with their introns cleanly removed and with their ends variably truncated, perhaps by incomplete reverse transcription, constitute one such category of element (27)(28)(29). The Alu sequences, with an internal promoter and efficient self-priming system, appear to be especially well adapted to movement in this manner (30,31), and the F family of mobile elements in Drosophila provides yet another example of oligo (dA)-terminated mobile sequences (32). Because long transcripts of Kpn I elements have indeed been detected (8,11,33), this mode of transposition would seem plausible, although it remains to be demonstrated.…”

Section: Discussionmentioning

confidence: 99%

Rearranged sequences of a human Kpn I element.

Potter¹

1984

Proc. Natl. Acad. Sci. U.S.A.

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The complete nucleotide sequence of a human Kpn I element inserted into a-satellite DNA is presented.This sequence reveals several features of interest. First, a large block of DNA normally associated with Kpn I elements has been deleted. Second, the order of the remaining sequences is permuted in a manner that cannot be accounted for by simple inversion. Third, a significant open reading frame of 675 bases is detected. (5,8,11,12). This laboratory has isolated and characterized human DNA segments carrying unusual monomeric domains of asatellite sequence (13). Of particular interest are the nonsatellite sequences that have been found occasionally interrupting the long tandem arrays of satellites (10,13,14). Because satellite sequences undergo continual rectification by unequal crossover (15) and gene conversion, it seems possible that the interrupting sequences represent mobile elements that have inserted into satellite relatively recently in evolutionary time. In this study I focused on a part of the pa7 clone, which has been shown to carry a nonsatellite sequence inserted into a-satellite DNA (13). The invading sequence is shown here to be an unusual Kpn I element.The Kpn I elements are abundant (about 30,000 copies per haploid genome) and particularly interesting structurally. No terminal repeats have yet been found, making them unlike most transposable elements (16,17), and their variable constructions include deletions and inversions (11). In this paper the complete nucleotide sequence of an element inserted into human a-satellite DNA is presented. The sequence reveals the presence of a large sequence permutation, thereby describing yet another type of polymorphism found in the Kpn I family of primate dispersed repetitive elements. Moreover, a large open reading frame is found, suggesting a coding function. MATERIALS AND METHODSEnzymes and polynucleotide linkers were purchased from New England BioLabs, and isotopes were from New England Nuclear. DNA Sequence Determination. DNA sequence was determined by using the partial chemical cleavage method of Maxam and Gilbert (18). DNA was labeled at the 3' end with the Klenow fragment of DNA polymerase 1 and at the 5' end by polynucleotide kinase.Subcloning. The 4.0-kilobase (kb) Sal I-EcoRI DNA segment carrying a Kpn I element with flanking a-satellite DNA was purified from the previously described pa7 clone (13) and ligated into pBR322 DNA cut with Sal I and EcoRI.In order to facilitate the sequence determination, two experiments designed to introduce restriction sites at useful locations were performed. In the first experiment the subclone was opened at the Bgl II site and then treated for various periods with the exonuclease BAL-31. Progress of the digestion was followed by gel electrophoresis. Cla I linkers were blunt-end-ligated to the ends and cleaved by Cla I, and the molecules were recircularized by ligation. After transformation of Escherichia coli HB101 and selection on ampicillin plates, random colonies were used for "miniprep" (19) and restrict...

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“…One common feature of all these RNAs is a tract of uridylates (Us) at their 3Ј ends that signals pol III to terminate transcription. Apart from pol III termination, these oligo(U) tracts have no known function, although the B1-Alu tail might hybridize with an internal A tract to provide a primer for reverse transcriptase (3)(4)(5).In a number of documented cases, large portions of the 3Ј end of certain pol III transcripts are removed during the course of transcription by the pol III transcription complex (6 -8). Binding of the nuclear autoantigen La protein to the oligo(U) tract of the nascent transcript appears to stabilize it against processing.…”

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confidence: 99%

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confidence: 99%

Identification and Characterization of a Nuclease Specific for the 3′ End of the U6 Small Nuclear RNA

Booth¹,

Pugh

1997

Journal of Biological Chemistry

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The U6 small nuclear RNA is post-transcriptionally processed by the addition and removal of nontemplate uridylates (Us) at its 3 end prior to incorporation into the U4⅐U6 small nuclear ribonucleoprotein complex. An enzyme responsible for removing Us from the U6 3 end has not been previously identified. Here we biochemically isolate and characterize an exonuclease activity from HeLa cells that removes template and nontemplate 3 -nucleotides specifically from U6 RNA. We also report the isolation of an inhibitor of this U6 nuclease. U6 nuclease rapidly removes the four terminal 3 Us found in the human U6 coding sequence in a magnesium-dependent manner. Mutagenesis studies on the U6 RNA define regions essential for processing. U6 nuclease recognizes specific sequences on both strands near the base of the major intramolecular stem loop of the U6 RNA. The preprocessed 3 Us form part of the base of the stem loop, but neither specific sequences nor secondary structure at the four terminal nucleotides are required to achieve processing.RNA polymerase (pol) 1 III produces numerous small RNAs that have a variety of functions (1, 2). pol III transcripts include tRNAs, adenovirus VA 1 RNA, U6 snRNA, 5 S rRNA, and other RNAs such as B1-Alu, which might be involved in retrotransposition of short interspersed elements. One common feature of all these RNAs is a tract of uridylates (Us) at their 3Ј ends that signals pol III to terminate transcription. Apart from pol III termination, these oligo(U) tracts have no known function, although the B1-Alu tail might hybridize with an internal A tract to provide a primer for reverse transcriptase (3)(4)(5).In a number of documented cases, large portions of the 3Ј end of certain pol III transcripts are removed during the course of transcription by the pol III transcription complex (6 -8). Binding of the nuclear autoantigen La protein to the oligo(U) tract of the nascent transcript appears to stabilize it against processing. In other reports of shortened transcripts, the last few nucleotides are absent, which might be due to pol III pausing (9). In this case, the La protein promotes proper termination and transcript release (9).The U6 snRNA transcript undergoes major 3Ј end processing in vivo before it is incorporated into the U4⅐U6 snRNP splicing complex, and the 3Ј region is essential for splicing function (10). At the completion of U6 synthesis, the La protein associates with the 3Ј uridylate tract of U6 (UUUU -OH ) as long as it contains a 3Ј-OH (11). What role the La protein serves in binding to the released transcript is not known, although it may stabilize U6 against degradation. The 3Ј end of La-associated U6 becomes heterogeneous through nontemplate 3Ј addition of Us (11-13). What happens next is unclear; however, the 3Ј end is eventually processed back to five Us in which the terminal U contains a 2Ј,3Ј-cyclic phosphate (UUUU(U)ϾP) (14). The activity responsible for the generation of the 2Ј,3Ј-cyclic phosphate has not been biochemically identified. Formation of the 2Ј,3Ј-cyclic ph...

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Direct repeats flank three small nuclear RNA pseudogenes in the human genome

Cited by 308 publications

References 37 publications

Species-specific amplification of tRNA-derived short interspersed repetitive elements (SINEs) by retroposition: a process of parasitization of entire genomes during the evolution of salmonids.

Species-specific amplification of tRNA-derived short interspersed repetitive elements (SINEs) by retroposition: a process of parasitization of entire genomes during the evolution of salmonids.

Rearranged sequences of a human Kpn I element.

Identification and Characterization of a Nuclease Specific for the 3′ End of the U6 Small Nuclear RNA

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