Novel structure of a human U6 snRNA pseudogene

Theissen, H.; Rinke, Jutta; Traver, Christopher N.; Lührmann, Reinhard; Appel, Bernd

doi:10.1016/0378-1119(85)90086-1

Cited by 11 publications

(11 citation statements)

References 19 publications

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“…The fission yeast Schizosaccharomyces pombe also contains a potentially functional B block homology within the intron of its U6 gene (11,32). However, in all cases studied thus far, the transcription of U6 relies wholly or in part on sequences upstream of the coding region.The human genome contains approximately 200 copies of U6-related sequences (14), only five of which have been sequenced and only three of which have been studied for transcriptional activity (20,33,37 …”

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“…The human genome contains approximately 200 copies of U6-related sequences (14), only five of which have been sequenced and only three of which have been studied for transcriptional activity (20,33,37). The consensus U6 gene originally cloned by Kunkel et al (wtU6 [20]) has been shown to utilize an exclusively 5' flanking promoter (22).…”

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“…The consensus U6 gene originally cloned by Kunkel et al (wtU6 [20]) has been shown to utilize an exclusively 5' flanking promoter (22). Another genomic U6 sequence containing an internal duplication of 16 bp has been shown to be transcriptionally inactive in vitro and does not protect any full-length RNA from HeLa cells (33). Previously, we described a variant of the human U6 gene (87U6) that differs from the consensus human U6 sequence by nine base substitutions and a single-base deletion within the coding region but has no homology in the 5' flanking region to wtU6 (37).…”

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Transcription of a variant human U6 small nuclear RNA gene is controlled by a novel, internal RNA polymerase III promoter.

Tichelaar¹,

Knerer²,

Vrabel³

et al. 1994

Mol. Cell. Biol.

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Promoter elements in the 5' flanking regions of vertebrate U6 RNA genes have been shown to be both necessary and sufficient for transcription by RNA polymerase III. We have recently isolated and characterized a variant human U6 gene (87U6) that can be transcribed by RNA polymerase III in vitro in the absence of any natural 5' or 3' flanking sequences. This gene contains 10 nucleotide differences from the previously characterized human U6 gene (wtU6) within the coding region but has no homology to wtU6 in the upstream promoter region. By constructing chimeras between these two genes, we have shown that mutation of as few as two nucleotides in the coding region of the human U6 RNA gene is sufficient to create an internal promoter that is functional in vitro. A T-to-C transition at position 57 and a single T deletion at position 52 produce an internal U6 promoter that is nearly as active in vitro as the external U6 polymerase III promoter utilized by wtU6. Neither of these residues is absolutely conserved during evolution, and both of these nucleotide changes occur within the previously noted A box homology. Deletion and linker scanning mutations within the coding region of this variant U6 gene suggest that, in addition to the central region including bp 52 and 57, sequences at the extreme 5' end of the gene are critical for efficient transcription. In contrast, flanking sequences have a minor effect on transcriptional efficiency. This arrangement is unique among internal RNA polymerase III promoters and may indicate unique regulation of this gene.The transcription of the small nuclear RNA U6 has been well characterized in both vertebrate (2,8,17,21,22,28) and yeast (6, 7, 9) species. In the three vertebrate species in which a U6 gene has been cloned (humans, mice, and Xenopus tropicalis), transcription has been shown to be entirely dependent on 5' flanking sequences, including a classical TATA box and the U small nuclear RNA specific proximal sequence element (for review, see references 19 and 38). Both of these elements are normally found in RNA polymerase II promoters but have been shown to function in the RNA polymerase III promoter of U6. Indeed, the TATA box has been shown to be the element responsible for conferring RNA polymerase III specificity to the U6 promoter (23,24). In yeast species, the promoter structure is more complex, consisting of both external and internal elements. The U6 gene in Saccharomyces cerevisiae requires a 5' flanking TATA box, but transcription in vivo requires the presence of an internal A block and a B block located 120 nucleotides downstream (4, 6, 7, 9). The fission yeast Schizosaccharomyces pombe also contains a potentially functional B block homology within the intron of its U6 gene (11,32). However, in all cases studied thus far, the transcription of U6 relies wholly or in part on sequences upstream of the coding region.The human genome contains approximately 200 copies of U6-related sequences (14), only five of which have been sequenced and only three of which have been stud...

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Transcription of a variant human U6 small nuclear RNA gene is controlled by a novel, internal RNA polymerase III promoter.

Tichelaar¹,

Knerer²,

Vrabel³

et al. 1994

Mol. Cell. Biol.

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“…2b. ) This clone therefore appears to be an authentic gene for human U6 RNA, as opposed to a U6 pseudogene (21,39).…”

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U6 small nuclear RNA is transcribed by RNA polymerase III.

Kunkel¹,

Maser²,

Calvet³

et al. 1986

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

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124

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A DNA fragment homologous to U6 small nuclear RNA was isolated from a human genomic library and sequenced. The immediate 5'-flanking region of the U6 DNA clone had significant homology with a potential mouse U6 gene, including a "TATA box" at a position 26-29 nucleotides upstream from the transcription start site. Although this sequence element is characteristic of RNA polymerase II promoters, the U6 gene also contained a polymerase III "box A" intragenic control region and a typical run of five thymines at the 3' terminus (noncoding strand). The human U6 DNA clone was accurately transcribed in a HeLa cell S100 extract lacking polymerase II activity. U6 RNA transcription in the S100 extract was resistant to a-amanitin at 1 ,gg/ml but was completely inhibited at 200 ,.g/ml. A comparison of fingerprints of the in vitro transcript and of U6 RNA synthesized in vivo revealed sequence congruence. U6 RNA synthesis in isolated HeLa cell nuclei also displayed low sensitivity to a-amanitin, in contrast to Ul and U2 RNA transcription, which was inhibited >90% at 1 ,ug/ml. In addition, U6 RNA synthesized in isolated nuclei was efficiently immunoprecipitated by an antibody against the La antigen, a protein known to bind most other RNA polymerase m transcripts. These results establish that, in contrast to the polymerase 11-directed transcription of mammalian genes for U1-U5 small nuclear RNAs, human U6 RNA is transcribed by RNA polymerase m.The U series of small nuclear RNAs (snRNAs) consists at present of eight species, U1-U8 (1-3), of which at least three, U1, U2, and U7, are cofactors for messenger RNA processing reactions (2, 4-7). Several lines of evidence indicate that Ul-U5 snRNAs are transcribed by RNA polymerase II (8-16). However, U6 snRNA has features that distinguish it from other U snRNAs. It does not contain a 2,2,7-trimethylguanosine cap structure at its 5' end (17, 18), and it lacks "domain A," a single-stranded region containing the sequence RA(U)nGR (R = purine nucleoside; n > 3) flanked by hairpin structures, which is present in U1, U2, U4, and U5 snRNAs (19).These facts prompted us to investigate the possibility that the transcription of U6 snRNA differs from that of the other snRNAs. In this paper we report the isolation and sequencing of a human U6 snRNA gene and describe experiments demonstrating that U6 snRNA is transcribed by RNA polymerase III. (Brief accounts ofthis work were presented at the

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Differential alterations in metabolic pattern of the spliceosomal uridylic acid‐rich small nuclear RNAs (UsnRNAs) during malignant transformation of 20‐methylcholanthrene‐induced mouse CNCI‐PM‐20 embryonic fibroblasts

Mukherjee

Manna

Mukherjee

et al. 2009

Molecular Carcinogenesis

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Differential alterations of the spliceosomal Uridylic acid rich small nuclear RNAs (UsnRNAs) (U1, U2, U4, U5, and U6) are reported to be associated with cellular proliferation and development, but definitive information is scarce and also elusive. An attempt is made in this study to analyze the metabolic patterns of major spliceosomal UsnRNAs, during tumor development, in an in vitro carcinogenesis model of 20-methylcholanthrene (MCA)-transformed Swiss Mouse Embryonic Fibroblast (MEF), designated as CNCI-PM-20. MEF cells, after treatment with 20-MCA, progressed through a sequence of passages with distinct and heritable changes, finally becoming neoplastic at passage-42 (P42). A differential expression pattern of major UsnRNAs was observed during this process. The abundance of U1 was 20% below control (P1) at passage-20 (P20), followed by a gradual increase up until P42 (approximately 12% above the P1 value). The abundance of U2 was more or less constant during the cellular transformation. U4 showed a trend of increase, with above 30% abundance than control at P20, followed by a significant increase at P36 and P42 (1.5- and 2-fold, respectively, P-value <0.01). U5 also followed an identical pattern, with an increase of 70% compared to control (P-value <0.05) at P42. Interestingly, U6 gradually decreased from P20 onwards up until P42, with 22% at P20 and 67% at P42 (P-value <0.01). An overall significant quantitative alteration in abundance of U4, U5, and U6, observed in our study, contributes to the understanding of the fact that, the metabolism of major spliceosomal UsnRNAs is differentially regulated during the process of neoplastic transformation.

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Novel structure of a human U6 snRNA pseudogene

Cited by 11 publications

References 19 publications

Transcription of a variant human U6 small nuclear RNA gene is controlled by a novel, internal RNA polymerase III promoter.

Transcription of a variant human U6 small nuclear RNA gene is controlled by a novel, internal RNA polymerase III promoter.

U6 small nuclear RNA is transcribed by RNA polymerase III.

Differential alterations in metabolic pattern of the spliceosomal uridylic acid‐rich small nuclear RNAs (UsnRNAs) during malignant transformation of 20‐methylcholanthrene‐induced mouse CNCI‐PM‐20 embryonic fibroblasts

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