scholarly journals Human U1 small nuclear RNA genes: extensive conservation of flanking sequences suggests cycles of gene amplification and transposition.

1985 ◽  
Vol 5 (9) ◽  
pp. 2159-2171 ◽  
Author(s):  
L B Bernstein ◽  
T Manser ◽  
A M Weiner
Keyword(s):  
Gene Amplification ◽  
Multigene Family ◽  
Large Fraction ◽  
Class I ◽  
Chromosome 1 ◽  
Small Nuclear Rna ◽  
Coding Region ◽  
Perfect Sequence ◽  
Flanking Sequences ◽  
Rna Genes

The DNA immediately flanking the 164-base-pair U1 RNA coding region is highly conserved among the approximately 30 human U1 genes. The U1 multigene family also contains many U1 pseudogenes (designated class I) with striking although imperfect flanking homology to the true U1 genes. Using cosmid vectors, we now have cloned, characterized, and partially sequenced three 35-kilobase (kb) regions of the human genome spanning U1 homologies. Two clones contain one true U1 gene each, and the third bears two class I pseudogenes 9 kb apart in the opposite orientation. We show by genomic blotting and by direct DNA sequence determination that the conserved sequences surrounding U1 genes are much more extensive than previously estimated: nearly perfect sequence homology between many true U1 genes extends for at least 24 kb upstream and at least 20 kb downstream from the U1 coding region. In addition, the sequences of the two new pseudogenes provide evidence that class I U1 pseudogenes are more closely related to each other than to true genes. Finally, it is demonstrated elsewhere (Lindgren et al., Mol. Cell. Biol. 5:2190-2196, 1985) that both true U1 genes and class I U1 pseudogenes map to chromosome 1, but in separate clusters located far apart on opposite sides of the centromere. Taken together, these results suggest a model for the evolution of the U1 multigene family. We speculate that the contemporary family of true U1 genes was derived from a more ancient family of U1 genes (now class I U1 pseudogenes) by gene amplification and transposition. Gene amplification provides the simplest explanation for the clustering of both U1 genes and class I pseudogenes and for the conservation of at least 44 kb of DNA flanking the U1 coding region in a large fraction of the 30 true U1 genes.

Human U1 small nuclear RNA genes: extensive conservation of flanking sequences suggests cycles of gene amplification and transposition

1985 ◽  
Vol 5 (9) ◽  
pp. 2159-2171 ◽  
Author(s):  
L B Bernstein ◽  
T Manser ◽  
A M Weiner
Keyword(s):  
Gene Amplification ◽  
Multigene Family ◽  
Large Fraction ◽  
Class I ◽  
Chromosome 1 ◽  
Small Nuclear Rna ◽  
Coding Region ◽  
Perfect Sequence ◽  
Flanking Sequences ◽  
Rna Genes

The DNA immediately flanking the 164-base-pair U1 RNA coding region is highly conserved among the approximately 30 human U1 genes. The U1 multigene family also contains many U1 pseudogenes (designated class I) with striking although imperfect flanking homology to the true U1 genes. Using cosmid vectors, we now have cloned, characterized, and partially sequenced three 35-kilobase (kb) regions of the human genome spanning U1 homologies. Two clones contain one true U1 gene each, and the third bears two class I pseudogenes 9 kb apart in the opposite orientation. We show by genomic blotting and by direct DNA sequence determination that the conserved sequences surrounding U1 genes are much more extensive than previously estimated: nearly perfect sequence homology between many true U1 genes extends for at least 24 kb upstream and at least 20 kb downstream from the U1 coding region. In addition, the sequences of the two new pseudogenes provide evidence that class I U1 pseudogenes are more closely related to each other than to true genes. Finally, it is demonstrated elsewhere (Lindgren et al., Mol. Cell. Biol. 5:2190-2196, 1985) that both true U1 genes and class I U1 pseudogenes map to chromosome 1, but in separate clusters located far apart on opposite sides of the centromere. Taken together, these results suggest a model for the evolution of the U1 multigene family. We speculate that the contemporary family of true U1 genes was derived from a more ancient family of U1 genes (now class I U1 pseudogenes) by gene amplification and transposition. Gene amplification provides the simplest explanation for the clustering of both U1 genes and class I pseudogenes and for the conservation of at least 44 kb of DNA flanking the U1 coding region in a large fraction of the 30 true U1 genes.

scholarly journals Human U1 small nuclear RNA pseudogenes do not map to the site of the U1 genes in 1p36 but are clustered in 1q12-q22.

1985 ◽  
Vol 5 (9) ◽  
pp. 2172-2180 ◽  
Author(s):  
V Lindgren ◽  
L B Bernstein ◽  
A M Weiner ◽  
U Francke
Keyword(s):  
In Situ Hybridization ◽  
Class I ◽  
Chromosome 1 ◽  
Small Nuclear Rna ◽  
Coding Region ◽  
Cell Biol ◽  
Gene Copies ◽  
Nuclear Rna ◽  
Human Chromosome 1

Human U1 small nuclear RNA is encoded by approximately 30 gene copies. All of the U1 genes share several kilobases of essentially perfect flanking homology both upstream and downstream from the U1 coding region, but remarkably, for many U1 genes excellent flanking homology extends at least 24 kilobases upstream and 20 kilobases downstream. Class I U1 RNA pseudogenes are abundant in the human genome. These pseudogenes contain a complete but imperfect U1 coding region and possess extensive flanking homology to the true U1 genes. We mapped four class I pseudogenes by in situ hybridization to the long arm of chromosome 1, bands q12-q22, a region distinct from the site on the distal short arm of chromosome 1 to which the U1 genes have been previously mapped (Lund et al., Mol. Cell. Biol. 3:2211-2220, 1983; Naylor et al., Somat. Cell Mol. Genet. 10:307-313, 1984). We confirmed our in situ hybridization results by genomic blotting experiments with somatic cell hybrid lines with translocation products of human chromosome 1. These experiments provide further evidence that class I U1 pseudogenes and the true U1 genes are not interspersed. The results, along with those published elsewhere (Bernstein et al., Mol. Cell. Biol. 5:2159-2171, 1985), suggest that gene amplification may be responsible for the sequence homogeneity of the human U1 gene family.

Human U1 small nuclear RNA pseudogenes do not map to the site of the U1 genes in 1p36 but are clustered in 1q12-q22

1985 ◽  
Vol 5 (9) ◽  
pp. 2172-2180 ◽  
Author(s):  
V Lindgren ◽  
L B Bernstein ◽  
A M Weiner ◽  
U Francke
Keyword(s):  
In Situ Hybridization ◽  
Class I ◽  
Chromosome 1 ◽  
Small Nuclear Rna ◽  
Coding Region ◽  
Cell Biol ◽  
Gene Copies ◽  
Nuclear Rna ◽  
Human Chromosome 1

Human U1 small nuclear RNA is encoded by approximately 30 gene copies. All of the U1 genes share several kilobases of essentially perfect flanking homology both upstream and downstream from the U1 coding region, but remarkably, for many U1 genes excellent flanking homology extends at least 24 kilobases upstream and 20 kilobases downstream. Class I U1 RNA pseudogenes are abundant in the human genome. These pseudogenes contain a complete but imperfect U1 coding region and possess extensive flanking homology to the true U1 genes. We mapped four class I pseudogenes by in situ hybridization to the long arm of chromosome 1, bands q12-q22, a region distinct from the site on the distal short arm of chromosome 1 to which the U1 genes have been previously mapped (Lund et al., Mol. Cell. Biol. 3:2211-2220, 1983; Naylor et al., Somat. Cell Mol. Genet. 10:307-313, 1984). We confirmed our in situ hybridization results by genomic blotting experiments with somatic cell hybrid lines with translocation products of human chromosome 1. These experiments provide further evidence that class I U1 pseudogenes and the true U1 genes are not interspersed. The results, along with those published elsewhere (Bernstein et al., Mol. Cell. Biol. 5:2159-2171, 1985), suggest that gene amplification may be responsible for the sequence homogeneity of the human U1 gene family.

Localization of human U1 small nuclear RNA genes to band p36.3 of chromosome 1 by in situ hybridization

1984 ◽  
Vol 10 (3) ◽  
pp. 307-313 ◽  
Author(s):  
S. L. Naylor ◽  
B. U. Zabel ◽  
T. Manser ◽  
R. Gesteland ◽  
A. Y. Sakaguchi
Keyword(s):  
In Situ Hybridization ◽  
Chromosome 1 ◽  
Small Nuclear Rna ◽  
Nuclear Rna ◽  
Rna Genes

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

1994 ◽  
Vol 14 (8) ◽  
pp. 5450-5457 ◽  
Author(s):  
J W Tichelaar ◽  
B Knerer ◽  
A Vrabel ◽  
E D Wieben
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Iii ◽  
Minor Effect ◽  
Small Nuclear Rna ◽  
Coding Region ◽  
Polymerase Iii ◽  
Flanking Sequences ◽  
U6 Gene ◽  
U6 Rna

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.

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

1994 ◽  
Vol 14 (8) ◽  
pp. 5450-5457
Author(s):  
J W Tichelaar ◽  
B Knerer ◽  
A Vrabel ◽  
E D Wieben
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Iii ◽  
Minor Effect ◽  
Small Nuclear Rna ◽  
Coding Region ◽  
Polymerase Iii ◽  
Flanking Sequences ◽  
U6 Gene ◽  
U6 Rna

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.

U1 small nuclear RNA genes are located on human chromosome 1 and are expressed in mouse-human hybrid cells

1983 ◽  
Vol 3 (12) ◽  
pp. 2211-2220
Author(s):  
E Lund ◽  
C Bostock ◽  
M Robertson ◽  
S Christie ◽  
J L Mitchen ◽  
...  
Keyword(s):  
Human Chromosome ◽  
Chromosome 1 ◽  
Hybrid Cells ◽  
Small Nuclear Rna ◽  
Human Genes ◽  
Nuclear Rna ◽  
Flanking Region ◽  
Human Chromosome 1 ◽  
Rna Genes ◽  
Human Specific

The majority, and perhaps all, of the genes for human U1 small nuclear RNA (U1 RNA) were shown to be located on the short arm of human chromosome 1. These genes were mapped by Southern blot analysis of DNA from rodent-human somatic cell hybrids, using the 5' region of a human U1 RNA gene as a human-specific probe. This probe hybridized to DNA fragments present only in digests of total human DNA or to the DNAs of cell lines which contained human chromosome 1. The major families of human U1 RNA genes were identified, but some human genes may have gone undetected. Also, the presence of a few U1 RNA genes on human chromosome 19 could not be ruled out. In spite of the lack of extensive 5'-flanking-region homology between the human and mouse U1 RNA genes, the genes of both species were efficiently transcribed in the hybrid cells, and the U1 RNAs of both species were incorporated into specific ribonucleoprotein particles.

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