Either Gene Amplification or Gene Conversion May Maintain the Homogeneity of the Multigene Family Encoding Human U1 Small Nuclear RNA

Weiner, Alan M.; Denison, R A

doi:10.1101/sqb.1983.047.01.129

Cited by 47 publications

(17 citation statements)

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“…arrays, sequences of repetitive DNA tend to be homogenized by DNA conversion, unequal sister chromatid exchange, or DNA amplification (12,13,31,32). The rate of homogenization of RPS sequences in a chromosome might be very much higher than the rate of recombination at alt regions, which might produce internal diversity of RPS units.…”

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Diversity of tandemly repetitive sequences due to short periodic repetitions in the chromosomes of Candida albicans

et al. 1994

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Diversity of tandemly repetitive sequences due to short periodic repetitions in the chromosomes of Candida albicans

et al. 1994

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“…In particular, it is difficult to imagine that the entire 6 kb of each U2 tandem repeat unit could be under such stringent selection as to prevent the average sequence divergence from exceeding 0.4%. Thus, the existence of homogeneous multigene families implies that cells possess a mechanism for actively homogenizing genes; in this way, natural selection can work not so much on the individual genes as on the homogenized family as a unit (40). The extensive conservation of both 5' and 3' flanking sequences surrounding human Ul genes (19), as well as the large number of Ul pseudogenes having flanking homology with the bona fide genes (9), originally led us to speculate that the homogeneity of the Ul multigene family could be maintained by successive rounds of gene conversion or gene amplification or both.…”

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Human genes for U2 small nuclear RNA are tandemly repeated.

Arsdell¹,

Weiner²

1984

Mol. Cell. Biol.

122

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We found that the genes for human U2 small nuclear RNA (snRNA) are organized as a nearly perfect tandem array of 10 to 20 copies per haploid genome. Although the coding region for the mature form of U2 RNA was only 188 base pairs (bp) long, the basic repeating unit of the tandem array was 6 kilobase pairs in length. Comparison of DNA sequences immediately upstream from human Ul and U2 genes revealed two regions of strong homology: region I (15 bp long) lay upstream of region II (20 bp long) and was separated from it by about the same distance in Ul genes (25 bp) as in U2 genes (21 bp); however, region I and region II were located 174 bp further upstream from the 5' end of the snRNA coding sequence in Ul genes than in U2 genes. Homologs of region II were also found upstream of the snRNA coding region in a mouse U2 gene and two rat Ul genes. Murphy et al. (Cell 29:265-274, 1982) U2 RNA is an abundant small nuclear RNA (snRNA) found in both plant and animal cells (5). The primary sequence of this snRNA species has been highly conserved through evolution as judged by nucleotide sequence analysis of U2 RNA from rat (30), chicken, pheasant (4), and wheat embryo (J. M. Skuzeski, personal communication), fingerprint analysis of U2 RNA from mouse and man (17,26), and DNA sequence analysis of a gene for mouse (27) and frog U2 snRNA (20). U2, like Ul, has a 5' terminal 2,2,7-trimethylguanosine cap structure, and both Ul and U2 appear to be transcribed by RNA polymerase 11 (5, 25). U2 RNA, as well as the snRNAs Ul, U4, U5, and U6 exist as components of small nuclear ribonucleoprotein particles (13,14,17). Indirect evidence suggests that Ul small nuclear ribonucleoproteins play a role in the nuclear splicing of mRNA precursors (16,23), and a similar role for U2 small nuclear ribonucleoproteins has been proposed (28; but see reference 4).The initial characterization of the multigene families for human Ul, U2, U3, U4, and U6 snRNAs has established that most of the human chromosomal loci complementary to these snRNAs are actually defective gene copies, or pseudogenes, which appear to be dispersed in the genome (2,8,9,11,12,19,22,36,41 Fig. 2A and C) was labeled in vitro with [c-32P]dATP by primed synthesis of the complementary strand.Blotting procedures. Genomic blots were prepared by the method of Southern (34) except that the DNA was depurinated by soaking the gel in 0.25 N HCl before denaturation (37).on May 10, 2018 by guest

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“…To date, only a few tRNA pseudogenes have been reported, in contrast to many complete tRNA genes. Are the pseudogenes evolutionary intermediates bound for homogenization (45) or deletion? Have they become functional in their own right?…”

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Transcription factor binding is limited by the 5'-flanking regions of a Drosophila tRNAHis gene and a tRNAHis pseudogene.

Cooley¹,

Schaack²,

Burke³

et al. 1984

Mol. Cell. Biol.

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We determined the sequence of a Drosophila tRNA gene cluster containing a tRNAHis gene and a tRNAHis pseudogene in close proximity on the same DNA strand. The pseudogene contains eight consecutive base pairs different from the region of the bona fide gene which codes for the 3' portion of the anticodon stem of tRNAHis. The tRNAHis gene is transcribed efficiently in Drosophila Kc cell extract, whereas the pseudogene is not. The pseudogene is also a much poorer competitor than the real gene in a stable transcription complex formation assay, even though the sequence alteration in the pseudogene does not affect the sequence or spacing of the putative internal transcription control regions. Recombinant clones were constructed in which the 5'-flanking regions are exchanged. The transcription efficiencies and competitive abilities of the recombinant clones resemble those of the genes from which the 5' flank was derived; for example, the tRNAHis pseudogene with the 5'-flanking sequence of the tRNAHis gene is now efficiently transcribed. Deletion analysis of the pseudogene 5' flank failed to uncover an inhibitory element. Deletion analysis of the real gene showed very high dependence on the presence of the wild-type 5'-flanking sequence for factor binding to the internal control regions and stable complex formation. The 5'-flanking sequence of a Drosophila tRNAArg gene active in the Drosophila Kc cell extract does not restore transcriptional activity or stable complex formation. The tRNAHis gene and pseudogene behave atypically in HeLa cell extract. Both genes compete for HeLa transcription factors, but neither of them is efficiently transcribed. Removal of the 5'-flanking sequences of each gene and replacement with various sequences, including the tRNAArg gene 5' flank, does not allow increased transcription in HeLa cell extract.

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Either Gene Amplification or Gene Conversion May Maintain the Homogeneity of the Multigene Family Encoding Human U1 Small Nuclear RNA

Cited by 47 publications

References 0 publications

Diversity of tandemly repetitive sequences due to short periodic repetitions in the chromosomes of Candida albicans

Diversity of tandemly repetitive sequences due to short periodic repetitions in the chromosomes of Candida albicans

Human genes for U2 small nuclear RNA are tandemly repeated.

Transcription factor binding is limited by the 5'-flanking regions of a Drosophila tRNAHis gene and a tRNAHis pseudogene.

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