Selective Expression of Cloned Middle-Repetitive Sequences in Nuclear RNA of Mouse Organs (original) (raw)
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Nucleic Acids Research, 1979
Total single-copy DNA and single-copy DNA contiguous to middle repetitive sequences were isolated from mouse brain by successive hydroxylapatite column chromatographies. These DNAs, termed repeat-contiguous single-copy DNA, were found to constitute 48% of the total single-copy DNA. The saturation hybridization values of these two DNA probes to nuclear RNA and cytoplasmic RNA containing polyA of mouse brain and liver were measured. The saturation hybridization levels of total singlecopy DNA to brain and liver nuclear RNA were 13.5% and 8.8%, respectively, and those of repeat-contiguous single-copy DNA to the same RNA samples were 13.3% and 8.5%, respectively.
Characterization of a highly repetitive sequence DNA family in rat
Journal of Molecular Biology, 1981
A 92 to 93 base-pair highly reiterated DNA from rat liver has been isolated by digestion with EcoRI and cloned in pBR322. Three recombinant plasmids have been studied in detail; these are p93-2 and p93-10, both of which contain two 93 base-pair inserts, and p93-15, which contains one 92 base-pair and two 93 base-pair inserts. Analysis of these seven cloned DNA fragments reveals that 93 base-pair highly repetitive DNA exhibits as much aa 50% overall sequence heterogeneity although several families can be identified on the basis of a high degree of sequence homology among particular cloned inserts. Individual families have also been identified on the basis of specific restriction endonucleaae sites. This property, coupled with a limited degree of cross-hybridization among the groups of inserts in filter hybridizations, has been utilized to demonstrate that the three 93(2) base-pair families identified here are repeated in a regularly interspersed, tandem manner with each family repeated no more frequently than once every fourth sequence. Similar conclusions have been reached by analysis of a specific fraction of 370 basepair rat repeated DNA .
A family of moderately repetitive sequences in mouse DNA
Nucleic Acids Research, 1980
When mouse DNA is digested to completion with restriction endonuclease Eco Rl, a distinct band of 1.3 kb segments comprising about 0.5-3% of thegenomeis observed upon agarose gel electrophoresis. This DNA is not tandemlyrepeated in the genome and is not derived from mouse satellite DNA. Restriction endonuclease analysis suggested that the 1.3 kb segments are heterogeneous. Specific sequences were selected from the 1.3 kb segments and amplified by cloning in plasmid pBR322. Southern transfer experiments indicated that three separately cloned mouse DNA inserts hybridized predominantly to the Eco R1 1.3 kbband and to the conspicuous subsegments generated by secondary restriction endonuclease cleavage of the sucrose gradient purified 1.3 kb segments. Segments were also excised by Hha I (Hha I segments) from the chimeric plasmids containing mouse DNA inserts and subjected to restriction endonuclease and cross-hybridization analysis. It was found that the three Hha I segments were different, although two of them exhibited partial sequence homology. Cot analysis indicated that each of the Hha I segments are repeated about 104 times in the mouse genome. These findings indicate that a family of related but non-identical, moderately repetitive DNA sequences, rather than a single homogeneous repeat, is present in the 1.3 kb Eco RI band.
Studies of a novel repetitive sequence family in the genome of mice
European Journal of Biochemistry, 1988
A new middle repetitive sequence is described in the mouse genome. It has been revealed with a recombinant clone isolated from a Mus musculus BamHI gene library constructed in pBR322 and containing an insertion of 1.73 kb. When digests of genomic DNA were subjected to Southern blot hybridization, using the 1.73-kb insert as probe, we obtained a light smear and discrete bands, indicating a dispersion in the mouse genome of this sequence. This 1.73-kb sequence seems to be a part of a greater repetitive sequence at least 6 kb in length.
Mammalian genome contains a wide variety of repetitive DNA sequences of relatively unknown function. We report a novel 227 bp simple repeat DNA (3.3 DNA) with a d {(GA) 7 A (AG) 7 } dinucleotide mirror repeat from the rat (Rattus norvegicus) genome. 3.3 DNA showed 75-85% homology with several eukaryotic mRNAs due to (GA/CU) n dinucleotide repeats by nBlast search and a dispersed distribution in the rat genome by Southern blot hybridization with [ 32 P]3.3 DNA. The d {(GA) 7 A (AG) 7 } mirror repeat formed a triplex (H-DNA)-like structure in vitro. Two large RNAs of 9.1 and 7.5 kb were detected by [ 32 P]3.3 DNA in rat brain by Northern blot hybridization indicating expression of such simple sequence repeats at RNA level in vivo. Further, several cDNAs were isolated from a rat cDNA library by [ 32 P]3.3 DNA probe. Three such cDNAs showed tissue-specific RNA expression in rat. pRT 4.1 cDNA showed strong expression of a 2.39 kb RNA in brain and spleen, pRT 5.5 cDNA showed strong expression of a 2.8 kb RNA in brain and a 3.9 kb RNA in lungs, and pRT 11.4 cDNA showed weak expression of a 2.4 kb RNA in lungs. Thus, genomic simple sequence repeats containing d (GA/CT) n dinucleotides are transcriptionally expressed and regulated in rat tissues. Such d (GA/CT) n dinucleotide repeats may form structural elements (e.g., triplex) which may be sites for functional regulation of genomic coding sequences as well as RNAs. This may be a general function of such transcriptionally active simple sequence repeats widely dispersed in mammalian genome.
Proceedings of The National Academy of Sciences, 1982
We have investigated the organization and the distribution of a family of interspersed DNA repeats in the mouse genome. The repeats are at least 5600 base pairs (bp) in size and contain two contiguous BamHI endonuclease fragments, 4000 and 540 bp in size, the larger of which includes a 1350-bp EcoRI fragment studied by previous authors. The repeats are polymorphic in their restriction maps, and represent the major family of interspersed repeats in the mouse genome. The repeats are present almost exclusively in the two light major components of mouse DNA, and the base composition of their large BamHI fragments matches that ofthose components. The genomic distribution ofthe repeats is different from that of structural genes, which are present not only in the two light components but also in the two heavy components of mouse DNA. This distribution indicates that the repeats are not involved, at least in any simple way, in the regulation of gene expression.
A cluster of repetitive elements within a 700 base pair region in the mouse genome
Nucleic Acids Research, 1983
Approximately 39% of the dones from a BALB/c mouse genomic library hybridized with polyadenylated cytoplasmic RNA extracted from anemic mouse spleen. The DNA sequence of a portion of one such clone revealed the presence of three repetitive sequence elements within a 700 bp span. All three elements contain putative RNA polymerase III control regions oriented in the same direction and oligo(dA) tracts at their 3' ends. The first element is a member of the murine Bl family. A comparison of this element with other Bl family members indicates that the Bl family can be divided Into two subclasses based on commonly held base changes and deletions. The second element within this 700 bp region may be a member of a new murine Alu family. Its structure is analogous to other murine Alu-equivalent sequences with respect to overall length, the presence of a 3' oligo(dA) tract and putative RNA pdymerase HI control regions. The third element is a murine type 2 Alu-equivalent sequence.
Complete sequence of the 45-kb mouse ribosomal DNA repeat: analysis of the intergenic spacer☆
Genomics, 2003
DNA from a single bacterial artificial chromosome clone was used to sequence the mouse ribosomal DNA intergenic spacer from the 3Ј end of the 45S pre-RNA to the spacer promoter (Accession No. AF441733). This made possible the assembly of a complete mouse ribosomal DNA repeat unit (45,309 bp long, TPA Accession No. BK000964). Analysis of the intergenic spacer (IGS) showed a high density of simple sequence repeats and transposable elements. The IGS contains two long sequence blocks, which are repeated tandemly. Some of the sequences in these blocks are also present in other parts of the IGS. A difference in the mutation rate along the mouse IGS was observed. The significance of sequence motifs in the IGS for transcription enhancement, transcription termination, origin of replication, and nucleolar organization is discussed.