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R Kominami

Publications and source records attributed to R Kominami.

At least 127 records · Page 7Linked to original sources
PubMed1987

Transcription termination and RNA processing in the 3'-end spacer of mouse ribosomal RNA genes.

The 3' termini of ribosomal RNA precursors from mouse FM3A cultured cells are mapped to eight sites within 625 bp downstream from the 3' terminus of 28 S rRNA. Three additional sites are mapped in liver RNA from C3H/He strain mice. Two of them, the sites at 570 bp and 625 bp are assumed to be termination sites in vivo, because they correspond to in vitro termination sites of RNA polymerase I, and 45 S RNAs having these 3' termini decay with kinetics distinct from others. The amount of 45 S RNA having the 3' terminus at other sites is variable among several mouse strains, despite their having the same DNA sequence in these regions. The ability to produce 3' termini in these sites seems to follow Mendel's law of inheritance. Therefore, we postulate that these nine sites are RNA processing sites which are controlled genetically.

Animals↗
PubMed1987

Amplified ribosomal spacer sequence: structure and evolutionary origin.

A novel class of repeated sequences consisting of tandem arrays of ribosomal spacer sequence has been discovered in a mouse genome. Comparison to normal ribosomal DNA reveals that one repeat unit consists of two separate parts of spacer sequence. This amplified spacer sequence has a pseudogene-like structure but is distinct from the previously reported pseudogenes and orphons in regions lacking coding sequences. So far the amplified spacer sequence has been found only in the BALB/c mouse genome but not in ten other laboratory strains and several wild-type mouse stocks. Surprisingly, a part of the amplified spacer sequence unit had a higher homology to the corresponding part of the ribosomal DNA sequence of Mus musculus molossinus, a Japanese wild-type mouse, than to the corresponding part of the rDNA of the BALB/c mouse. These findings suggest that the amplified spacer sequence of the BALB/c mouse might have partly originated in M. m. molossinus or in a related subspecies.

Animals↗
PubMed1987

Variation among mouse ribosomal RNA genes within and between chromosomes.

We compared nucleotide sequences of the transcription-initiation region of five mouse ribosomal DNA (rDNA) clones. Two clones were isolated from Japanese wild mice, Mus musculus molossinus, and the other three from BALB/c mice originating in M. m. domesticus. Two BALB/c clones that are derived from the same chromosome are very similar, suggesting the occurrence of intrachromosomal homogenization of rDNA repeats. However, the other clone of BALB/c was approximately as different from the former two clones as from the rDNA clones of M. m. molossinus. These results suggest that, compared with intrachromosomal homogenization, homogenization among rDNA repeats on nonhomologous chromosomes occurs relatively infrequently after the mouse subspecies separation.

Animals↗
PubMed1987

Sequestration analysis for RNA polymerase I transcription factors with various deletion and point mutations reveals different functional regions of the mouse rRNA gene promoter.

We compared the ability of various deletion and substitution mutants of the mouse rRNA gene promoter to bind essential factors required for accurate transcription initiation by RNA polymerase I. Different amounts of a competitor template were first incubated with a mouse cell extract containing the whole complement of factors and RNA polymerase I, and then a tester template was added for the second incubation. Transcription was started by adding nucleoside triphosphates (one labeled), and the accurate transcripts were determined on a gel. The results indicated that the ability of 5' deletion mutants to sequester essential factors decreased almost concurrently with the impairment of in vitro transcription activity, whereas when the promoter sequence was removed from the 3' side, the transcription activity decreased earlier and more drastically than the sequestration ability. Similar, though not identical, results were obtained by preincubation with fraction D separated on a phosphocellulose column, indicating that the major factor which was sequestered was TFID, the species-dependent transcription initiation factor that binds first to the promoter in the initiation reaction (H. Kato, M. Nagamine, R. Kominami, and M. Muramatsu, Mol. Cell. Biol. 6:3418-3427, 1986). Compilation of the data suggests that a region inside the 5' half of the core promoter (-40 to -1) is essential for the binding of TFID. The 3' half of the promoter (-1 to downstream) is not essential for the binding of TFID but is highly important for an efficient transcription initiation. A strong down-mutant with a one-base substitution at -16 (G to A) had a reduced ability to bind to TFID, whereas a null mutant with a single base substitution at -7 (G to A) showed a binding ability similar to that of the wild-type promoter when tested with whole-cell extract. This null mutant, however, could not sequester the TFID well when incubated with fraction D alone, suggesting that the binding of TFID with this mutant is unstable in the absence of another factor(s) present in cell extract. The factor is not TFIA, which binds after TFID, because the addition of fraction A containing TFIA did not cause TFID to bind to the mutant. The availability of different mutants having lesions at different steps of transcription initiation will provide a powerful tool for the dissection of the initiation reaction of the RNA gene.

Animals↗
PubMed1986

Evolutionary implication of heterogeneity of the nontranscribed spacer region of ribosomal DNA repeating units in various subspecies of Mus musculus.

Genetic variability of the nontranscribed spacer (NTS) region within ribosomal DNA repeating units in the various subspecies of Mus musculus was determined. Mice belonging to several laboratory mouse strains were examined by means of Southern blot hybridization with a mouse ribosomal DNA probe. This probe encompasses the 3' end of the 28S ribosomal RNA (rRNA) gene and the following spacer. Restriction enzyme digestions of the liver DNAs from various wild mice revealed that each of the subspecies has a unique pattern in the spacer encompassing a distance approximately 10 kb downstream from the ribosomal gene. These restriction patterns permit the classification of mouse subspecies and also provide insights into the origin of the laboratory mouse strains.

Animals↗
PubMed1986

Formation of the transcription initiation complex on mammalian rDNA.

Steps for the formation of transcription initiation complex on the human rRNA gene (rDNA) in vitro were analyzed with partially purified transcription factors and RNA polymerase I. The reaction requires at least two factors besides RNA polymerase I for maximal efficiency. Preincubation and short-pulse analyses of the accurate transcripts revealed the following steps. First, the species-dependent factor, designated TFID, bound to the rDNA template, forming a preinitiation complex (PIC-1) which was resistant to a moderate concentration (0.015 to 0.02%) of Sarkosyl. Other factors, designated TFIA and RNA polymerase I, were then added to convert it to the final preinitiation complex PIC-3. This complex incorporated the first two nucleoside triphosphates of the starting site to complete the initiation complex (IC), which was resistant to a high concentration (0.2%) of Sarkosyl. Binding of TFID was rate limiting in the overall initiation reaction in vitro. Together with the kinetics of incorporation, the results are interpreted to mean that TFID, one bound, remains complexed with rDNA together with TFIA as the PIC-2 for many rounds of transcription by RNA polymerase I. Thus, the formation of PIC-2 may be a prerequisite for the stable opening of rDNA for transcription in vivo.

Animals↗
PubMed1985

A polymorphic repetitive-sequence PR1 family. Evidence for meiotic instability.

When EcoRI digests of mouse genomic DNA were subjected to Southern blot analysis with the polymorphic repetitive sequence PR1 as a probe, one satellite-like band of 3.5 X 10(3) base-pairs, designated as PR1 family B, was detected in BALB/c-strain mice, but not in the DDD/1- or MOA-strain mice. Analysis of recombinant phage clones revealed that the repeating unit of the PR1 family B was 13.5 X 10(3) base-pairs long. This family consisted of a tandem array of repeating units and occupied as much as 2% of one BALB/c chromosome. Since the BALB/c-specific PR1 family B is not present in DDD/1 or MOA mice, the unpaired portion of the BALB/c chromosome may be looped out in a synaptonemal complex during meiosis in F1 hybrids of the BALB/c strain with DDD/1 or MOA. To determine the fate of this extra DNA, we examined the genotypes of the F1 hybrid mice and of the segregating populations. Although the PR1 patterns of F1 and most N2 mice are consistent with typical Mendelian inheritance, some N2 progeny showed an abnormal 3.5 X 10(3) base-pair band of unexpectedly reduced intensity. This indicated that the extra DNA of PR1 family B occasionally underwent recombination during meiosis in F1 mice, resulting in its apparent excision. Examination of PstI digests supported this interpretation.

Animals↗
PubMed1985

Presence of a limited number of essential nucleotides in the promoter region of mouse ribosomal RNA gene.

Point mutations are introduced into a mouse rDNA fragment containing the promoter region by a sodium bisulfite method and the mutants are tested for the ability of accurate transcription initiation in vitro. The results indicate that the change, G to A, at -7 completely eliminates the promoter activity, and those at -16 and at -25 decrease it to about 10% and 50%, respectively. On the other hand, the substitutions at +9, +4, -2, -9 and -39 do not alter the template activity significantly. It is concluded that there are limited but distinct nucleotides that are essential for the transcription initiation of this gene. This sort of absolute requirement for single specific bases is not reported in protein coding genes transcribed by RNA polymerase II. We propose that these rigid recognition signals which we have found are the molecular basis for the strong species-dependency of the transcription machinery of RNA polymerase I system. A model is presented in which a transcription factor interacts with the rDNA promoter from one side of the DNA double-helix with essential contacts at these bases.

Animals↗
PubMed1985

Ribosomal RNA synthesis in mammalian cells permealized by diethylaminoethyl (DEAE)-dextran treatment.

Ehrlich ascites tumor cells were made permeable to nucleoside triphosphates by treating them with diethylaminoethyl (DEAE)-dextran. Permeable cells incorporated labeled UTP into RNA at a constant rate for at least 30 min at 37 degrees C and 100 min at 25 degrees C, whereas no incorporation was detected without DEAE-dextran treatment. This RNA synthesis is dependent on added nucleoside triphosphates and is affected differentially by different concentrations of alpha-amanitin. The results of both hybridization and S1-nuclease protection mapping experiments with pulse-labeled RNA synthesized in this system indicate that reinitiation of rRNA transcription takes place from the physiological initiation site in cells made permeable by treatment with DEAE-dextran. By using this system, we examined the kinetics of rRNA synthesis in mouse FM3A cells during inhibition of protein synthesis. The results reflected those previously obtained by analyses of nucleolar RNA synthesis in vivo during protein synthesis inhibition. This permeable cell system should provide a rapid and reproducible assay method for rRNA synthesis in mammalian cells.

Animals↗
PubMed1984

The 6S RNA transcribed from rodent total DNA in vitro is the transcript of the type 2 Alu family.

We have performed in vitro transcription, using total DNA isolated from mouse and a cloned mouse DNA fragment containing a representative type 2 Alu sequence characterized by Kominami et al. (1983) as templates. From each template, 6S RNA was transcribed. The fingerprint of the 6S RNA produced from in vitro transcription of total DNA showed a very clear pattern of oligonucleotides. By comparing the oligonucleotides of the 6S RNA produced from each template, we demonstrated that the 6S RNA transcribed from mouse total DNA is the in fact the transcript of type 2 Alu sequences. The composition of the oligonucleotides of the 6S RNA transcribed from mouse total DNA seems to reflect well that of the consensus sequence of the type 2 Alu family proposed by Krayev et al. (1982). In vitro transcripts of rat or hamster total DNA showed fingerprint patterns nearly identical to that of mouse DNA, confirming that rodents have equivalent type 2 Alu sequences whose transcripts have the same length and similar compositions of oligonucleotides. Thus total DNA transcription provides a novel approach to the detection and analysis of type 2 Alu sequences transcribed in vitro.

Animals↗
PubMed1984

Determination of the promoter region of mouse ribosomal RNA gene by an in vitro transcription system.

Sequences required for a faithful and efficient transcription of a cloned mouse ribosomal RNA gene (rDNA) are determined by testing a series of deletion mutants in an in vitro transcription system utilizing two kinds of mouse cellular extract. Deletion of sequences upstream of -40 or downstream of +52 causes only slight reduction in promoter activity as compared with the "wild-type" template. For upstream deletion mutants, the removal of a sequence between -40 and -35 causes a significant decrease in the capacity to direct efficient initiation. This decrease becomes more pronounced when the deletion reaches -32 and the sequence A-T-C-T-T-T, conserved among mouse, rat, and human rDNAs, is lost. Residual template activity is further reduced as more upstream sequence is deleted and finally becomes undetectable when the deletion is extended from -22 down to -17, corresponding to the loss of the conserved sequence T-A-T-T-G. As for downstream deletion mutants, the removal of the sequence downstream of +23 causes some (and further deletions up to +11 cause a more) serious decrease in template activity in vitro. These deletions involve other conserved sequences downstream of the transcription start site. However, the removal of the original transcription start site does not abolish the transcription initiation completely, provided that the whole upstream sequence is intact.

Cell-Free System↗
PubMed1983

Novel repetitive sequence families showing size and frequency polymorphism in the genomes of mice.

A middle repetitive sequence, PR1, originally found in mouse rDNA appeared as satellite-like bands when EcoRI and BglII digests of genomic DNA were subjected to Southern blot hybridization using PR1 as probe. The copy number and sizes of PR1-related satellite-like bands, designated as PR1 families, differed remarkably among the subspecies and laboratory strains of mice when the EcoRI digests of genomic DNAs were compared. These bands were not detected in rat and human DNAs. A unit of PR1 sequence was determined by examining cloned EcoRI 3.5 kb (kb, 10(3) bases) fragment and 6.6 kb rDNA by cross-hybridization and sequence analysis: 3.5 kb and 6.6 kb DNAs are composed of homologous PR1 regions and the flanking non-homologous sequences. The results indicate that amplification of different sequences containing PR1 has occurred in different subspecies and strains of mice, and that the segments of satellite-like bands are likely to have been created by recombination of the PR1 sequence with other DNA segments before amplification. The chromosomal distribution of the 3.5 kb PR1 family was studied by back-crossing the female F1 between BALB/c and DDD/1 to male DDD/1. The segregation data strongly suggest that most, if not all, of this family are located on a single chromosome. The stability of these PR1 families in the genomes of cultured cells of a given strain was also examined. An extra band homologous to PR1 appeared in their genomes, but was not detected in other tissues, indicating that some PR1 families may change even during cell propagation.

Animals↗
PubMed1983

A mouse type 2 Alu sequence (M2) is mobile in the genome.

The Alu and its equivalent families of interspersed repetitive DNA sequences have been found in various mammalian genomes. It has been proposed that some of them might move around the genome like known prokaryotic and eukaryotic transposable elements, as most of these sequences are flanked by short direct repeats at both ends. To prove that this is the case, however, one must demonstrate the existence of homologous sequences of DNA with and without Alu insertion among the genomes of different strains or individuals of a species. While studying a polymorphic repetitive sequence (PR1) originally found in the spacer region of mouse ribosomal RNA genes, we have now found that a sequence similar to the CHO type 2 Alu-equivalent element, designated M2, is inserted within a PR1 sequence which is located outside the ribosomal RNA gene and that this M2 segment is flanked by a short direct repeat at both ends. Furthermore, this PR1 segment containing M2 is detected only in the BALB/c strain among the laboratory mice and wild mouse subspecies examined. These facts suggest that the M2 sequence has been inserted into PR1 sequence relatively recently during evolution of mouse strains and support the idea that at least some of the Alu-equivalent families are mobile in the genome. Recently, Grimaldi and Singer reported an African green monkey alpha-satellite sequence that was interrupted by an Alu element.

Animals↗