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At least 325 records · Page 18Linked to original sources
PubMed1990

Nucleotide sequence of circular DNA molecules homologous to the 240 bp tandem repeats of the intergenic spacer of Drosophila melanogaster ribosomal DNA.

We have determined the nucleotide sequence of ten 240 bp repeated sequences of the DNA intergenic spacer present in circular DNA molecules purified from D melanogaster embryos. No significant difference was found with the sequence of the chromosomal units. This suggests that most of the circular molecules homologous to the 240 bp repeats are generated by homologous recombination between adjacent chromosomal units.

Animals↗
PubMed1993

In planta deletion of DNA inserts from the large intergenic region of cauliflower mosaic virus DNA.

RNA splicing and copy-choice recombination lead to deletions in the DNA of cauliflower mosaic virus (CaMV). To assess the relative importance of these mechanisms of nucleotide sequence change, free of constraints imposed by the "relay race" mode of translation of CaMV RNA, we examined the stability of inserts in the large intergenic region. The insertions had, in various combinations, splicing signals and directly repeated sequences that could facilitate deletion. Most modified DNAs were infectious. Viral DNA recovered from infected plants was analyzed by restriction and, in some cases, cloned for nucleotide sequencing to determine deletion endpoints. Deletions from a DNA containing introduced splicing signals occurred primarily at direct repeats, although deletion apparently by splicing was also detected. Both types of deletion were also observed with insertions containing a 5' splice donor but no known functional 3' splice acceptor. One DNA, whose insertion lacked splicing signals and short repeated sequences, was stable in one of two plants infected. Total insert deletions were bounded by repeats or pseudorepeats, while partial insert deletions apparently occurred by splicing. The results suggest that the two mechanisms for deletion of nucleotides are equally important in the evolution of caulimoviral nucleotide sequences.

Base Sequence↗
PubMed1996

The structure of the semenogelin gene locus--nucleotide sequence of the intergenic and the flanking DNA.

The sequence of 15.7 kb from the human semenogelin gene locus has been determined. Together with previously published sequences, this gives the structure of a 28-kb region encompassing the two semenogelin genes. The two transcription units are separated by 11616 bp intergenic DNA comprising more than 40% repetitive DNA sequences, predominantly located to a 4-kb block of L1 and Alu repeats. Two more blocks of L1 sequences are present in the DNA flanking the genes, so that approximately 20% of the completed sequence consists of long interspersed repeated sequences, so called LINES. A comparison of the SgI gene and the SgII gene suggests that they evolved by the duplication of an approximately 8 kb DNA segment about 61 million years ago, probably by a mechanism involving recombination between L1 elements.

Base Sequence↗
PubMed1984

Tandem repeated DNA in an intergenic region of herpes simplex virus type 1 (Patton).

When the entire US region of HSV-1 (Patton) was cloned as an EcoRI fragment in bacteriophage lambda gtWES, the BamHI B6B5 fragment was observed to vary in size among independent isolates [Umene and Enquist, Gene 13 (1981) 251-268]. This fragment polymorphism also occurred in DNA of HSV-1 single plaque isolates. We report here that this heterogeneity is due to variation in copy number of a 15-bp tandem repeat of sequence 5'-CCACTCCCCACCCAC-3', which apparently lies in an intergenic region of the HSV-1 DNA.

Base Sequence↗
PubMed1996

Integration of foreign DNA in an intergenic region of the archaeon Methanosarcina mazei without effect on transcription of adjacent genes.

Transformation systems for methanogenic archaea are scarce, none has been reported for the genus Methanosarcina, and plasmids useful as vectors for cloning foreign DNA into methanogens that stably replicate as extrachromosomal elements are not available. We developed an integration vector for transformation of a member of the genus Methanosarcina, i.e. Methanosarcina mazei, using a segment (Int alpha; 1015 bp) which encompasses the intergenic region (431 bp) between the stress (heat-shock) genes grpE and dnaK. This segment also includes the 3' end (270 bp) of the grpE protein-coding region and the 5' end (314 bp) of the dnaK protein-coding region. Int alpha has an EcoRI site, useful for cloning, situated in the 3' direction beyond the grpE transcription termination region, and far upstream from the dnaK promoter. This location of the site, and the monocistronic mode of transcription of grpE and dnaK in M. mazei, suggested to us that a foreign insert in the site would not affect transcription of either flanking gene. A puromycin-resistance cassette (pac cassette) was inserted in the EcoRI site of Int alpha already inserted in pUC18, to obtain a vector which integrated the pac cassette in the chromosome between grpE and dnaK. The pac gene was transcribed and the transformants acquired puromycin resistance. Constitutive and heat-shock-induced transcription of grpE and dnaK in the transformants was the same as in wild-type cells. The two vectors found with transforming ability differed in the orientation of the pac cassette but both had M. mazei's DNA on each flank of the cassette, with the same orientation as that of the homologous segments in the chromosome.

Bacterial Proteins↗
PubMed1995

Complete sequence of the 43-kb human ribosomal DNA repeat: analysis of the intergenic spacer.

We have sequenced the remaining 12.4 kb of the 30-kb human ribosomal DNA intergenic spacer (IGS), which allows us to piece together both a complete IGS and a 43-kb rDNA unit. The sequence of the complete IGS reveals a collection of sequence motifs that can be correlated with functions known or expected to reside in the rDNA repeat: modulation of transcription, recombination, initiation of DNA replication, and chromosomal organization. Finally, we find that IGS accumulates variation at a much higher rate than the transcribed regions. This finding leads us to correlate sequence character with types of mutation and sequence context with rate of mutation.

Animals↗
PubMed1995

Bent DNA in the large intergenic region of wheat dwarf geminivirus.

Wheat dwarf virus (WDV) is a member of the geminivirus group, unique plant DNA viruses which replicate exclusively via dsDNA replication intermediates. The large intergenic region (LIR), a nontranscribed regulatory region, contains an inverted repeat with the potential to form a stem-loop structure in which the initiation site for WDV (+)strand (virion-sense) DNA replication has been mapped. In this work, we have studied by two-dimensional electrophoresis and by electron microscopy the DNA structure of the WDV LIR and we have identified a DNA sequence which confers a static DNA curvature. This is the first report of the occurrence of DNA bending in the regulatory region of a geminivirus genome. The bending locus, defined by an 80-bp cluster of A(T) tracts, is located downstream from the potential stem-loop. The A(T) tract proximal to the stem-loop structure is separated by 14 bp from the inverted repeat, and deletion of distal A(T) tracts abolished the curvature of the new WDV deltaLIR. The bending center maps approximately 80 bp downstream from the putative initiation site for (+)strand DNA replication and approximately 70 bp upstream from the TATA box for virion-sense transcription. The possible implications of the DNA bending locus as a regulatory element of WDV DNA replication and/or virion-sense transcription are discussed.

Base Sequence↗
PubMed2005

Phylogeography and conservation genetics of Hygrophila pogonocalyx (Acanthaceae) based on atpB-rbcL noncoding spacer cpDNA.

Genetic variation in the atpB-rbcL intergenic spacer region of chloroplast DNA (cpDNA) was investigated in Hygrophila pogonocalyx Hayata (Acanthaceae), an endangered and endemic species in Taiwan. In this aquatic species, seed dispersal from capsules via elasticity is constrained by gravity and is thereby confined within populations, resulting in limited gene flow between populations. In this study, a total of 849 bp of the cpDNA atpB-rbcL spacer were sequenced from eight populations of H. pogonocalyx. Nucleotide diversity in the cpDNA is low (theta = 0.00343+/-0.00041). The distribution of genetic variation among populations agrees with an "isolation-by-distance" model. Two geographically correlated groups, the western and eastern regions, were identified in a neighbor-joining tree and a minimum-spanning network. Phylogeographical analyses based on the cpDNA network suggest that the present-day differentiation between western and eastern groups of H. pogonocalyx resulted from past fragmentation. The differentiation between eastern and western populations may be ascribed to isolation since the formation of the Central Mountain Range about 5 million years ago, which is consistent with the rate estimates based on a molecular clock of cpDNA.

Acanthaceae↗
PubMed2003

Identification of the biological species of Armillaria associated with Wynnea and Entoloma abortivum using PCR-rFLP analysis of the intergenic region (IGR) of ribosomal DNA.

Polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) analysis of the first intergenic region (IGR1) of nuclear ribosomal DNA was used to clarify the relationship between IGR1 variations and six Japanese biological species of Armillaria: A. gallica, A. nabsnona, A. ostoyae, A. cepistipes, A. mellea and Nagasawa's E (Nag. E: taxonomically unknown species). The procedure was then used to identify Armillaria species associated with Wynnea species (W. americana and W. gigantea) and Entoloma abortivum. By combining the RFLP patterns obtained using three endonucleases, HaeIII, HinfI and MspI, the IGR1s from 18 isolates of six Armillaria species were assigned to nine different RFLP phenotypes and the six species were distinguished from each other. Each of the RFLP phenotypes from the Armillaria isolates associated with Wynnea species or E. abortivum matched a corresponding phenotypes observed among the six Armillaria species. Based on this, all four isolates from W. gigantea were identified as A. mellea, two from W. americana as A. cepistipes, and all three from E. abortivum as Nag. E. These results provide new information on the biological species of Armillaria associated with Wynnea and E. abortivum.

Agaricales↗
PubMed2000

Identification of acetic acid bacteria by RFLP of PCR-amplified 16S rDNA and 16S-23S rDNA intergenic spacer.

DNA corresponding to 16S rDNA and the 165-23S rDNA intergenic spacer (ITS) from 22 reference strains of acetic acid bacteria, representing the diversity of the family Acetobacteraceae, and 24 indigenous acetic acid bacteria isolated from wine fermentations were analysed by PCR-RFLP. Frateuria aurantia LMG 1558T and Escherichia coli ATCC 11775T were included as outgroups. PCR-amplified products of about 1450 bp were obtained from the 16S rDNA of all the strains and products of between 675 and 800 bp were obtained from the 16S-23S rDNA ITS. PCR products were digested with 4-base-cutting restriction enzymes in order to evaluate the degree of polymorphism existing among these strains. Of the enzymes tested, Taql and Rsal were the most discriminatory and showed no intraspecific variations in the restriction patterns. Restriction analysis of the 16S rDNA with these enzymes is proposed as a rapid and reliable method to identify acetic acid bacteria at the level of genus and species (or related species group) and its applicability to identification of indigenous acetic acid bacteria was demonstrated. The same degree of distinction as that for the 16S rDNA analysis was obtained within reference strains of acetic acid bacteria by PCR-RFLP of the 16S-23S rDNA ITS. However, 16S-23S rDNA ITS restriction patterns of strains isolated from wine did not match those of any of the reference strains. Thus, PCR-RFLP of the 16S-23S rDNA ITS is not a useful method to identify isolates of acetic acid bacteria at the species level, although it may be an adequate method to detect intraspecific differentiation.

Acetobacteraceae↗
PubMed1999

Sequence Characterization of a Unique Intergenic Spacer in Gadiformes Mitochondrial DNA.

: The nucleotide sequences of intergenic spacers located between the tRNA(Thr) and tRNA(Pro) genes in mitochondrial DNA of cod fishes (order Godiformes) were determined. Spacers from eight species representing two families of cod fishes were analyzed and found to vary in size from 25 to 99 bp. Each spacer sequence contains one or two copies of a conserved 17-bp motif. Four to five central nucleotides of this motif constitute a substitutional hot spot as observed from interspecific and intraspecific comparisons. The substitution rate of the spacer is approximately twice that of the variable part I of the mitochondrial DNA control region, making this sequence region interesting as a molecular marker in population studies or stock assessments of cod fishes. We propose that the spacer originated in a duplication event and evolved into a functional domain, perhaps by binding regulatory proteins.

Journal Article↗
PubMed2006

Seasonal influences on fungal community structure in unimproved and improved upland grassland soils.

Seasonal and management influences on the fungal community structure of two upland grassland soils were investigated. An upland site containing both unimproved floristically diverse (U4a) and improved mesotrophic (MG7b) grassland types was selected. Samples from both grassland types were taken at five times in one year. Soil fungal community structure was assessed using fungal automated ribosomal intergenic spacer analysis (ARISA), a DNA-profiling approach. A grassland management regime was found to strongly affect fungal community structure, with fungal ARISA profiles from unimproved and improved grassland soils differing significantly. The number of fungal ribotypes found was higher in unimproved than improved grassland soils, providing evidence that improvement may reduce the suitability of upland soil as a habitat for specific groups of fungi. Seasonal influences on fungal community structure were also noted, with samples taken in autumn (October) more correlated with change in ribotype profiles than samples from other seasons. However, seasonal variation did not obscure the measurement of differences in the fungal community structure that were due to agricultural improvement, with canonical correspondence analysis indicating grassland type had a stronger influence on fungal profiles than did season.

Analysis of Variance↗
PubMed2003

Selection on human genes as revealed by comparisons to chimpanzee cDNA.

To better understand the evolutionary forces that affect human genes, we sequenced 5055 expressed sequence tags from the chimpanzee and compared them to their human counterparts. In conjunction with intergenic chimpanzee DNA sequences and data on human single-nucleotide polymorphisms in the genes studied, this allows us to gauge the extent to which selection affects human genes at a genome-wide scale. The comparison to intergenic DNA sequences indicates that about 39% of silent sites in protein-coding regions are deleterious and subject to negative selection. Further, when the divergence between human and chimpanzee is compared with the extent of nucleotide polymorphisms among humans in the same sequences, there is significantly higher divergence in the 5' untranslated regions (UTRs) but not in other parts of the transcript. This indicates that positive selection may have had a considerable influence on 5'UTRs. The dinucleotide CG (CpG) also exhibits a different substitution pattern within 5'UTRs as compared with other parts of the genome.

Amino Acid Substitution↗
PubMed2004

Assessment of intra-species diversity among strains of Acinetobacter baumannii isolated from sites contaminated with petroleum hydrocarbons.

A total of 96 crude oil-degrading bacterial strains were isolated from 5 geographically diverse sites in India that were contaminated with different types of petroleum hydrocarbons. The strains were identified by sequencing the genes that encode for 16S rRNA. Out of the 96 isolates, 25 strains were identified as Acinetobacter baumannii and selected for the study. All of the selected strains could degrade the total petroleum hydrocarbon fractions of crude oil. These 25 strains were biochemically profiled and grouped into 8 phenovars on the basis of multivariate analysis of their substrate utilization profiles. PCR-based DNA fingerprinting was performed using intergenic repetitive DNA sequences, which divided the selected 25 strains into 7 specific genomic clusters. tRNA intergenic spacer length polymorphism was performed to determine the intra-species relatedness among these 25 strains. It delineated the strains into 8 genomic groups. The present study detected specific variants among the A. baumannii strains with differential degradation capacities for different fractions of crude oil. This could play a significant role in in situ bioremediation. The study also revealed the impact of environmental factors that cause intra-species diversity within the selected strains of A. baumannii.

Acinetobacter baumannii↗
PubMed1983

Yeast H3 and H4 histone messenger RNAs are transcribed from two non-allelic gene sets.

The genes coding for the H3 and H4 histones of Saccharomyces cerevisiae have been isolated by recombinant DNA cloning. The genes were detected in a bacteriophage lambda library of the yeast genome by hybridization with plasmids containing the cloned Psammechinus miliaris sea urchin histone genes (pCH7) and the cloned Drosophila histone genes (cDM500). Two non-allelic sets of the H3 and H4 genes have been isolated. Each set consists of one H3 gene and one H4 gene arranged as a divergently transcribed pair separated by an intergene spacer DNA. The histone genes were located on the cloned yeast fragments by S1 nuclease mapping, as was a gene (SMT1) of unknown function that does not code for a histone but is closely linked to one of the histone sets. Sequence homology between the two non-allelic sets is confined to the coding regions of the respective genes while the flanking DNA and intergene spacer DNA are extensively divergent. Cellular RNA homologous to the histone genes, including transcribed non-coding sequences unique to each of the four genes, was detected by S1 mapping, thus demonstrating that all four genes are transcribed in vegetative cells.

Base Sequence↗
PubMed2005

Sap1p binds to Ter1 at the ribosomal DNA of Schizosaccharomyces pombe and causes polar replication fork arrest.

Eukaryotic DNA replication forks stall at natural replication fork barriers or Ter sites located within the ribosomal DNA (rDNA) intergenic spacer regions during unperturbed DNA replication. The rDNA intergenic spacer of the fission yeast Schizosaccharomyces pombe contains four polar or orientation-specific fork barriers, Ter1-3 and RFP4. Whereas the transcription terminator Reb1p binds Ter2 and Ter3 to arrest replication, the factor(s) responsible for fork arrest at Ter1 and RFP4 remain unknown. Using linker scanning mutagenesis, we have narrowed down minimal Ter1 to 21 bp. Sequence analysis revealed the presence of a consensus binding motif for the essential switch-activating and genome-stabilizing protein Sap1p within this region. Recombinant Sap1p bound Ter1 with high specificity, and endogenous Ter1 binding activity contained Sap1p and comigrated with the Sap1p-Ter1 complex. Circular permutation analysis suggested that Sap1p bends Ter1 and SAS1 upon binding. Targeted mutational analysis revealed that Ter1 mutations, which prevent Sap1p binding in vitro, are defective for replication fork arrest in vivo, whereas mutations that do not affect Sap1p binding remain competent to arrest replication. The results confirm the hypothesis that the chromatin organizer Sap1p binds site-specifically to genomic regions other than SAS1 and support the notion that Sap1p binds the rDNA fork barrier Ter1 to cause polar replication fork arrest at this site but not at SAS1.

Base Sequence↗
PubMed2004

Chromatin structure at the flanking regions of the human beta-globin locus control region DNase I hypersensitive site-2: proposed nucleosome positioning by DNA-binding proteins including GATA-1.

The human beta-globin locus control region DNase I hypersensitive site-2 (LCR HS-2) is erythroid-specific and is located 10.9 kb upstream of the epsilon-globin gene. Most studies have only examined the core region of HS-2. However, previous studies in this laboratory indicate that positioned nucleosomes are present at the 5'- and 3'-flanking regions of HS-2. In addition, footprints were observed that indicated the involvement of DNA-binding proteins in positioning the nucleosome cores. A consensus GATA-1 site exists in the region of the 3'-footprint. In this study, using an electrophoretic mobility shift assay (EMSA) and DNase I footprinting, we confirmed that GATA-1 binds in vitro at the 3'-end of HS-2. An additional GATA-1 site was found to bind GATA-1 in vitro at a site positioned 40 bp upstream. At the 5'-end of HS-2, DNase I footprinting revealed a series of footprints showing a marked correlation with the in vivo footprints. EMSA indicated the presence of several erythroid-specific complexes in this region including GATA-1 binding. Sequence alignment for 12 mammalian species in HS-2 confirmed that the highest conservation to be in the HS-2 core. However, a second level of conservation extends from the core to the sites of the proposed positioning proteins at the HS-2 flanking regions, before declining rapidly. This indicates the importance of the HS-2 flanking regions and supports the proposal of nucleosome positioning proteins in these regions.

3' Flanking Region↗