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Nuclear DNA
About: Nuclear DNA is a research topic. Over the lifetime, 3933 publications have been published within this topic receiving 185830 citations.
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TL;DR: By interrogating a library of ordered YAC clones, this work provides evidence for a chromosomal copy of the rDNA on chromosome 4, and suggests that this locus may provide master copies for the stable transmission of the extrachromosomal elements.
Abstract: Ribosomal RNAs (rRNAs) are encoded by multicopy families of identical genes. In Dictyostelium and other protists, the rDNA is carried on extrachromosomal palindromic elements that comprise up to 20% of the nuclear DNA. We present the sequence of the 88 kb Dictyostelium rDNA element, noting that the rRNA genes are likely to be the only transcribed regions. By interrogating a library of ordered YAC clones, we provide evidence for a chromosomal copy of the rDNA on chromosome 4. This locus may provide master copies for the stable transmission of the extrachromosomal elements. The extrachromosomal elements were also found to form chromosome-sized clusters of DNA within nuclei of nocodazole-treated cells arrested in mitosis. These clusters resemble true chromosomes and may allow the efficient segregation of the rDNA during mitosis. These rDNA clusters may also explain the cytological observations of a seventh chromosome in this organism.
57 citations
TL;DR: Processes such as triacylglycerol metabolism, energy production, protein folding, response to unfolded proteins, and cellular detoxification were found to be altered in these cells.
Abstract: Purpose
Sperm DNA fragmentation has been suggested as a marker for infertility diagnosis and prognosis Hence, understanding its impact on male physiology and post-genomic pathways would be clinically important We performed the proteomics and functional enrichment analyses of viable spermatozoa from ejaculates with low and high sperm DNA fragmentation to identify protein expression and pathways altered in association with sperm DNA fragmentation
57 citations
TL;DR: The nuclear DEB protein Ku plays an essential role in nuclear DNA double-strand break repair, and the DEB activity described herein may therefore play a similar role in mitochondrial DNA repair.
Abstract: Mammalian mitochondrial protein extracts possess DNA end-binding (DEB) activity. Protein binding to a 394 bp double-stranded DNA molecule was measured using an electrophoretic mobility shift assay. Mitochondrial DEB activity was highly specific for linear DNA. Inclusion of a vast excess of non-radioactive circular DNA did not disrupt binding to radioactive f394. In contrast, binding was abolished by the inclusion of linear competitor DNA. In mammals, nuclear DEB activity is due to Ku, a hetero-dimer composed of the Ku70 and Ku86 proteins. To determine whether mitochondrial DEB activity was also due to Ku, protein extracts were prepared from the Chinese hamster XR-V15B cell line, which lacks this protein. As anticipated, nuclear extracts prepared from these cells lacked DEB activity. In contrast, mitochondrial extracts prepared from these cells had wild-type levels of DEB activity, demonstrating that this latter activity is not a consequence of nuclear contamination. Although the nuclear and mitochondrial DEB activities are independent of each other, they are nevertheless closely related, since mitochondrial DEB activity was 'supershifted' by both anti-Ku70 and anti-Ku86 antisera. The nuclear DEB protein Ku plays an essential role in nuclear DNA double-strand break repair. The DEB activity described herein may therefore play a similar role in mitochondrial DNA repair.
57 citations
TL;DR: Functional studies revealed that cells expressing recombinant hOGG1 were more proficient at repairing NO-induced mtDNA damage, which led to increased cellular survival following NO exposure, and the results described here show that conditional expression of hogG1 in mitochondria decreases NO- induced inhibition of ATP production and protects cells from NO- induces apoptosis.
57 citations
TL;DR: The hypothesis that rDNA regions are preferentially accessible to carcinogen modification because of the diffuse conformation maintained within transcribed genes is supported.
Abstract: The in vivo formation of covalent aflatoxin B1 (AFB1)-DNA adducts within the rRNA gene sequences of nuclear DNA has been studied in AFB1-treated rats. Liver nuclear DNA, enriched in ribosomal DNA (rDNA) by one round of cesium salt density gradient centrifugation, was treated under buffered alkaline conditions to convert unstable AFB1-N7-guanine adducts to stable AFB1-formamidopyrimidine derivatives. The alkali-treated DNA was hybridized to 18S and 28S rRNA in 70% formamide buffer to form rRNA X rDNA hybrids. These hybrids were separated from the bulk of nuclear DNA by two rounds of centrifugation in CsCl, and the level of AFB1 adduction to rDNA versus total nuclear DNA was compared as a function of dose 2 hr after AFB1 administration. Over an 8-fold dose range (0.25-2.0 mg of AFB1 per kg of body weight), rDNA contained 4- to 5-fold more AFB1 residues than nuclear DNA, indicating that rDNA is preferentially accessible to carcinogen modification in vivo. While aflatoxin B1 forms adducts with DNA principally at guanine residues, the guanine enrichment of rDNA was insufficient to explain the magnitude of observed preferential AFB1 modification of rDNA. These results support the hypothesis that rDNA regions are preferentially accessible to carcinogen modification because of the diffuse conformation maintained within transcribed genes. This experimental approach permits the quantitative description of carcinogen modification within a defined gene sequence; further refinement of this approach may be useful in defining the precise relationships between covalent chemical-DNA interactions and the alterations in gene expression that result.
56 citations