Nuclear DNA

About: Nuclear DNA is a research topic. Over the lifetime, 3933 publications have been published within this topic receiving 185830 citations.

Concise Reviews: Assisted Reproductive Technologies to Prevent Transmission of Mitochondrial DNA Disease

Abstract: While the fertilized egg inherits its nuclear DNA from both parents, the mitochondrial DNA is strictly maternally inherited. Cells contain multiple copies of mtDNA, each of which encodes 37 genes, which are essential for energy production by oxidative phosphorylation. Mutations can be present in all, or only in some copies of mtDNA. If present above a certain threshold, pathogenic mtDNA mutations can cause a range of debilitating and fatal diseases. Here, we provide an update of currently available options and new techniques under development to reduce the risk of transmitting mtDNA disease from mother to child. Preimplantation genetic diagnosis (PGD), a commonly used technique to detect mutations in nuclear DNA, is currently being offered to determine the mutation load of embryos produced by women who carry mtDNA mutations. The available evidence indicates that cells removed from an eight-cell embryo are predictive of the mutation load in the entire embryo, indicating that PGD provides an effective risk reduction strategy for women who produce embryos with low mutation loads. For those who do not, research is now focused on meiotic nuclear transplantation techniques to uncouple the inheritance of nuclear and mtDNA. These approaches include transplantation of any one of the products or female meiosis (meiosis II spindle, or either of the polar bodies) between oocytes, or the transplantation of pronuclei between fertilized eggs. In all cases, the transferred genetic material arises from a normal meiosis and should therefore, not be confused with cloning. The scientific progress and associated regulatory issues are discussed. Stem Cells 2015;33:639–645

Repair of N-methylpurines in the mitochondrial DNA of xeroderma pigmentosum complementation group D cells.

Abstract: Previous work from our laboratory has shown that mitochondria are able to repair N-methylpurines formed by methylnitrosourea (MNU). However, it is unclear as to whether repair mechanisms that remove this type of lesion in nuclear DNA also remove these adducts in mitochondria. To address this question, we studied repair of MNU-induced N-methylpurines in the mitochondrial DNA from xeroderma pigmentosum complementation group D (XP-D) cells using quantitative Southern blot analysis and 32P-end-labeling techniques. These cells have been reported to be defective in the repair of this type of lesion in their nuclear genome. WI 38 cells were used as normal controls for these studies. Both XP-D fibroblasts and WI 38 cells were exposed to 0.5 mM MNU for 1 h. Following an 8 h repair period, 61% of N-methylpurines were repaired in the mitochondrial genome of XP-D cells and 39% of these lesions were repaired in WI 38 cells. After 24 h, XP-D cells had repaired 77% of the N-methylpurines in their mitochondrial genome, while WI 38 cells had 44% repair of this type of damage. During this same 24 h time period, 81.5% of the N7-methylguanines had been removed from the total cellular DNA of the WI 38 cells compared to only 38.3% repair of this lesion in the XP-D cells. Thus, XP-D cells, though deficient in the repair of N-methylpurines in their nuclear genome, are proficient in the repair of this type of damage in their mitochondria, suggesting that the mechanisms to repair N-methylpurines in the nuclear and mitochondrial genomes of these cells are different.

Identification of ancient remains through genomic sequencing

Abstract: Studies of ancient DNA have been hindered by the preciousness of remains, the small quantities of undamaged DNA accessible, and the limitations associated with conventional PCR amplification. In these studies, we developed and applied a genomewide adapter-mediated emulsion PCR amplification protocol for ancient mammalian samples estimated to be between 45,000 and 69,000 yr old. Using 454 Life Sciences (Roche) and Illumina sequencing (formerly Solexa sequencing) technologies, we examined over 100 megabases of DNA from amplified extracts, revealing unbiased sequence coverage with substantial amounts of nonredundant nuclear sequences from the sample sources and negligible levels of human contamination. We consistently recorded over 500-fold increases, such that nanogram quantities of starting material could be amplified to microgram quantities. Application of our protocol to a 50,000-yr-old uncharacterized bone sample that was unsuccessful in mitochondrial PCR provided sufficient nuclear sequences for comparison with extant mammals and subsequent phylogenetic classification of the remains. The combined use of emulsion PCR amplification and high-throughput sequencing allows for the generation of large quantities of DNA sequence data from ancient remains. Using such techniques, even small amounts of ancient remains with low levels of endogenous DNA preservation may yield substantial quantities of nuclear DNA, enabling novel applications of ancient DNA genomics to the investigation of extinct phyla.