Project description:Mitochondrial genomes are separated from the nuclear genome for most of the cell cycle by the nuclear double membrane, intervening cytoplasm and the mitochondrial double membrane. Despite these physical barriers we show that somatically acquired mitochondrial-nuclear genome fusion sequences are present in cancer cells. Most occur in conjunction with intranuclear genomic rearrangements and the features of the fusion fragments indicate that non-homologous end joining and/or replication-dependent DNA double strand break repair are the dominant mechanism involved. This study includes 12 pairs of whole-genome sequences (tumour and paired-normal), which present somatic mitochondrial DNA integrations in tumour genomes. Reference: Young Seok Ju et al., Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells, Genome Research (2015).

| EGAS00001001234 | EGA

Interactions between mitochondrial and nuclear DNA in mammalian cells are non-random

Project description:There is evidence for the on-going recurrent transfer of mitochondrial DNA (mtDNA) into the nucleus in both germ line and somatic cells. However, the outcomes associated with the transfer of mtDNA into somatic cell nuclei are poorly understood. High-resolution Chromosome Conformation Capture (HiC) techniques, which are used to identify global patterns of chromatin interactions, regularly capture physical interactions between mitochondrial and nuclear DNA (i.e. mito-nDNA interactions) in mammalian cells. These mito-nDNA interactions are routinely considered a consequence of nonspecific ligation events during chromatin library preparation. Here, we have evaluated mito-nDNA interactions captured by HiC in six human cell lines, and by Circular Chromosome Conformation Capture (4C) in mouse cortical astrocytes. We show that mito-nDNA interactions are statistically significant and shared between biological and technical replicates in the HiC and 4C experiments. The most frequent interactions between mtDNA and nuclear loci in the HiC and 4C data occur with repetitive DNA sequences including the centromeric regions in the six human cell lines and 18S rDNA in mouse cortical astrocytes. Such findings confirm previous observations of mtDNA forming interactions with rDNA genes in budding yeast and centomeres in rat bone marrow cells. Finally the mitochondrial D-loop tends to be enriched in the captured mito-nDNA interactions. Collectively our results imply a degree of selective regulation in the identity of the interacting mitochondrial partners confirming that mito-nDNA interactions in mammalian cells are not random.

2017-11-21 | GSE77610 | GEO

Mesenchymal Stem Cells Transfer Mitochondria to the Cells with Virtually Absent Mitochondrial Function but Not to the Cells Harboring Pathogenic Mitochondrial DNA Mutations

Project description:It has been reported that human mesenchymal stem cells (MSCs) can transfer mitochondria to the cells with severely compromised mitochondrial function. We tested whether MSCs transfer mitochondria to the cells under several different conditions of mitochondrial dysfunction, including human pathogenic mitochondrial DNA (mtDNA) mutations. Using biochemical selection methods, we found that exponentially growing cells in restrictive media (uridine and bromodeoxyuridine [BrdU]+) after coculture of MSCs (uridine-independent and BrdU-sensitive) and 143B-derived cells with severe mitochondrial dysfunction induced by either long-term ethidium bromide treatment or short-term rhodamine 6G (R6G) treatment (uridine-dependent but BrdU-resistant). The exponentially growing cells had nuclear DNA fingerprint patterns identical to 143B, and a sequence of mtDNA identical to the MSCs. Since R6G causes rapid and irreversible damage to mitochondria without the removal of mtDNA, the mitochondrial function appears to be restored through a direct transfer of mitochondria rather than mtDNA alone. Conditioned media, which were prepared by treating mtDNA-less 143B 0 cells under uridine-free condition, induced increased chemotaxis in MSC, which was also supported by transcriptome analysis. A chemotaxis inhibitory agent blocked mitochondrial transfer phenomenon in the above condition. However, we could not find any evidence of mitochondrial transfer to the cells harboring human pathogenic mtDNA mutations (A3243G mutation or 4,977 bp deletion). Thus, the mitochondrial transfer is limited to the condition of a near total absence of mitochondrial function. Elucidation of the mechanism of mitochondrial transfer will help us create a potential “cell therapy-based mitochondrial restoration or mitochondrial gene therapy” for human diseases caused by mitochondrial dysfunction. time series

2011-11-22 | E-GEOD-33831 | biostudies-arrayexpress

Transfer of mitochondrial DNA into the nuclear genome during gene editing [ND5.3 PEM-seq]

Project description:Mitochondria serve as the cellular powerhouse, and their distinct DNA makes them a prospective target for gene editing to treat genetic disorders. However, the impact of genome editing on mitochondrial DNA (mtDNA) stability remains a mystery. Our study reveals previously unknown risks of genome editing that both nuclear and mitochondrial editing cause broad transfer of mitochondrial DNA segments into the nuclear genome in various cell types including human cell lines, primary T cells, and mouse embryos. Furthermore, drug-induced mitochondrial stresses and mtDNA breaks exacerbate this transfer of mtDNA into the nuclear genome. Notably, we observe that mitochondrial targeting editors, mitoTALEN and recently developed base editor DdCBE, can also induce widespread mtDNA integrations. However, we provide a practical solution to suppress mtDNA transfer by co-expressing TREX1 or TREX2 exonucleases during DdCBE editing. These findings also shed light on the origins of mitochondrial-nuclear DNA segments.

2024-09-24 | GSE248511 | GEO

Transfer of mitochondrial DNA into the nuclear genome during gene editing [mitoTALEN_ND4 PEM-seq]

2024-09-24 | GSE248510 | GEO

Transfer of mitochondrial DNA into the nuclear genome during gene editing [CBE_ND4 PEM-seq]

2024-09-24 | GSE248509 | GEO

Transfer of mitochondrial DNA into the nuclear genome during gene editing [PEM-seq]

2024-09-24 | GSE248164 | GEO