Pathological ribonuclease H1 causes R-loop depletion and aberrant DNA segregation in mitochondria

Abstract

The genetic information in mammalian mitochondrial DNA is densely packed; there are no introns and only one sizeable noncoding, or control, region containing key cis-elements for its replication and expression. Many molecules of mitochondrial DNA bear a third strand of DNA, known as "7S DNA," which forms a displacement (D-) loop in the control region. Here we show that many other molecules contain RNA as a third strand. The RNA of these R-loops maps to the control region of the mitochondrial DNA and is complementary to 7S DNA. Ribonuclease H1 is essential for mitochondrial DNA replication; it degrades RNA hybridized to DNA, so the R-loop is a potential substrate. In cells with a pathological variant of ribonuclease H1 associated with mitochondrial disease, R-loops are of low abundance, and there is mitochondrial DNA aggregation. These findings implicate ribonuclease H1 and RNA in the physical segregation of mitochondrial DNA, perturbation of which represents a previously unidentified disease mechanism.RNase H1 | R-loop | mitochondrial DNA | DNA segregation | mitochondrial disease

LETM 1 couples mitochondrial DNA metabolism and nutrient preference

“…A growing number of mitochondrial disorders are now understood to feature mtDNA aggregation or clustering (Almalki et al , ; Akman et al , ; Desai et al , ; Nicholls et al , and this report). Clustering of the different complexes appears to be remarkably well tolerated, in that OXPHOS subunits continue to be produced and assembled correctly in the vicinity of the mtDNA aggregates, as respiratory capacity can remain at normal levels ().…”

DNA Topoisomerase I differentially modulates R-loops across the human genome

“…Increased R-loop formation in RNase H-deficient yeast strains subjected to Top1 inhibition led to origin-independent DNA replication initiation in the rDNA [28]. Finally, the mitochondrial genome is thought to initiate DNA replication priming through R-loop intermediates [70][71][72] and a recent study showed that replication origins are specified in an R-loop dependent manner at murine class switch immunoglobulin regions [73].…”

Assisted reproductive technologies to prevent human mitochondrial disease transmission

“…However, D-loop functionality also depends on factors encoded by the nucleus, including RNASEH1 (ref. 49), which might affect the risk of reversion. Another suggestion is that perinuclear mitochondria are somehow preferentially replicated 50 .…”