The Mitochondrial Genome Is a “Genetic Sanctuary” during the Oncogenic Process

Since Otto Warburg linked mitochondrial physiology and oncogenesis in the 1930s, a number of studies have focused on the analysis of the genetic basis for the presence of aerobic glycolysis in cancer cells. However, little or no evidence exists today to indicate that mtDNA mutations are directly responsible for the initiation of tumor onset. Based on a model of gliomagenesis in the mouse, we aimed to explore whether or not mtDNA mutations are associated with the initiation of tumor formation, maintenance and aggressiveness. We reproduced the different molecular events that lead from tumor initiation to progression in the mouse glioma. In human gliomas, most of the genetic alterations that have been previously identified result in the aberrant activation of different signaling pathways and deregulation of the cell cycle. Our data indicates that mitochondrial dysfunction is associated with reactive oxygen species (ROS) generation, leading to increased nuclear DNA (nDNA) mutagenesis, but maintaining the integrity of the mitochondrial genome. In addition, mutational stability has been observed in entire mtDNA of human gliomas; this is in full agreement with the results obtained in the cancer mouse model. We use this model as a paradigm of oncogenic transformation due to the fact that mutations commonly found in gliomas appear to be the most common molecular alterations leading to tumor development in most types of human cancer. Our results indicate that the mtDNA genome is kept by the cell as a “genetic sanctuary” during tumor development in the mouse and humans. This is compatible with the hypothesis that the mtDNA molecule plays an essential role in the control of the cellular adaptive survival response to tumor-induced oxidative stress. The integrity of mtDNA seems to be a necessary element for responding to the increased ROS production associated with the oncogenic process

Reconstructing the Indian Origin and Dispersal of the European Roma: A Maternal Genetic Perspective

Previous genetic, anthropological and linguistic studies have shown that Roma (Gypsies) constitute a founder population dispersed throughout Europe whose origins might be traced to the Indian subcontinent. Linguistic and anthropological evidence point to Indo-Aryan ethnic groups from North-western India as the ancestral parental population of Roma. Recently, a strong genetic hint supporting this theory came from a study of a private mutation causing primary congenital glaucoma. In the present study, complete mitochondrial control sequences of Iberian Roma and previously published maternal lineages of other European Roma were analyzed in order to establish the genetic affinities among Roma groups, determine the degree of admixture with neighbouring populations, infer the migration routes followed since the first arrival to Europe, and survey the origin of Roma within the Indian subcontinent. Our results show that the maternal lineage composition in the Roma groups follows a pattern of different migration routes, with several founder effects, and low effective population sizes along their dispersal. Our data allowed the confirmation of a North/West migration route shared by Polish, Lithuanian and Iberian Roma. Additionally, eleven Roma founder lineages were identified and degrees of admixture with host populations were estimated. Finally, the comparison with an extensive database of Indian sequences allowed us to identify the Punjab state, in North-western India, as the putative ancestral homeland of the European Roma, in agreement with previous linguistic and anthropological studies

Transcriptional activity and strain-specific history of mouse pseudogenes

Abstract: Pseudogenes are ideal markers of genome remodelling. In turn, the mouse is an ideal platform for studying them, particularly with the recent availability of strain-sequencing and transcriptional data. Here, combining both manual curation and automatic pipelines, we present a genome-wide annotation of the pseudogenes in the mouse reference genome and 18 inbred mouse strains (available via the mouse.pseudogene.org resource). We also annotate 165 unitary pseudogenes in mouse, and 303, in human. The overall pseudogene repertoire in mouse is similar to that in human in terms of size, biotype distribution, and family composition (e.g. with GAPDH and ribosomal proteins being the largest families). Notable differences arise in the pseudogene age distribution, with multiple retro-transpositional bursts in mouse evolutionary history and only one in human. Furthermore, in each strain about a fifth of all pseudogenes are unique, reflecting strain-specific evolution. Finally, we find that ~15% of the mouse pseudogenes are transcribed, and that highly transcribed parent genes tend to give rise to many processed pseudogenes

Role of Pleiotropy in the Evolution of a Cryptic Developmental Variation in Caenorhabditis elegans

Using vulval phenotypes in Caenorhabditis elegans, the authors show that cryptic genetic variation can evolve through selection for pleiotropic effects that alter fitness, and identify a cryptic variant that has conferred enhanced fitness on domesticated worms under laboratory conditions

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.

We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains and find extensive strain-specific haplotype variation. We identify and characterize 2,567 regions on the current mouse reference genome exhibiting the greatest sequence diversity. These regions are enriched for genes involved in pathogen defence and immunity and exhibit enrichment of transposable elements and signatures of recent retrotransposition events. Combinations of alleles and genes unique to an individual strain are commonly observed at these loci, reflecting distinct strain phenotypes. We used these genomes to improve the mouse reference genome, resulting in the completion of 10 new gene structures. Also, 62 new coding loci were added to the reference genome annotation. These genomes identified a large, previously unannotated, gene (Efcab3-like) encoding 5,874 amino acids. Mutant Efcab3-like mice display anomalies in multiple brain regions, suggesting a possible role for this gene in the regulation of brain development

Specificity of mtDNA-directed PCR-influence of NUclear MTDNA insertion (NUMT) contamination in routine samples and techniques.

Nuclear mitochondrial insertions (NUMTs) are sequences homologous to mtDNA, which are present throughout the human nuclear genome. The possibility that these sequences may be accidentally amplified in reactions directed to mtDNA has been raised and evaluated by different groups and by different means. Despite that, data is still missing on the specificity of PCRs in routine procedures in what concerns contamination with nuclear mtDNA insertions (NUMTs). In this work, we performed PCR sequencing reactions with primers directed either to mitochondrial or to NUMT DNA with different annealing temperatures and in different tissues. We observed that (a) contamination with NUMTs depends on the sample and tissue, and (b) employing routine techniques, there is no risk of co-amplification. Only when mtDNA is almost completely removed from the samples does the number of NUMT copies exceed mitochondrial sequences, i.e., only in samples with virtually no mtDNA, such as those resulting from preferential semen lysis, is there a risk of accidental amplification of NUMTs. We suggest that to evaluate a possible co-amplification of NUMT DNA, it is more relevant to take into account sample processing and original tissue of the samples, and consequently the relative proportions of NUMT and mtDNA, rather than the presence of NUMTs by itself, irrespectively of its proportion.This work was partially supported by Fundação para a Ciência e a Tecnologia through a research grant to A.G. (SFRH/BD/16518/2004) and by “Programa Operacional Ciência, e Inovação 2010” (POCI 2010), VI Programa-Quadro (2002–2006)

MtDNA single macrodeletions associated with myopathies: absence of haplogroup-related increased risk

As for any non-recombining genome, any mutation at mtDNA, if not recurrent, appears on a particular haplotype background, allowing its detection by haplogroup association studies. It has been shown that the propensity for occurrence of single macrodeletions at a level beyond the pathological threshold is associated with super-haplogroup U/K. However, in this report, we present evidence for the absence of preferential haplogroup backgrounds for single macrodeletions. We have analysed how haplogroup diagnostic polymorphisms could disrupt direct repeats usually flanking the deleted segment, and we have concluded that for the Common Deletion, no such polymorphisms are observed in humans, but they do occur in other primates. Furthermore, we also report five new single macrodeletions.This work was partially supported by a PhD grant to AG (SFRH/BD/16518/2004) from Fundacao para a Ciencia e a Tecnologia and IPATIMUP by Programa Operacional Ciencia, Tecnologia e Inovacao (POCTI), Quadro Comunitario de Apoio III