Journal Article

The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser

Attimonelli, Marcella, Calabrese, Francesco Maria, Lang, Martin, Gasparre, Giuseppe, Simone, Domenico

2011

Overview

Background Eukaryotic nuclear genomes contain fragments of mitochondrial DNA called NumtS (Nuclear mitochondrial Sequences), whose mode and time of insertion, as well as their functional/structural role within the genome are debated issues. Insertion sites match with chromosomal breaks, revealing that micro-deletions usually occurring at non-homologous end joining loci become reduced in presence of NumtS. Some NumtS are involved in recombination events leading to fragment duplication. Moreover, NumtS are polymorphic, a feature that renders them candidates as population markers. Finally, they are a cause of contamination during human mtDNA sequencing, leading to the generation of false heteroplasmies. Results Here we present RHNumtS.2, the most exhaustive human NumtSome catalogue annotating 585 NumtS, 97% of which were here validated in a European individual and in HapMap samples. The NumtS complete dataset and related features have been made available at the UCSC Genome Browser. The produced sequences have been submitted to INSDC databases. The implementation of the RHNumtS.2 tracks within the UCSC Genome Browser has been carried out with the aim to facilitate browsing of the NumtS tracks to be exploited in a wide range of research applications. Conclusions We aimed at providing the scientific community with the most exhaustive overview on the human NumtSome, a resource whose aim is to support several research applications, such as studies concerning human structural variation, diversity, and disease, as well as the detection of false heteroplasmic mtDNA variants. Upon implementation of the NumtS tracks, the application of the BLAT program on the UCSC Genome Browser has now become an additional tool to check for heteroplasmic artefacts, supported by data available through the NumtS tracks.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Animal Genetics and Genomics / Biomedical and Life Sciences / Cell Nucleus - metabolism / Chromosomes, Human / Cloning / Contamination / Databases, Genetic / Deoxyribonucleic acid / DNA / DNA, Mitochondrial - chemistry / DNA, Mitochondrial - genetics / Genetic variation / Genetics / Genomes / Genomics / heteroplasmy / Human and rodent genomics / Humans / Karyotype / Life Sciences / Microarrays / Microbial Genetics and Genomics / Mitochondria - genetics / Mitochondrial DNA / Non-homologous end joining / Nucleotide sequence / Physiological aspects / Plant Genetics and Genomics / Polymerase chain reaction / Proteomics / Protocol / Recombination / Reproducibility of Results / Research Article / Reviews / Software / Structure-function relationships