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. 2014 Jan;42(Database issue):D1261-8.
doi: 10.1093/nar/gkt982. Epub 2013 Oct 28.

MitoBreak: the mitochondrial DNA breakpoints database

Joana Damas  1 , João Carneiro, António Amorim, Filipe Pereira
Affiliations

MitoBreak: the mitochondrial DNA breakpoints database

Joana Damas et al. Nucleic Acids Res. 2014 Jan.

Abstract

Mitochondrial DNA (mtDNA) rearrangements are key events in the development of many diseases. Investigations of mtDNA regions affected by rearrangements (i.e. breakpoints) can lead to important discoveries about rearrangement mechanisms and can offer important clues about the causes of mitochondrial diseases. Here, we present the mitochondrial DNA breakpoints database (MitoBreak; http://mitobreak.portugene.com), a free, web-accessible comprehensive list of breakpoints from three classes of somatic mtDNA rearrangements: circular deleted (deletions), circular partially duplicated (duplications) and linear mtDNAs. Currently, MitoBreak contains >1400 mtDNA rearrangements from seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Macaca mulatta, Drosophila melanogaster, Caenorhabditis elegans and Podospora anserina) and their associated phenotypic information collected from nearly 400 publications. The database allows researchers to perform multiple types of data analyses through user-friendly interfaces with full or partial datasets. It also permits the download of curated data and the submission of new mtDNA rearrangements. For each reported case, MitoBreak also documents the precise breakpoint positions, junction sequences, disease or associated symptoms and links to the related publications, providing a useful resource to study the causes and consequences of mtDNA structural alterations.

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Figures

Figure 1.
Figure 1.
Schematic representation of a circular deleted (A), circular partially duplicated (B), full-length linear (C) and short linear (D) mtDNA molecule. The first (5′) and second (3′) breakpoints in the reference mtDNA L-strand define an mtDNA deletion or duplication. The proximal retained regions of the 5′ breakpoint (5fl; 5′ flanking; dark blue section) and 3’ breakpoint (3fl; 3′ flanking; dark red section) are found in mtDNA deletions and duplications (occurring twice in duplicated mtDNA). The proximal deleted regions of the 5′ breakpoint (5del; 5′ deleted; light blue section) and 3′ breakpoint (3del; 3′ deleted; light red section) are removed in mtDNA deletions. Full-length linear mtDNA is defined by a single breakpoint and has no deleted sections. Shorter linear mtDNAs are defined by two breakpoints.
Figure 2.
Figure 2.
The positioning of the breakpoints in the presence of direct repeats. (A) The precise location of the 5′ and 3′ breakpoints is unknown for several reported mtDNA rearrangements because of the presence of direct repeats (underlined, bold letters). (B) When only one copy of the direct repeat is maintained, the 5′ and 3′ breakpoints were placed downstream (on the right) of the homology, according to the L-strand numbering. (C) Representation of the possible number of direct repeats (DR) retained in the rearrangement junction of mtDNA deletions and duplications. When the breakpoints are located in a DR, the resulting junction sequence can retain 0, 1 or 2 copies of the repeated motif (green box).
Figure 3.
Figure 3.
The general statistics section of MitoBreak for a dataset with mtDNA deletions. This section provides a series of descriptive analyses such as (A) deletion lengths, (B) breakpoint distributions, (C) analysis by group, (D) locations of the deleted regions and (E) mtDNA circular visualization. The button opening each analysis is shown in grey.
Figure 4.
Figure 4.
The individual page section of MitoBreak for a mtDNA deletion. This section describes for each rearrangement: (A) general characteristics of the selected rearrangement, (B) clinical or phenotypical groups where the rearrangement was found, (C) flanking sequences with highlighted direct repeats, (D) location of the 5′ and 3′ breakpoints in a 2D plot, (E) circular representation of the rearranged mtDNA region, (F) rearrangement length in comparison with the full dataset and (G) references.
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