Continued colonization of the human genome by mitochondrial DNA

Abstract

Integration of mitochondrial DNA fragments into nuclear chromosomes (giving rise to nuclear DNA sequences of mitochondrial origin, or NUMTs) is an ongoing process that shapes nuclear genomes. In yeast this process depends on double-strand-break repair. Since NUMTs lack amplification and specific integration mechanisms, they represent the prototype of exogenous insertions in the nucleus. From sequence analysis of the genome of Homo sapiens, followed by sampling humans from different ethnic backgrounds, and chimpanzees, we have identified 27 NUMTs that are specific to humans and must have colonized human chromosomes in the last 4-6 million years. Thus, we measured the fixation rate of NUMTs in the human genome. Six such NUMTs show insertion polymorphism and provide a useful set of DNA markers for human population genetics. We also found that during recent human evolution, Chromosomes 18 and Y have been more susceptible to colonization by NUMTs. Surprisingly, 23 out of 27 human-specific NUMTs are inserted in known or predicted genes, mainly in introns. Some individuals carry a NUMT insertion in a tumor-suppressor gene and in a putative angiogenesis inhibitor. Therefore in humans, but not in yeast, NUMT integrations preferentially target coding or regulatory sequences. This is indeed the case for novel insertions associated with human diseases and those driven by environmental insults. We thus propose a mutagenic phenomenon that may be responsible for a variety of genetic diseases in humans and suggest that genetic or environmental factors that increase the frequency of chromosome breaks provide the impetus for the continued colonization of the human genome by mitochondrial DNA.

Figure 1. Polymorphism of NUMTs 18-192, 1-74, and 2-53

The polymorphism of NUMTs 18-192, 1-74, and 2-53 as revealed by PCR amplification and electrophoresis of the products on 2% agarose gels. For each locus, the upper arrow indicates the fragment that contains the NUMT, and the lower arrow indicates the fragment that does not contain the NUMT. The individual tested is indicated above. The (+/+) are homozygous positive, (+/−) are heterozygotes, and (−/−) are homozygous negative.

Figure 2. Sequence Insertion Polymorphism of Six NUMTs

Sequence of NUMTs 1-74, 2-53, 2-132, 12-89,13-75 and 18-192 are indicated in lower case and the flanking sequences in capital letters. Underlined letters represent nucleotides homologous to both the mt and the chromosomal sequences (microhomology). Bold and italicized letters correspond to nucleotide additions, following the NUMTs insertion, which are absent from the −/− individuals. The individuals sequenced are indicated in Table 2. In all cases the sequence corresponded to the one available on the human genome public Web sites. Boxes represent exon sequences. In 12-89, the exon sequence would extend till the stop codon (taa).

Figure 3. Distribution of Human-Specific NUMTs in Chromosomes

A scale representation of the human chromosomes. The location of human-specific NUMTs is indicated with a red arrow. A green arrow indicates the position of NUMTs showing insertion polymorphism in humans, and a blue arrow indicates a previously described NUMT (11-541).

Figure 4. Human-Specific NUMTs in Human Chromosomes

For each human chromosome, indicated on the x-axis, the number of NUMTs (y-axis, on the left) common to human and chimpanzee (white columns) and specific to humans (black columns) are shown. An open circle indicates the chromosome size in millions of base pairs (Mbp; y-axis on the right).

Figure 5. Insertion Sites of NUMTs in the Human Genome

Histogram of the insertion sites of NUMTs in the human genome. Only NUMTs tested in human and in chimpanzee samples are shown. This includes the 27 NUMTs specific to humans and absent from chimpanzees (21 present in all individuals tested and 6 with insertion polymorphism in humans), one additional NUMT with insertion polymorphism, previously described, see text, and 14 NUMTs common to human and chimpanzee, out of 183 found by BLAST search. Colors of the blocks indicate the different target sites. For details see Table 3.

Figure 6. Scheme Representing Some NUMT Insertions in Genes

Four known or predicted genes, found in loci with NUMT insertion in humans, have been schematically represented either in the absence (A) or in the presence (B) of the insertion. Boxes represent exons, and thick lines represent introns. Red boxes and lines indicate the sequence corresponding to the NUMT, which has been identified for each case. A dotted line in (A) indicates that, in the absence of insertion, the exon/intron pattern was not identified by gene identification programs. Representation not to scale.