The normal situation is that all the copies of mtDNA within the cell are identical and have wild-type mtDNA sequence.
Cell lines with 4 copies of the DRIM gene (SK-BR-3, MCF7, T47D) had only ~25% of NM2C5 DRIM transcript levels and half of that expressed by M4A4 cells, even though these cell lines had double the copies of DRIM within their genome.
The enhanced green fluorescent protein (GFP) gene was cloned between the unique sites such that the inserted gene was transcribed from TRS2 which was located upstream within ORF1b, while the copy of TRS6 drives ORF2a/b transcription.
We first challenge the hypothesis that the conserved motifs they observed in 5'UTRs are present within the genomic copies of numerous unrelated RP genes.
This is typical of recent or active TE families, in which the copy number increases faster than the accumulation of mutations within the copies (Lerat et al. 2011; Staton et al. 2012).
In single individuals, more than one different deletion has been found in one and the same patient, either within the same copy of chromosome 7 with retention of sequences between the deleted regions or within different cell clones [ 28, 29].
Because GRIMM cannot deal with duplicated genes and requires that the compared genomes have the same gene content, genes within one of the two copies of the IR were excluded and only the genes common to all the compared genomes were analysed.
The large repeat regions within the genome (two copies of the 33.9 kb pathogenicity island, together with three copies of a ∼3 kb repeat region consisting of a gene with no known homologues, flanked by an ISFtu1 element and an ISFtu2 element) were resolved by long PCR amplification of the entire repeats (using two overlapping long PCRs in the case of the 33.9 kb islands).
For these analyses, genes within one of the two copies of the IR were excluded from the data set, and the SSC and LSC + IR regions were considered as two separate chromosomes.
For these analyses, genes within one of the two copies of the IR were excluded from the data set and only the genes common to all compared genomes were analyzed.
