As shown in Figure 4A, the average rate of non-synonymous changes (dN) observed in human mouse alignments is 51% higher in the most closed chromatin regions of the genome than in the most open regions.
Predicted CpG islands acquired from the UCSC Genome Browser are shown in green, and chained human-mouse alignments are shown in olive green.
However, intriguingly, when human-mouse alignments are examined, the introns of tissue-specific genes have been shown to contain a greater proportion of conserved sequence than those of housekeeping genes [ 12] (in contradiction to what is observed in human-chimpanzee alignments).
Whole genome pairwise human-mouse alignments were downloaded from the UCSC Genome Bioinformatics website ([ 18]; build 32, Nov. 2003).
The human-mouse alignment was created by aligning both genomes using blastz [ 104].
The tables for gene mapping, SNP mapping and Human-Mouse alignment were obtained from ensemble, dbSNP, HGVBASE and UCSC and installed locally.
UCSC alignments, on the other hand, are based on blastz pairwise alignments, which are not symmetric – a human-mouse alignment is different from a mouse-human alignment in general.
Only the mouse-rat pairwise alignments are used for comparisons with the human genome and all other sequence regions from mouse and rat are discarded.
When identical breakpoint regions fell into different categories according to the human or mouse alignments, they were discarded from the global analysis because they could represent regions of breakpoint reuse.
Multiple alignments between human, mouse and fugu sequences were preferred over pair-wise alignments between human and fugu sequences, because multiple alignments are generally more selective (fewer false positives) than pair-wise alignments in the detection of regulatory elements [ 26].
Matches corresponding to the coordinates of the retained intron plus parts of the flanking exons (at least -20 nt upstream and +20 nt downstream) were accepted as evidence of intron retention in the mouse (only spliced alignments were accepted).
