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Many of these differentially expressed miRNA genes are clustered together in the mouse genome (Figure 1B).
To test this hypothesis, we performed E2f4 chromatin immunoprecipitations in seven primary mouse tissues and a mouse cell line using promoter microarrays representing 13,000 regions in the mouse genome (Figure 2B).
To investigate the pattern of imprinting status for all the transcripts covered by our study, we plotted the 5,076 unique Entrez genes with counts of four or more in both reciprocal crosses across the mouse genome (Figure 5; Figure S1.14).
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Proximal promoter arrays targeted to transcription start sites capture the large majority of E2F4-chromatin interactions in the genome [8], [14]; we confirmed this result using whole-chromosome arrays that indicated that E2F4 binds largely at transcriptional start sites within the human and mouse genomes (Figure S1).
The marker genes are scattered over the entire mouse genome [see Figure 3 in Additional file 1].
We detected breakpoints on the human genome using the software Cassis [ 7], and grouped them by pairs such that each distant pair in the human genome corresponds to adjacent loci in the mouse genome (see Figure 1 and Methods).
These results were compared to the initial number of human genomes in Figure 4B and percent of initial mouse genomes in Figure 4C.
Two of these three sites are highly conserved in the human and mouse genomes (SI. Figure S4b).
A simple comparison between the surveys of mouse and human homeobox loci highlights the higher number of homeobox loci found in the mouse genome, although this figure is heavily influenced by the extensive Obox and Rhox arrays.
HIV integration sites were mapped to the mouse genome (Supplementary information, Figure S1I).
This site was located between the two upstream untranslated Cbx5 exons at position 103,049,787 bp (mouse genome assembly NCBI37/mm9; Figure 1A) on chromosome 15 (Kent et al. 2002; Fujita et al. 2011).
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