Trends in Genetics
Genome AnalysisA significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions
Section snippets
MAR in the J-C intron of Igκ gene
MARs in the rabbit and mouse Igκ genes (MARIgκ) were identified experimentally next to the intronic enhancer, and in human MARIgκ was predicted on the basis of sequence conservation [12]. MARIgκ performs important biological functions: the mouse Igκ gene construct without MARIgκ exhibits low and erratic expression in transgenic mice [17] and somatic hypermutation is reduced in MARIgκ-knockout mice [18]. The dot matrix alignment (ftp://ncbi.nih.gov/pub/kondrashov/MAR/align.zip) revealed
Predicted MARs in human–mouse orthologous genomic contigs
As already mentioned, MARs are among the few functionally characterized long noncoding sequences in eukaryotic genomes. Because the functions of the human–mouse HITs are largely unknown, we sought to determine whether these regions overlapped with MARs. To this end, we predicted MARs using the ChrClass program (ftp://ncbi.nih.gov/pub/kondrashov/MAR/Chrclass.zip; [9]). The observed frequencies of predicted MARs per 1000 bases (1 kb) did not differ significantly between mouse and human
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