The mapping of cis-elements to genes was obtained using motif discovery algorithms, PhyloCon and Converge, with binding p-value less than 0.001 and conservation in at least 0, 1 or 2 other yeast species [ 26].
Our results provide an example where inter-individual variation in DNA methylation acts as a modifier of genetic influences on gene expression and may interfere with genetic mapping of cis-regulatory polymorphisms by attenuating the genetic effect on transcription and thereby the significance of genetic association results as in the case of the ZPBP2 gene.
One recent study reports the mapping of cis-regulatory variants in a small set of genes to haplotype blocks in human samples [ 60], and another recent study reports the investigation of cis-regulatory variations in 3' UTRs of a set of genes showing cis-acting regulation in a panel of mouse recombinant congenic strains [ 61].
We used the observed/expected Hi-C maps, which we calculated from the 20 kb iteratively corrected interaction maps of cis-interactions by dividing each diagonal of a matrix by its chromosome-wide average value.
In the line of previous studies [1] [5], we could build a detailed map of cis-regulated eQTLs in monocytes.
They combined these data with an improved epigenetic map of cis-regulatory elements for immune cell (34).
To derive a more complete map of cis-eQTLs in this population, we used publicly available SNP data from 48 classical inbred strains to map SNP-based eQTLs http://www.broadinstitute.org/mouse/hapmap/.org/mouse/hapmap/
Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S,, 2012, A draft map of cis-regulatory sequences in the mouse genome, GSE29184 ; http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi acc=GSE29184, Publicly available at NCBI GEO (http://www.ncbi.nlm.nih.gov/geo/ ).nih.gov/geo/
We have mapped thousands of cis- and trans-eQTLs in four tissues (fat, kidney, adrenal and left ventricle) in a large panel of rat recombinant inbred (RI) strains.
The simultaneous availability of genome-wide SNP analysis enabled further fine mapping of the cis-eQTLs, which showed that common SNPs accounted for 45% of the loci with AEI (when sequences up to 250 kb upstream and downstream were included) [ 5].
