In Genome Biology this week, two papers describe methods for sequence capture. In one, scientists led by Olivier Harismendy and Kelly Frazer at the University of California, San Diego, used oligo capture probes in solution to select for approximately 3.6 megabases of sequence target. The approach, they say, generated sequence data with sensitivity to detect 93 percent of SNPs with a calling accuracy greater than 99 percent. In another, Broad Institute researchers used targeted RNA-Seq to probe gene expression in cancer. Upon hybridizing tumor cDNA and oligos specific for 467 cancer-related genes, the method "showed high selectivity, improved mutation detection enabling discovery of novel chimeric transcripts, and provided RNA expression data," they say.
The Dana-Farber Cancer Institute's Xiaobo Xia and Andrew Kung used ChIP-chip and gene expression profiling to study the genes activated by hypoxia. Looking at two cell lines, they discovered that under hypoxic conditions, the transcription factor hypoxia-inducible factor 1 (HIF-1) binds first to loci that are already active and that are "characterized by the presence of histone H3 lysine 4 methylation, the presence of RNA polymerase II, and basal production of mRNA," they say, suggesting that genes active in a cell defines genes that can be activated by transcription factors that respond to stimuli.
Korean scientists led by Beom-Seok Park at the National Academy of Agricultural Science have used comparative tiling sequencing to compare the genomes of Arabidopsis and Brassica rapa, a widely cultivated plant. Looking at 65.8 megabases of assembled sequence data, they found that even though it's been triplicated, the B. rapa genome has only twice the content gene-wise of Arabidopsis and that whole genome triplication occurred recently. "Based on a comparative analysis of the B. rapa sequences and the Arabidopsis genome, it appears that polyploidy and chromosomal diploidization are ongoing processes that collectively stabilize the B. rapa genome and facilitate its evolution," they write.
Finally, Cizhong Jiang at Tongji University, Shanghai, and B. Franklin Pugh at Penn State have created a reference map of nucleosome positions across the Saccharomyces cerevisiae genome. They referred to six different high-resolution, genome-wide maps of nucleosome positions to build it, and the data, software, and browser are available for download here.