In a paper published online in advance in Genome Research this week, researchers at Belgium's Katholieke Universiteit Leuven and their colleagues at Harvard report on the existence of "disallowed genes" — those, that until now, have been considered ubiquitously expressed, housekeeping genes, but are not expressed in one tissue. In constructing a multi-tissue panel of genome-wide mRNA expression data, the team found that the tissue-specific repression of housekeeping genes can lead to disease. "We propose that disallowed genes need to be repressed in the specific target tissue to ensure correct tissue function," the authors write.
In another Genome Research preprint, investigators at Switzerland's University of Lausanne show that "copy number variation modifies expression time-courses" in a somewhat dose-dependent manner, such that they affect genes located on their flanks and sometimes even "those at a great distance from their boundary." The Lausanne team monitored the effects of CNVs on gene expression during mouse development. The researchers found that "some brain-expressed genes mapping within CNVs appear to be under compensatory loops only at specific time-points, indicating that the effect of CNVs on these genes is modulated during development," which implies that expression timing may be as relevant as its level.
The University of Washington's Can Alkan and his colleagues at the National Cancer Institute and elsewhere have characterized centromeric repeats across the horse, dog, elephant, and armadillo genomes. Alkan et al. describe their computational method, RepeatNet, online in Genome Research this week. RepeatNet, the authors write, uses unassembled whole-genome shotgun sequences "to systematically identify higher-order repeat structures ... and test whether these sequence elements correspond to functional centromeric sequences." In their analyses, the team found the greatest diversity of centromeric sequences in horse and dog, whereas the elephant and armadillo "showed high-centromeric sequence homogeneity."
An international research team led by investigators at the Dana-Farber Cancer Institute reports its use of SAGE-seq to profile gene expression in human breast cancer samples as well as a new data analysis pipeline that enables the "mapping of sense and antisense strands of mitochondrial and RefSeq genes, the normalization between libraries, and the identification of differentially expressed genes." Based on their protocol, the researchers advice a "minimum desired sequencing depth around 5 million reads" when using SAGE-seq to detect genes that are less-abundant, including those they identified that are "abnormally activated in breast cancer."