In PLoS Genetics this week, the Harvard School of Public Health's Marilyn Cornelis and her colleagues "report the first genome-wide association study of habitual caffeine intake," in which they genotyped 47,341 individuals of European descent and identified 7p21 near AHR and 15q24 between CYP1A1 and CYP1A2 as two loci significantly associated with consumption. "Both the AHR and CYP1A2 genes are biologically plausible candidates as CYP1A2 metabolizes caffeine and AHR regulates CYP1A2," Cornelis et al. report.
Tanya Vavouri and Ben Lehner at the Centre for Genomic Regulation in Barcelona propose in a PLoS Genetics paper that "chromatin organization in sperm may be the major functional consequence of base composition variation in the human genome." Using sequencing and microarray analysis, Vavouri and Lehner found that "base composition is the major determinant of nucleosome retention in human sperm, predicting retention very well in both genic and non-genic regions of the genome" as well as a "striking link between the retention of nucleosomes in sperm and the establishment of DNA methylation-free regions in the early embryo."
An international team led by investigators at the Hans Knöll Institute in Jena, Germany, reports in PLoS One this week that "the Candida albicans-specific gene EED1 encodes a key regulator of hyphal extension" and maintenance. Using transcriptional profiling techniques, the team found that, during infection of oral tissue, Eed1 and "Ume6 act in a pathway regulating maintenance of hyphal growth thereby repressing hyphal-to-yeast transition and permitting dissemination of C. albicans within epithelial tissues."
Investigators at the Ludwig Institute for Cancer Research in Lausanne, Switzerland, along with their international colleagues, report their use of karyotyping, SNP arrays, CGH arrays, and RNA-seq on seven human metastatic melanoma cell lines, through which they "identified 28 significantly enriched pathway modules." Of these, the WNT signaling, cadherin signaling, angiogenesis, and melanogenesis pathways were frequently altered, the team reports in PLoS One. Further, the team writes, "our results emphasize the potential of the EPHA3 and FRS2 gene products, involved in angiogenesis and migration, as possible therapeutic targets in melanoma."