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Ben Tycko and colleagues report the identification of genotype-dependent allele-specific methylation at many loci through the use of genomic methylation-sensitive SNP array analysis. Using independent assays, they confirm allele-specific methylation at 16 SNP-tagged loci on various chromosomes.
Keji Zhao and colleagues report genome-wide maps of 18 histone lysine acetylations in human CD4+ T cells as detected by ChIP-sequencing. Analysis of the data along with genome-wide maps of histone lysine methylations revealed a common module of 17 modifications associated with 25% of genes.
Eugenio Sangiorgi and Mario Capecchi use lineage tracing in mice to identify Bmi1 as a specific marker of a stem cell population located at the +4 position of the small intestinal crypt. Their findings address a long-standing debate in the field and support the existence of two distinct intestinal stem cell populations near the crypt base.
George Daley and colleagues show that ectopic Ras activation diverts embryonic stem cells towards trophoblastic fates, and conversely, that inhibition of MAPK signaling reduces trophectoderm outgrowth from embryo explants. These results implicate Ras-MAPK signaling in this early and critical cell fate decision.
Bernhard Weber and colleagues identify a previously unknown insertion-deletion polymorphism in ARMS2 (LOC387715), a gene associated with age-related macular degeneration. The variant leads to rapid mRNA turnover of the ARMS2 transcript, suggesting a role for this gene in AMD.
Maria Karayiorgou and colleagues report that de novo mutations in DNA copy number are strongly associated with nonfamilial cases of schizophrenia. The authors observed no such enrichment among familial cases, suggesting that this type of mutation contributes primarily to sporadic forms of the disease.
Evan Eichler and colleagues assess copy number variation of the C57BL/6J duplicated regions in 15 mouse strains used for genetic association studies. They report that mice show comparable copy number polymorphism when compared to humans, but that it is more locally restricted, specifically to regions containing gene families associated with spermatogenesis, pregnancy, viviparity, pheromone signaling and the immune response.
Gudbjartsson et al. report that variants near two genes, ASIP and TYR, are associated with risk of cutaneous melanoma and basal cell carcinoma. These loci are among several loci initially discovered for their role in human pigmentation, as reported by Sulem et al. In a separate study, Brown et al. independently discover an association between variants near ASIP and melanoma risk.