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Elisabeth Mangold and colleagues carried out a genome-wide association study for nonsyndromic cleft lip with or without cleft palate, and report a locus on 8q24.21 that is strongly associated with this phenotype.
Alexandre Reymond, Henrik Kaessman and colleagues report a high-resolution survey of copy number variation in mice and assess the impact of such variation on gene expression across multiple tissues and strains. They conclude that CNVs substantially influence global transcription, including long-range cis effects extending up to several hundred kilobases.
Timothy Graubert and colleagues report a high-resolution survey of copy number variation in mouse inbred strains and assess the impact of such variation on gene expression. They find that up to 26% of strain-dependent expression variation in hematopoietic stem/progenitor cells is associated with copy number variation.
Thomas Drake and colleagues report the results of knockout or transgene introduction for nine obesity candidate genes in mice. Eight of the nine mutations result in significant changes in obesity-related traits, validating their previously developed approach for identifying candidate genes involved in particular phenotypes. They further identify related metabolic pathways that are altered by manipulation of the eight genes.
Michael Taylor and colleagues identify copy number aberrations of genes with critical roles in writing, reading, removing and blocking the state of histone lysine methylation, indicating that defective control of the histone code contributes to the pathogenesis of medulloblastoma.
Jung Kyoon Choi and Young-Joon Kim analyze published genome-wide datasets and show that a nucleosome is commonly positioned at a critical gene regulatory region flanking promoters that respond variably to external signals. The preference for nucleosome binding at this position is encoded by the DNA sequence itself.
Marie-Paule Roth and colleagues report that targeted disruption of Bmp6 in mice leads to a rapid and massive accumulation of iron in several tissues, showing that it is critical for iron homeostasis.
Jodie Babitt and colleagues report that Bmp6-null mice have a phenotype that resembles hereditary hemochromatosis, with increased serum iron concentration and tissue iron overload. Administration of Bmp6 increases hepcidin expression and reduces serum iron, suggesting that Bmp6 is a key endogenous regulator or iron metabolism in vivo
Eran Segal and colleagues report that promoters driving expression of cellular respiration genes in aerobic yeast species encode relatively open chromatin, whereas promoters associated with the same genes in anaerobic yeast species encode relatively closed chromatin. These results suggest that phenotypic diversity may in part be influenced by changes in the DNA-encoded nucleosome organization of promoters.
Trudy Mackay and colleagues measure sleep phenotypes in 40 wild-derived Drosophila lines, and report candidate genes and transcriptional networks associated with sleep regulation.
Stanislas Lyonnet and colleagues report a new locus associated with Pierre Robin sequence, an important subgroup of cleft palate. They find that translocations, deletions and point mutation affecting highly conserved noncoding elements (HCNEs) found at distances on either side of SOX9 are associated with PRS.
Ernest Fraenkel and colleagues present ResponseNet, a method used to integrate analysis of genetic and transcriptional datasets, and its application characterizing yeast cellular responses to alpha-synuclein toxicity.
Trudy Mackay and colleagues present a resource of 40 Drosophila melanogaster wild-derived inbred lines. The authors quantify genome-wide variation in transcript abundance for six ecologically relevant traits, characterize the transcriptome and identify transcriptional modules.
Wei Zheng and colleagues carried out a genome-wide association study of breast cancer in Chinese women and discovered risk variants on 6q25.1 located upstream of the gene encoding estrogen receptor 1 (ESR1). They also found a similar association between the 6q25.1 locus and breast cancer in samples of European ancestry.
Manel Esteller and colleagues report truncating mutations in TARBP2, an integral component of a DICER1-containing complex, in human colorectal cancers. This is the first report of a mutation in one of the genes involved in miRNA processing in human cancer.
Haruhiko Koseki and colleagues identify a gain-of-function mutation in Fgf9 in mice with elbow knee synostosis. They further show that this mutation prevents homodimerization of Fgf9, allowing increased diffusion of the altered protein through developing tissues.
Christopher Newton-Cheh and colleagues report the identification of common variants at the NPPA-NPPB locus associated with plasma atrial natriuretic peptide concentration, as well as with lower systolic and diastolic blood pressure, and reduced risk of hypertension.
Jeanette Erdmann and colleagues identify a locus on chromosome 3q22.3 associated with coronary artery disease. The SNP with the strongest association is in MRAS, which encodes a membrane-anchored GTP-binding protein.
Using a haplotype-based approach, David-Alexandre Trégouët and colleagues report that the SLC22A3-LPAL2-LPA gene cluster is associated with risk of coronary artery disease.
Toshihiro Tanaka and colleagues report the identification of variants in BRAP, which encodes a galectin-2–binding protein, that are associated with risk of myocardial infarction in two Asian populations.