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Richard Houlston and colleagues identify variants at six loci associated with risk of chronic lymphocytic leukemia. These findings confirm that common, low-penetrance susceptibility alleles contribute to this hematological malignancy and provide new insights into disease etiology.
Gil McVean and colleagues examine recombination hot spots in the human genome, using new search methods and drawing on HapMap II to identify an extended family of hot spot–associated motifs. They report a common sequence motif estimated to be found in ∼40% of recombination hot spots.
Mark Daly, Ramnik Xavier and colleagues report that a 20-kb deletion polymorphism upstream of IRGM is associated with altered IRGM expression and Crohn's disease. They also show that manipulation of IRGM levels in cells modulated the efficiency of autophagic responses to internalized bacteria, suggesting a mechanism by which the deletion variant might influence disease risk.
Masato Kasuga and colleagues and Shiro Maeda and colleagues each report the independent identification of SNPs in KCNQ1 associated with type 2 diabetes in the Japanese population. Each group replicated the associations in other populations of East Asian and European descent.
Frank Baas and colleagues report mutations in three of the four subunits of the tRNA-splicing endonuclease complex in families with two subtypes of pontocerebellar hypoplasia. The findings implicate tRNA processing in neurological disorders.
Masato Kasuga and colleagues and Shiro Maeda and colleagues each report the independent identification of SNPs in KCNQ1 associated with type 2 diabetes in the Japanese population. Each group replicated the associations in other populations of East Asian and European descent.
Miltos Tsiantis and colleagues examine leaf formation in Arabidopsis thaliana, which has simple, undivided leaves, and Cardamine hirsuta, which has a subdivided leaf blade with individual leaflets. Using genetics, marker gene expression and cell lineage tracing, the authors show that lateral leaflet formation in C. hirsuta requires establishment of growth foci that form after leaf initiation.
Stefan Schreiber and colleagues report the results of a genome-wide association study for sarcoidosis, a complex chronic inflammatory disorder. Variants near ANXA11 and PLAC9 are associated with elevated risk of the disease, with ANXA11 as the stronger candidate.
Valerie Cormier-Daire and colleagues report mutations in ADAMTSL2 in geleophysic dysplasia, a connective tissue disorder. The authors present evidence that ADAMTSL2 is an extracellular matrix protein regulating the bioavailability of TGF-β.
Gray horses are born colored but gradually lose hair pigmentation and become white, a trait that is transmitted in an autosomal dominant manner. Leif Andersson and colleagues report that the the mutation causing the Gray phenotype is a 4.6-kb duplication in intron 6 of STX17, which promotes overexpression of both STX17 and the neighboring gene NR4A3 in melanomas from Gray horses.
Shiro Ikegawa and colleagues identify a variant in a newly identified gene, DVWA, that is associated with susceptibility to knee osteoarthritis. DVWA contains von Willebrand factor domains and is expressed specifically in cartilage.
Mitinori Saitou and colleagues report that Prdm14, which encodes a transcription factor expressed exclusively in the germ cell lineage, is essential for re-acquisition of pluripotency and epigenetic reprogramming of primordial germ cells.
Takeshi Izawa and colleagues report the cloning of a gene underlying a rice quantitative trait locus influencing grain width. A deletion in qSW5 increases yield of rice grains, and the authors show that this mutation has likely been selected for during the domestication of rice.
Helen McNeill and colleagues show that loss of Fat4, a homolog of the Drosophila planar cell polarity protein Fat, disrupts oriented cell division, leading to a failure of tubule elongation and cystic kidney disease in mice. The findings suggest that loss of planar cell polarity may underlie some forms of cystic kidney disease in humans.
Daniel Cohn and colleagues identify mutations in the gene encoding the calcium-permeable cation channel TRPV4 in families with autosomal dominant brachyolmia. Functional studies show that the mutations result in gain-of-function of channel activation.
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.