Volume 44 Issue 2, February 2012

A new study reports SNP genotypes of over 1,300 Arabidopsis thaliana accessions from throughout Eurasia, providing a resource for genome-wide association studies and studies of local adaptation. The extensive data are also used to identify targets of natural selection and to describe genome-wide patterns of recombination.

The sequencing of the genome and transcriptome of Schistosoma haematobium, a highly prevalent blood fluke and human parasite with a proven link to malignant bladder cancer, marks the 160^th anniversary of its discovery as the first schistosome known to infect humans. Comparative genomic analyses of S. haematobium and the more prevalent human-schistosomiasis pathogens (Schistosoma mansoni and Schistosoma japonicum) identified both shared and distinct genomic features.

One of the most striking properties of RNA interference (RNAi) in Caenorhabditis elegans is its persistence in offspring after the triggering double-stranded RNA (dsRNA) has disappeared. A new study reveals that a heterochromatic silencing mark is deposited around the targets of RNAi and is transmitted through generations. These results show that RNAi can induce stable and heritable chromatin modifications in animals.

Teresa Zelinski and colleagues identify null alleles of ABCG2 in individuals with the Jr(a–) blood group phenotype.

Sergey Nikolaev, Stylianos Antonarakis and colleagues report exome sequencing of seven melanoma cell lines and matched germline cells. They identify recurring somatic mutations in MAP2K1 and MAP2K2 occurring at an overall frequency of 8%.

Catherine André, Judith Fischer and colleagues report that mutations in PNPLA1 cause congenital ichthyosis in humans and golden retriever dogs. Their findings suggest a role for PNPLA1 in the formation of the epidermal lipid barrier.

Eileen Furlong and colleagues report the development and application of BiTS-ChIP (batch isolate tissue specific chromatin immunoprecipitation), in which a tagged nuclear protein is expressed in developing cells of interest. They apply this method to investigate six chromatin markers and RNA Pol II occupancy in mesodermal cells in developing Drosophila embryos and find that histone modifications and Pol II occupancy can predict enhancer activity.

Andy Fire and colleagues report the finding of histone H3 lysine 9 trimethylation footprints extending several kilobases from siRNA targets at specific loci across the C. elegans genome. Such exogenous RNA–induced chromatin modification was mediated by secondary amplification of siRNA and was maintained across two or more generations.

Nicholas Hayward and colleagues sequenced eight metastatic melanoma exomes and identified frequent somatic mutations in two MAP kinase family genes, MAP3K5 and MAP3K9. Mutation in MAP3K9 may confer resistance to temozolomide, a common chemotherapeutic drug.

Lionel Arnaud and colleagues identify ABCB6 as the genetic basis of the novel Lan blood group system.

Lionel Arnaud and colleagues identify null alleles of ABCG2 as the genetic basis of the Junior blood group system.

Xue-Qing Yu, Jian-Jun Liu and colleagues report results of a genome-wide association study of IgA nephropathy in Han Chinese. They identify two new susceptibility loci at 8p23 and 17p13 and replicate previously reported signals in the MHC region and at 22q12.

Jiahao Sha, Xinru Wang, Hongbing Shen and colleagues report a genome-wide association study of non-obstructive azoospermia in Chinese men. They identify common variants near three genes (PRMT6, PEX10 and SOX5) associated with this form of male infertility.

Lavinia Paternoster and colleagues report a meta-analysis of genome-wide association studies of atopic dermatitis. They report three newly identified associated loci near OVOL1 and ACTL9 and in KIF3A.

Joseph Gleeson and colleagues identify CEP41 mutations as a cause of Joubert syndrome. Their functional studies suggest that CEP41 regulates ciliary entry of TTLL6, an enzyme required for tubulin glutamylation at the cilium.

Rosa Rademakers and colleagues show that mutations in CSF1R cause hereditary diffuse leukoencephalopathy with spheroids, a central nervous system white-matter disease with variable clinical presentations that include personality and behavioral changes, dementia, depression, parkinsonism and seizures.

Huda Zoghbi and colleagues report that MECP2 transgenic mice display heightened anxiety and social approach deficits and that genetic and pharmacological inhibition of Crh or its receptor, Crhr1, suppresses the anxiety phenotypes. The authors also report that genetic reduction of Oprm1 improves social approach behaviors in MECP2 transgenic mice.

Joy Bergelson and colleagues characterize genome-wide patterns of genetic variation in a collection of 1,307 worldwide Arabidopsis thaliana accessions from the Regional Mapping (RegMap) panel, a publicly available genomic resource that includes large regional panels. They characterize signatures of selection and patterns of recombination and identify an enrichment of hotspots in intergenic regions and in repetitive DNA.

Albrecht Melchinger and colleagues report a complementary approach to phenotype-based screening for hybrid maize. The new approach accurately predicts the combining abilities of agronomical traits based on genomic and metabolomic information comprising 56,110 SNPs and 130 metabolite measurements.

Robin Gasser and his colleagues report the whole-genome sequence of Schistosoma haematobium. They include comparisons to the genome sequences of S. mansoni and S. japonicum, the two other species that cause schistosomiasis in humans.

Gil McVean and colleagues report algorithms for de novo assembly and genotyping of variants using colored de Bruijn graphs and provide these in a software implementation called Cortex. Their methods can detect and genotype both simple and complex genetic variants in either an individual or a population.