Reviews & Analysis

Three new studies report large-scale resequencing and comparative genomic analysis of diverse maize varieties. The authors conducted a comprehensive characterization of sequence variation in maize genomes and identified signals of selection in maize domestication and breeding.

A new study shows that alteration of poly(dA:dT) tracts in promoters offers a broadly applicable genetic mechanism for predictably tuning gene expression with high resolution. By systematically manipulating these tracts in a controlled yeast system, the authors demonstrate quantitative mechanistic relationships linking regulatory DNA sequences, nucleosome occupancy, transcription factor binding and gene expression.

Loss-of-function mutations in the gene encoding the cyclin-dependent kinase inhibitor CDKN1C cause Beckwith-Wiedemann syndrome and cancer. A new study now identifies potentially gain-of-function missense mutations in CDKN1C that cause the undergrowth-associated IMAGe syndrome.

A new study shows that three independent mutations in the Sh1 gene, which encodes a YABBY transcription factor, gave rise to the non-shattering seed phenotype in domesticated sorghum. This same gene may have also had a role in the domestication of other cereals, including maize and rice.

The clinical spectrum of prostate cancer ranges from curable, local disease to widely metastatic, lethal cancer. Two new prostate cancer genome studies provide the first glimpse at both ends of this spectrum.

We usually think of an individual's cells as sharing the same genome. Challenging this notion, two new studies show that somatic mosaicism is common and can be an early herald of cancer.

Shamil Sunyaev and colleagues present exome sequencing methods and their applications in studies to identify the genetic basis of human complex traits. They include analyses of the whole-exome sequences of 438 individuals from across several studies.

A new study reports the mapping of gene expression in primary immune cell subsets, showing the presence of cell type–specific cis and trans expression quantitative trait loci (eQTLs). The identification of cell type–specific trans-regulated networks can inform functional studies of susceptibility loci identified from genome-wide association studies for human complex diseases.

Three teams have applied whole-exome and proteome methods to identify a new cofactor of human RNA polymerase II that is required for the recovery of transcription on damaged templates. The identification of this new factor raises questions about the causal relationships between molecular mechanisms of transcription regulation and excision repair and developmental and neurological disease and nonmalignant skin photosensitivity.

A new study reports comparative genomic analysis of 52 geographically diverse strains of Chlamydia trachomatis. The authors reconstruct a genome-wide phylogeny of the species and report extensive genome-wide recombination across multiple lineages of this intracellular bacterial pathogen.

The reprogramming of somatic cells to a pluripotent state is prone to errors that could hamper the use of this technology. A new study now shows that vitamin C enhances the quality of somatic cell reprogramming in mice, highlighting the possibility that further manipulation of culture conditions could improve this technology for regenerative medicine.

Neuroendocrine cells, including those in the gut, have a vast array of functions. A new study shows that conditional inactivation of the gene encoding Foxo1 in mouse intestinal endocrine cells converts them into cells synthesizing and secreting insulin. Ectopic gut insulin production was sufficient to ameliorate glucose control in mice with conditional pancreatic β-cell loss and diabetes mellitus.

Mutations in CTC1, which encodes a key telomere component, have been identified as the cause of Coats plus syndrome. This discovery provides an important pathophysiological link between Coats plus and the clinically related telomere disorders dyskeratosis congenita, Revesz syndrome and Hoyeraal-Hreidarsson syndrome.

A new study reports a comprehensive survey of genetic diversity in natural populations of the nematode Caenorhabditis elegans. Their analyses suggest that recent chromosome-scale selective sweeps have reduced C. elegans genetic diversity worldwide and strongly structured genetic variation across its genome.

A new study refines the association signals for rheumatoid arthritis susceptibility in the major histocompatibility complex (MHC) region to five amino-acid positions encoded in three HLA genes, all within peptide-binding grooves. By adapting statistical methods from genome-wide association studies (GWAS) and using imputation from a large reference panel, they demonstrate the potential for this approach to identify functional variants in associated regions.

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.

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.