News & Views in 2011

DNA methylation is an epigenetic mark stably directing gene expression throughout development. A new study uncovers a role for the DNA methyltransferase Dnmt3a in silencing self-renewal genes in hematopoietic stem cells (HSCs) to permit efficient hematopoietic differentiation.

Recent studies, including two in this issue, report heterozygous missense mutations in the U2AF1 and SF3B1 genes that encode spliceosome subunits. U2AF1 is frequently mutated in myeloid hematopoietic malignancies, especially in myelodysplastic syndrome (MDS), and SF3B1 is frequently mutated in both MDS and chronic lymphocytic leukemia (CLL).

A new study reports the development of the 'morbidostat', a device that allows for continuous culture of bacteria under a constant drug selection pressure using computer feedback control of antibiotic concentration. This device, together with bacterial whole-genome sequencing, allowed the authors to follow the evolution of resistance-conferring mutations in Escherichia coli populations in real time, providing support for deterministic evolution of resistance in some situations.

A careful analysis of risk haplotypes in relation to age-related macular degeneration (AMD) susceptibility has led to the identification of a rare, high-penetrance variant in the complement factor H (CFH) gene that is also causally associated with atypical hemolytic uremic syndrome (aHUS) and related glomerulopathies. This finding provides a convincing causal mechanism linking the two diseases and develops a paradigm for the genetic architecture of a common and complex disease.

The combination of genomic, epidemiological and evolutionary analyses provides a powerful toolbox for understanding how pathogens adapt to their human hosts. By sequencing 112 Burkholderia dolosa genomes from an outbreak among patients with cystic fibrosis, a new study documents evolution in action and identifies a set of genes that contributed to the pathogen's adaptation.

An efficient way to design genotyping arrays for fine mapping is to group phenotypes with common biology. The first application of the Immunochip to celiac disease provides an insightful view of what this strategy can achieve.

The origin of DNA methylation patterns has been a mystery for many years. A new study identifies the DNA sequence itself as a key determinant and focuses attention on the role of transcription factors.

Diversification and specialization of high-throughput technologies demand assay-specific treatment of data for reliable interpretation. A new study shows that data generated using the Hi-C approach contain hidden features of interchromosomal DNA interactions, which are revealed through analysis with an integrated probabilistic model that corrects for multiple sources of bias in the data.

A new study shows an inserted retroelement in the regulatory sequences of the maize tb1 gene, which controls shoot branching, was the target of human selection during the domestication of maize from its wild relative teosinte. The insertion allele was already present at low frequency in teosinte populations before selection, highlighting the significance of standing genetic variation in the evolution of morphological diversity.

Two new studies describe germline mutations in BAP1 in putatively dissimilar cancer-related syndromes. The spectrum of neoplasms associated with these germline mutations suggest that BAP1 has an important tumor suppressor function in multiple tissues.

Several new studies report mutations in the gene GATA2 in three different familial syndromes characterized by predisposition to myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Before the onset of MDS and AML, patients with similar GATA2 mutations had distinct hematological abnormalities.

Two new studies take distinct population genetic approaches to analyzing whole-genome sequencing data sets in order to estimate human demographic parameters. These papers refine our understanding of the relationships among human populations while illustrating both the possibilities and the statistical challenges of fitting demographic models to whole-genome data sets.

Complex autoimmune diseases such as rheumatoid arthritis, systemic lupus erythematosus, type 1 diabetes, multiple sclerosis, psoriasis and inflammatory bowel disease have different pathological presentations but have overlapping genetic susceptibility variants. A new study using mice lacking Tnfaip3, whose ortholog is linked to autoimmune disease in humans, leads to insights in the role of one molecular driver of varied clinical symptomatology in disparate autoimmune disorders.

Advances in both pedigree-based and population-based genetic maps in recent years have helped unravel some of the mysteries of human meiotic recombination. The publication of the first admixture-derived human genetic maps offers a new approach for inferring recombination events and provides insight into variation in recombination rate patterns across populations.

A new study shows that the PTPN22 coding variant associated with autoimmunity is a loss-of-function allele that causes the protein tyrosine phosphatase encoded by PTPN22 to undergo accelerated degradation, resulting in enhanced signaling in several immune cell types.

New work has identified networks of protein interactions at the transition zones of cilia. These discoveries provide insights into the molecular pathogenesis of ciliopathies and illustrate the power of linking proteomics technologies with human genetics to uncover critical disease pathways.

Somatic mutations in mitochondrial DNA build up in aging tissues and are thought to contribute to physiological aging. Surprisingly, it is not known if these mutations occur early or late in life. A new study looks at mechanisms of accelerated mitochondrial aging in HIV-infected individuals treated with nucleoside analog anti-retroviral drugs and offers support for an early origin of mitochondrial DNA mutations.

The human genome contains large areas with hypervariable DNA methylation that are associated with deregulation of gene expression. This epigenetic variation may be necessary for differentiation, but it also provides a mechanism for Darwinian evolution at the cellular level that may underlie age-related diseases such as cancer.

Although there are only 22,000 human genes, most express multiple mRNA isoforms through alternative splicing and selection of alternative 5′ and 3′ ends. A new study identifies the role of alternative splicing in maintaining neuronal excitability in the adult mouse brain.

Large-scale mapping of chromatin state and transcription factor binding have uncovered many broad chromatin domains along linear genomic DNA, but it is unclear how these functional domains are organized in three-dimensional nuclear space. A new study now shows that many domains exist as loops connected by CCTC-binding factor (CTCF), providing new insights into the higher-order structure of chromatin organization in the nucleus.