Articles in 2009

The ATP-dependent chromatin assembly factor (ACF) generates and maintains nucleosome spacing by constantly moving a nucleosome towards the longer flanking DNA faster than the shorter flanking DNA. But how the enzyme moves back and forth between both sides of a nucleosome to accomplish bidirectional movement is unknown. Nucleosome movement is now shown to depend cooperatively on two ACF molecules, indicating that ACF functions as a dimer of ATPases.

The ATP-dependent chromatin assembly factor (ACF) generates regularly spaced nucleosomes, but the mechanism by which ACF mobilizes nucleosomes remains poorly understood. Here, single-molecule FRET is used to monitor the remodelling of individual nucleosomes by ACF in real time; the study reveals previously unknown remodelling intermediates and dynamics, and indicates that ACF is a highly processive and bidirectional nucleosome translocase.

Multiple somatic rearrangements are often found in cancer genomes, but the underlying processes of rearrangement and the effects of this are unclear. A paired-end sequencing strategy is now used to map somatic rearrangements in human breast cancer genomes. More rearrangements in some breast cancers are found than previously recognized, including frequent tandem duplications that may reflect a specific defect in DNA maintenance.

A mesenchymal phenotype is the hallmark of tumour aggressiveness in human malignant glioma, but the regulatory programs responsible for implementing the associated molecular signature are largely unknown. Reverse-engineering and an unbiased interrogation of a glioma-specific regulatory network now reveal the transcription factors that activate expression of mesenchymal genes in malignant glioma.

To elucidate regulatory mechanisms involved in reprogramming to generate pluripotent cells from somatic cells, this study generates interspecies heterokaryons (fused mouse ES cells and human fibroblasts) that induce reprogramming efficiently, rapidly and without cell division. SiRNA–mediated knockdown reveals that AID is required for active DNA demethylation and initiation of nuclear reprogramming towards pluripotency in human somatic cells.

The effect of sequence variants on phenotypes may depend on parental origin. Here, a method is developed that takes parental origin — the impact of which, to date, has largely been ignored — into account in genome-wide association studies. For 38,167 Icelanders genotyped, the parental origin of most alleles is determined; furthermore, a number of variants are found that show associations specific to parental origin, including three with type 2 diabetes.

The protein encoded by the breast cancer susceptibility gene BRCA1 participates in the DNA damage response and acts as a ubiquitin ligase; however, its regulation remains poorly understood. The ligase activity of BRCA1 is now shown to require PIAS-mediated modification with SUMO, and in the absence of PIAS SUMO ligases, DNA repair is impeded. The data demonstrate that the SUMOylation pathway has a significant role in the mammalian DNA damage response.

Sea levels during the last interglacial stage (about 125 kyr ago) are known to have been higher than today, and may serve as a partial analogue for anthropogenic warming scenarios. However, because local sea levels differ from global sea level, accurately reconstructing past global sea level requires an integrated analysis of globally distributed data sets. An extensive compilation of local sea level indicators and a statistical approach are now used to estimate global sea level during the last interglacial.

The quantitative description of microbial growth using a few measurable parameters is an important challenge in systems biology. Extracellular glucose sensing and uptake initiate the budding yeast's growth on glucose, but conventional growth models focus almost exclusively on glucose uptake. By uncoupling these two parameters, the interaction between glucose perception and import, rather than their individual actions, is now shown to determine the central features of growth.

Here, the genomes of a malignant melanoma and a lymphoblastoid cell line from the same person are sequenced, providing the first comprehensive catalogue of somatic mutations from an individual cancer. The data provide insight into the causes of tumour formation and the development of the cancer genome, with the dominant mutational signature reflecting DNA damage due to ultraviolet light exposure.

Tobacco smoke contains more than sixty carcinogens that bind and mutate DNA. Here, massively parallel sequencing technology is used to sequence a small-cell lung cancer cell line, exploring the mutational burden associated with tobacco smoking. Multiple mutation signatures from the cocktail of carcinogens in tobacco smoke are found, as well as evidence of transcription-coupled repair and another, more general, expression-linked repair pathway.

Here, a draft sequence of the giant panda genome is assembled using next-generation sequencing technology alone. Genome analysis reveals a low divergence rate in comparison with dog and human genomes and insights into panda-specific traits; for example, the giant panda's bamboo diet may be more dependent on its gut microbiome than its own genetic composition.

In living systems, the repair of genotoxic damage requires that the lesion first be detected in an excess of undamaged DNA. A base-excision DNA repair enzyme, MutM, is now captured and structurally elucidated at the stage of initial encounter with a damaged nucleobase within a DNA duplex. By combining structural biology and computational modelling, the pathway by which this encounter causes the damaged nucleobase to be extruded from the DNA duplex is defined.

During reconsolidation of memories, stored information is rendered labile after being retrieved and can be manipulated. Previous studies have used pharmacological intervention to disrupt retrieved memories; here, however, a non-invasive, behavioural technique is used to target the reconsolidation of fear memories in humans. Non-fearful information provided during the reconsolidation window appears to update old fear memories, causing a lack of expression of fear responses.

Conjugation of ubiquitin chains onto proteins is an important post-translational modification that regulates the stability, localization and activity of substrate proteins. A series of enzymes known as E1, E2 and E3 mediate assembly of ubiquitin chains but the pathway remains unclear. Theoretical and experimental methodologies are now introduced to study the formation of ubiquitin chains at millisecond time resolution, demonstrating that substrate polyubiquitylation proceeds sequentially.

The majority of excitatory neurotransmission in the central nervous system is mediated by ionotropic glutamate receptors, which function by opening a transmembrane ion channel upon binding of glutamate. However, despite this crucial role in neurobiology, the architecture and atomic structure of an intact isotropic glutamate receptor are unknown. The X-ray crystal structure of the rat GluA2 receptor in complex with a competitive antagonist is now reported and analysed.

Type IV secretion systems span the two membranes of Gram-negative bacteria, with three proteins —— VirB7, VirB9 and VirB10 — assembled into a 1.05 megadalton core spanning the inner and outer membranes. Here, the crystal structure of an outer-membrane complex is presented. The structure is the largest determined for an outer-membrane channel and is unprecedented in being composed of three proteins.

The formate–nitrite transporter family, of which FocA is a representative member, is known to transport short-chain acids in bacteria, archaea, fungi, algae and parasites; however, the structure and transport mechanism of these transporters remain unknown. Here, study of the crystal structure of Escherichia coli FocA reveals that the overall structure of FocA closely resembles that of aquaporin, suggesting that it is in fact a channel, rather than a transporter.

Despite the growing number of X-ray crystal structures of membrane proteins, direct structural information about proteins in their native membrane environment remains scarce. Neutron diffraction, solid-state nuclear magnetic resonance spectroscopy and molecular dynamics simulations are now used to investigate the structure and hydration of bilayer membranes containing S1–S4 voltage-sensing domains.

Mutations in the enzyme cytosolic isocitrate dehydrogenase 1 (IDH1) are commonly found in glioblastomas, a major subset of primary human brain cancers. However, only a single copy of the gene is mutated, suggesting that the mutation does not result in a simple loss of function. Here, IDH1 mutations are shown to act in a gain-of-function manner, resulting in a new ability of the enzyme to catalyse α-ketoglutarate to R(-)-2-hydroxyglutarate, an onco-metabolite.