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Genomes are organized into high-level three-dimensional structures, and DNA elements separated by long genomic distances can in principle interact functionally. Many transcription factors bind to regulatory DNA elements distant from gene promoters. Although distal binding sites have been shown to regulate transcription by long-range chromatin interactions at a few loci, chromatin interactions and their impact on transcription regulation have not been investigated in a genome-wide manner. Here we describe the development of a new strategy, chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) for the de novo detection of global chromatin interactions, with which we have comprehensively mapped the chromatin interaction network bound by oestrogen receptor α (ER-α) in the human genome. We found that most high-confidence remote ER-α-binding sites are anchored at gene promoters through long-range chromatin interactions, suggesting that ER-α functions by extensive chromatin looping to bring genes together for coordinated transcriptional regulation. We propose that chromatin interactions constitute a primary mechanism for regulating transcription in mammalian genomes. Gene regulation: the ER-α interactome Many transcription factors bind to regulatory DNA elements that are distant from gene promoters, and such distal binding sites are thought to regulate transcription through long-range chromatin interactions. In order to study how this remote control is organized in a complex genome, Fullwood et al . use a technique termed ChIA-PET (chromatin interaction analysis by paired-end tag sequencing) to detect and map the chromatin interaction network mediated by oestrogen receptor α (ER-α) in human cancer cells. In the resulting global chromatin interactome map, most high-confidence remote ER-α-binding sites are anchored at gene promoters through long-range chromatin interactions, suggesting that ER-α functions by extensive chromatin looping to bring genes together for coordinated transcriptional regulation. Many transcription factors bind to regulatory DNA elements that are distant from gene promoters. These distal binding sites are thought to regulate transcription through long-range chromatin interactions, but, until now, the impact of chromatin interactions on transcription regulation has not been investigated in a genome-wide manner. A new strategy — chromatin interaction analysis by paired-end tag sequencing — is now described for the de novo detection of global chromatin interactions.

Recording and transcribing interviews in qualitative social research is a vital but time-consuming and resource-intensive task. To tackle this challenge, researchers have explored various alternative approaches; automatic transcription utilising speech recognition algorithms has emerged as a promising solution. The question of whether automated transcripts can match the quality of transcripts produced by humans remains unanswered. In this paper we systematically compare multiple automatic transcription tools: Amberscript, Dragon, F4x, Happy Scribe, NVivo, Sonix, Trint, Otter, and Whisper. We evaluate aspects of data protection, accuracy, time efficiency, and costs for an English and a German interview. Based on the analysis, we conclude that Whisper performs best overall and that similar local-automatic transcription tools are likely to become more relevant. For any type of transcription, we recommend reviewing the text to ensure accuracy. We hope to shed light on the effectiveness of automatic transcription services and provide a comparative frame for others interested in automatic transcription.

Targeting KRAS cancers Mutations in genes of the RAS family are preset on about 20% of human cancers, making RAS proteins prime potential targets for cancer therapy. Direct targeting of RAS proteins has not so far been productive, but two papers published in this issue offer the prospect of alternative targets in a signalling pathway downstream of RAS. Using a synthetic lethality RNAi screen, Barbie et al . identify TBK1 as a kinase in the NF-κB signalling pathway that is essential for the survival of KRAS -transformed cells. TBK1 induces anti-apoptotic signals and may be a therapeutic cancer target. And in an elegant mouse model for lung cancer driven by Kras mutation and loss of p53, Meylan et al . show that NF-κB signalling is activated by the concerted actions of these two alterations and required for tumour initiation and tumour maintenance. NF-κB transcription factors have been implicated in cellular transformation and tumorigenesis, but despite extensive biochemical characterization of NF-κB signalling, its requirement in tumour development is not completely understood. Here, the NF-κB pathway is shown to be required for the development of tumours in a mouse model of lung adenocarcinoma in a p53-status-dependent manner, providing support for the development of NF-κB inhibitory drugs as targeted therapies. NF-κB transcription factors function as crucial regulators of inflammatory and immune responses as well as of cell survival 1 . They have also been implicated in cellular transformation and tumorigenesis 2 , 3 , 4 , 5 , 6 . However, despite extensive biochemical characterization of NF-κB signalling during the past twenty years, the requirement for NF-κB in tumour development in vivo , particularly in solid tumours, is not completely understood. Here we show that the NF-κB pathway is required for the development of tumours in a mouse model of lung adenocarcinoma. Concomitant loss of p53 (also known as Trp53) and expression of oncogenic Kras(G12D) resulted in NF-κB activation in primary mouse embryonic fibroblasts. Conversely, in lung tumour cell lines expressing Kras(G12D) and lacking p53, p53 restoration led to NF-κB inhibition. Furthermore, the inhibition of NF-κB signalling induced apoptosis in p53-null lung cancer cell lines. Inhibition of the pathway in lung tumours in vivo , from the time of tumour initiation or after tumour progression, resulted in significantly reduced tumour development. Together, these results indicate a critical function for NF-κB signalling in lung tumour development and, further, that this requirement depends on p53 status. These findings also provide support for the development of NF-κB inhibitory drugs as targeted therapies for the treatment of patients with defined mutations in Kras and p53.

Covalent DNA–protein cross-links (DPCs) are toxic DNA lesions that block replication and require repair by multiple pathways. Whether transcription blockage contributes to the toxicity of DPCs and how cells respond when RNA polymerases stall at DPCs is unknown. Here we find that DPC formation arrests transcription and induces ubiquitylation and degradation of RNA polymerase II. Using genetic screens and a method for the genome-wide mapping of DNA–protein adducts, DPC sequencing, we discover that Cockayne syndrome (CS) proteins CSB and CSA provide resistance to DPC-inducing agents by promoting DPC repair in actively transcribed genes. Consequently, CSB- or CSA-deficient cells fail to efficiently restart transcription after induction of DPCs. In contrast, nucleotide excision repair factors that act downstream of CSB and CSA at ultraviolet light-induced DNA lesions are dispensable. Our study describes a transcription-coupled DPC repair pathway and suggests that defects in this pathway may contribute to the unique neurological features of CS. Three studies identify a transcription-coupled DNA–protein cross-link repair pathway that depends on the Cockayne syndrome proteins and the proteasome.

The organization of biological materials into versatile three-dimensional assemblies could be used to build multifunctional therapeutic scaffolds for use in nanomedicine. Here, we report a strategy to design three-dimensional nanoscale scaffolds that can be self-assembled from RNA with precise control over their shape, size and composition. These cubic nanoscaffolds are only ∼13 nm in diameter and are composed of short oligonucleotides, making them amenable to chemical synthesis, point modifications and further functionalization. Nanocube assembly is verified by gel assays, dynamic light scattering and cryogenic electron microscopy. Formation of functional RNA nanocubes is also demonstrated by incorporation of a light-up fluorescent RNA aptamer that is optimally active only upon full RNA assembly. Moreover, we show that the RNA nanoscaffolds can self-assemble in isothermal conditions (37 °C) during in vitro transcription, which opens a route towards the construction of sensors, programmable packaging and cargo delivery systems for biomedical applications. Three-dimensional nanoscale scaffolds can be self-assembled from RNA with precise control over their shape, size and composition.

Development requires the establishment of precise patterns of gene expression, which are primarily controlled by transcription factors binding to cis -regulatory modules. Although transcription factor occupancy can now be identified at genome-wide scales, decoding this regulatory landscape remains a daunting challenge. Here we used a novel approach to predict spatio-temporal cis -regulatory activity based only on in vivo transcription factor binding and enhancer activity data. We generated a high-resolution atlas of cis -regulatory modules describing their temporal and combinatorial occupancy during Drosophila mesoderm development. The binding profiles of cis -regulatory modules with characterized expression were used to train support vector machines to predict five spatio-temporal expression patterns. In vivo transgenic reporter assays demonstrate the high accuracy of these predictions and reveal an unanticipated plasticity in transcription factor binding leading to similar expression. This data-driven approach does not require previous knowledge of transcription factor sequence affinity, function or expression, making it widely applicable. Gene expression in time and space Gene expression states are established through the integration of signalling and transcriptional networks converging on enhancer elements, or ' cis -regulatory modules' (CRMs). Methods of predicting the location of CRMs are now highly effective, so the pressure is now on to develop ways of predicting their spatio-temporal activity. A team from the European Molecular Biology laboratory has now developed a new approach to predicting how the combinatorial binding of transcription factors to enhancers translates into specific spatio-temporal patterns of gene expression. The approach uses transcription factor binding and in vivo activity data, and is demonstrated in an analysis of Drosophila mesoderm development. The precise patterns of gene expression required for development are primarily controlled by transcription factors binding to cis -regulatory modules; however, decoding this regulatory landscape remains challenging. Here, a novel approach is used to predict spatio-temporal cis -regulatory activity based only on in vivo transcription factor binding and enhancer activity data, and is then applied to Drosophila mesoderm development.

Alcohol consumption is a moderately heritable trait, but the genetic basis in humans is largely unknown, despite its clinical and societal importance. We report a genome-wide association study meta-analysis of

Global transcription machinery engineering (gTME) is an approach for reprogramming gene transcription to elicit cellular phenotypes important for technological applications. Here we show the application of gTME to Saccharomyces cerevisiae for improved glucose/ethanol tolerance, a key trait for many biofuels programs. Mutagenesis of the transcription factor Spt15p and selection led to dominant mutations that conferred increased tolerance and more efficient glucose conversion to ethanol. The desired phenotype results from the combined effect of three separate mutations in the SPT15 gene [serine substituted for phenylalanine (Phe¹⁷⁷Ser) and, similarly, Tyr¹⁹⁵His, and Lys²¹⁸Arg]. Thus, gTME can provide a route to complex phenotypes that are not readily accessible by traditional methods.

New validated cellular targets are needed to reinvigorate antibacterial drug discovery. This need could potentially be filled by riboswitches—messenger RNA (mRNA) structures that regulate gene expression in bacteria. Riboswitches are unique among RNAs that serve as drug targets in that they have evolved to form structured and highly selective receptors for small drug-like metabolites. In most cases, metabolite binding to the receptor represses the expression of the gene(s) encoded by the mRNA. If a new metabolite analog were designed that binds to the receptor, the gene(s) regulated by that riboswitch could be repressed, with a potentially lethal effect to the bacteria. Recent work suggests that certain antibacterial compounds discovered decades ago function at least in part by targeting riboswitches. Herein we will summarize the experiments validating riboswitches as drug targets, describe the existing technology for riboswitch drug discovery and discuss the challenges that may face riboswitch drug discoverers.

Cancer cells have diverse biological capabilities that are conferred by numerous genetic aberrations and epigenetic modifications. Today's powerful technologies are enabling these changes to the genome to be catalogued in detail. Tomorrow is likely to bring a complete atlas of the reversible and irreversible alterations that occur in individual cancers. The challenge now is to work out which molecular abnormalities contribute to cancer and which are simply 'noise' at the genomic and epigenomic levels. Distinguishing between these will aid in understanding how the aberrations in a cancer cell collaborate to drive pathophysiology. Past successes in converting information from genomic discoveries into clinical tools provide valuable lessons to guide the translation of emerging insights from the genome into clinical end points that can affect the practice of cancer medicine.