Experimentally characterized enhancer regions have previously been shown to display specific patterns of enrichment for several different histone modifications. We modelled these enhancer chromatin profiles in the human genome and used them to guide the search for novel enhancers derived from transposable element (TE) sequences. To do this, a computational approach was taken to analyze the genome-wide histone modification landscape characterized by the ENCODE project in two human hematopoietic cell types, GM12878 and K562. We predicted the locations of 2,107 and 1,448 TE-derived enhancers in the GM12878 and K562 cell lines respectively. A vast majority of these putative enhancers are unique to each cell line; only 3.5% of the TE-derived enhancers are shared between the two. We evaluated the functional effect of TE-derived enhancers by associating them with the cell-type specific expression of nearby genes, and found that the number of TE-derived enhancers is strongly positively correlated with the expression of nearby genes in each cell line. Furthermore, genes that are differentially expressed between the two cell lines also possess a divergent number of TE-derived enhancers in their vicinity. As such, genes that are up-regulated in the GM12878 cell line and down-regulated in K562 have significantly more TE-derived enhancers in their vicinity in the GM12878 cell line and vice versa. These data indicate that human TE-derived sequences are likely to be involved in regulating cell-type specific gene expression on a broad scale and suggest that the enhancer activity of TE-derived sequences is mediated by epigenetic regulatory mechanisms.

Cystic fibrosis (CF) is the most common genetic disease among Caucasians, and accordingly the cystic fibrosis transmembrane conductance regulator (CFTR) protein has perhaps the best characterized disease mutation spectrum with more than 1,500 causative mutations having been identified. In this study, we took advantage of that wealth of mutational information in an effort to relate site-specific evolutionary parameters with the propensity and severity of CFTR disease-causing mutations. To do this, we devised a scoring scheme for known CFTR disease-causing mutations based on the Grantham amino acid chemical difference matrix. CFTR site-specific evolutionary constraint values were then computed for seven different evolutionary metrics across a range of increasing evolutionary depths. The CFTR mutational scores and the various site-specific evolutionary constraint values were compared in order to evaluate which evolutionary measures best reflect the disease-causing mutation spectrum. Site-specific evolutionary constraint values from the widely used comparative method PolyPhen2 show the best correlation with the CFTR mutation score spectrum, whereas more straightforward conservation based measures (ConSurf and ScoreCons) show the greatest ability to predict individual CFTR disease-causing mutations. While far greater than could be expected by chance alone, the fraction of the variability in mutation scores explained by the PolyPhen2 metric (3.6%), along with the best set of paired sensitivity (58%) and specificity (60%) values for the prediction of disease-causing residues, were marginal. These data indicate that evolutionary constraint levels are informative but far from determinant with respect to disease-causing mutations in CFTR. Nevertheless, this work shows that, when combined with additional lines of evidence, information on site-specific evolutionary conservation can and should be used to guide site-directed mutagenesis experiments by more narrowly defining the set of target residues, resulting in a potential savings of both time and money.

There is a need for a comprehensive and sensitive method to test for a broad range of viral pathogens in samples without any identifiable pathogen detected. Real-time PCR assays are sensitive and rapid, but their specificity limits their utility in detecting divergent agents. Shotgun high-throughput sequencing methods provide unbiased sequence identification, however, they have limited sensitivity and require complex analyses. In order to meet the need for a sensitive, high-throughput virus detection and discovery platform with good sensitivity, we combine two existing technologies, broadly-reactive consensus-degenerate pan-viral group PCR and the MiSeq sequencer (Illumina), using the Access Array (Fluidigm), a commercially-available microfluidic PCR system. Pan-viral group primers target conserved regions of virus taxonomic groups and can amplify known and potentially novel species. The Access Array employs dozens of these assays in parallel, which are then sequenced all at once on the MiSeq. In this study, we run a respiratory panel of pan-viral group PCR assays using AA-PCR-Seq. We validate the panel on a collection of representative human and animal samples, comparing it to qPCR and shotgun next-generation sequencing (NGS). AA-PCR-Seq provides a robust, straightforward method for screening large numbers of samples for virus detection and discovery.

Corynebacterium minutissimum was first isolated in 1961 from infection sites of patients presenting with erythrasma, a common cutaneous infection characterized by a rash. Since its discovery, C. minutissimum has been identified as an opportunistic pathogen in immunosuppressed cancer and HIV patients. Here, we report the whole-genome sequence of C. minutissimum.