Transcriptome content and dynamics at single-nucleotide resolution

Massively parallel short-tag 'RNA sequencing' is giving new insights into the complexity of the eukaryotic transcriptome

The uniqueome: a mappability resource for short-tag sequencing

Summary: Quantification applications of short-tag sequencing data (such as CNVseq and RNAseq) depend on knowing the uniqueness of specific genomic regions at a given threshold of error. Here, we present the ‘uniqueome’, a genomic resource for understanding the uniquely mappable proportion of genomic sequences. Pre-computed data are available for human, mouse, fly and worm genomes in both color-space and nucletotide-space, and we demonstrate the utility of this resource as applied to the quantification of RNAseq data

The uniqueome: a mappability resource for short-tag sequencing

Summary: Quantification applications of short-tag sequencing data (such as CNVseq and RNAseq) depend on knowing the uniqueness of specific genomic regions at a given threshold of error. Here, we present the ‘uniqueome’, a genomic resource for understanding the uniquely mappable proportion of genomic sequences. Pre-computed data are available for human, mouse, fly and worm genomes in both color-space and nucletotide-space, and we demonstrate the utility of this resource as applied to the quantification of RNAseq data

X-MATE: a flexible system for mapping short read data

Summary: Accurate and complete mapping of short-read sequencing to a reference genome greatly enhances the discovery of biological results and improves statistical predictions. We recently presented RNA-MATE, a pipeline for the recursive mapping of RNA-Seq datasets. With the rapid increase in genome re-sequencing projects, progression of available mapping software and the evolution of file formats, we now present X-MATE, an updated version of RNA-MATE, capable of mapping both RNA-Seq and DNA datasets and with improved performance, output file formats, configuration files, and flexibility in core mapping software

Therapeutic Potential of Heme Oxygenase-1/Carbon Monoxide in Lung Disease

Heme oxygenase (HO), a catabolic enzyme, provides the rate-limiting step in the oxidative breakdown of heme, to generate carbon monoxide (CO), iron, and biliverdin-IXα. Induction of the inducible form, HO-1, in tissues is generally regarded as a protective mechanism. Over the last decade, considerable progress has been made in defining the therapeutic potential of HO-1 in a number of preclinical models of lung tissue injury and disease. Likewise, tissue-protective effects of CO, when applied at low concentration, have been observed in many of these models. Recent studies have expanded this concept to include chemical CO-releasing molecules (CORMs). Collectively, salutary effects of the HO-1/CO system have been demonstrated in lung inflammation/acute lung injury, lung and vascular transplantation, sepsis, and pulmonary hypertension models. The beneficial effects of HO-1/CO are conveyed in part through the inhibition or modulation of inflammatory, apoptotic, and proliferative processes. Recent advances, however, suggest that the regulation of autophagy and the preservation of mitochondrial homeostasis may serve as additional candidate mechanisms. Further preclinical and clinical trials are needed to ascertain the therapeutic potential of HO-1/CO in human clinical disease

The place of popular music in Scotland’s cultural policy

n the last two decades the status of popular music as both a cultural activity and creative industry has changed significantly in Scottish and UK cultural policy. The change is in line with a broader shift away from thinking of the arts as cultural activity in need of subsidy and towards treating them as part of the creative economy. The current cultural policy landscape pertaining to popular music is mapped out, drawing on interviews and an online survey with members of the Scottish Music Industry Association (SMIA) and complementary interviews with stakeholders from relevant government and arms-length funding and development bodies. The Scottish Government's (SG) White Paper on independence highlighted the creative industries as one of five growth sectors key to the Scottish economy, but for popular music – and in line with the global music industry – many working in the Scottish music industry face acute challenges. Given EU regulations (and the Scottish Government's preference to remain in the EU) and international agreements in areas like broadcasting and copyright, if they are to flourish many members of the SMIA will likely need to strengthen their relationships with the wider UK and global music industry, regardless of the outcome of the referendum on independence

RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data

Summary: Mapping of next-generation sequencing data derived from RNA samples (RNAseq) presents different genome mapping challenges than data derived from DNA. For example, tags that cross exon-junction boundaries will often not map to a reference genome, and the strand specificity of the data needs to be retained. Here we present RNA-MATE, a computational pipeline based on a recursive mapping strategy for placing strand specific RNAseq data onto a reference genome. Maximizing the mappable tags can provide significant savings in the cost of sequencing experiments. This pipeline provides an automatic and integrated way to align color-space sequencing data, collate this information and generate files for examining gene-expression data in a genomic context

Integrated Genome Analysis Suggests that Most Conserved Non-Coding Sequences are Regulatory Factor Binding Sites

More than 98% of a typical vertebrate genome does not code for proteins. Although non-coding regions are sprinkled with short (<200 bp) islands of evolutionarily conserved sequences, the function of most of these unannotated conserved islands remains unknown. One possibility is that unannotated conserved islands could encode non-coding RNAs (ncRNAs); alternatively, unannotated conserved islands could serve as promoter-distal regulatory factor binding sites (RFBSs) like enhancers. Here we assess these possibilities by comparing unannotated conserved islands in the human and mouse genomes to transcribed regions and to RFBSs, relying on a detailed case study of one human and one mouse cell type. We define transcribed regions by applying a novel transcript-calling algorithm to RNA-Seq data obtained from total cellular RNA, and we define RFBSs using ChIP-Seq and DNAse-hypersensitivity assays. We find that unannotated conserved islands are four times more likely to coincide with RFBSs than with unannotated ncRNAs. Thousands of conserved RFBSs can be categorized as insulators based on the presence of CTCF or as enhancers based on the presence of p300/CBP and H3K4me1. While many unannotated conserved RFBSs are transcriptionally active to some extent, the transcripts produced tend to be unspliced, non-polyadenylated and expressed at levels 10 to 100-fold lower than annotated coding or ncRNAs. Extending these findings across multiple cell types and tissues, we propose that most conserved non-coding genomic DNA in vertebrate genomes corresponds to promoter-distal regulatory elements

ToF-SIMS mediated analysis of human lung tissue reveals increased iron deposition in COPD (GOLD IV) patients

Chronic obstructive pulmonary disease (COPD) is a debilitating lung disease that is currently the third leading cause of death worldwide. Recent reports have indicated that dysfunctional iron handling in the lungs of COPD patients may be one contributing factor. However, a number of these studies have been limited to the qualitative assessment of iron levels through histochemical staining or to the expression levels of iron-carrier proteins in cells or bronchoalveolar lavage fluid. In this study, we have used time of flight secondary ion mass spectrometry (ToF-SIMS) to visualize and relatively quantify iron accumulation in lung tissue sections of healthy donors versus severe COPD patients. An IONTOF 5 instrument was used to perform the analysis, and further multivariate analysis was used to analyze the data. An orthogonal partial least squares discriminant analysis (OPLS-DA) score plot revealed good separation between the two groups. This separation was primarily attributed to differences in iron content, as well as differences in other chemical signals possibly associated with lipid species. Further, relative quantitative analysis revealed twelve times higher iron levels in lung tissue sections of COPD patients when compared to healthy donors. In addition, iron accumulation observed within the cells was heterogeneously distributed, indicating cellular compartmentalization