Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets

erefinder: Genome-wide detection of oestrogen response elements

Oestrogen response elements (EREs) are specific DNA sequences to which ligand-bound oestrogen receptors (ERs) physically bind, allowing them to act as transcription factors for target genes. Locating EREs and ER responsive regions is therefore a potentially important component of the study of oestrogen-regulated pathways. Here, we report the development of a novel software tool, erefinder, which conducts a genome-wide, sliding-window analysis of oestrogen receptor binding affinity. We demonstrate the effects of adjusting window size and highlight the program's general agreement with ChIP studies. We further provide two examples of how erefinder can be used for comparative approaches. erefinder can handle large input files, has settings to allow for broad and narrow searches, and provides the full output to allow for greater data manipulation. These features facilitate a wide range of hypothesis testing for researchers and make erefinder an excellent tool to aid in oestrogen-related research.

Comprehensive functional annotation of 77 prostate cancer risk loci

Genome-wide association studies (GWAS) have revolutionized the field of cancer genetics, but the causal links between increased genetic risk and onset/progression of disease processes remain to be identified. Here we report the first step in such an endeavor for prostate cancer. We provide a comprehensive annotation of the 77 known risk loci, based upon highly correlated variants in biologically relevant chromatin annotations--we identified 727 such potentially functional SNPs. We also provide a detailed account of possible protein disruption, microRNA target sequence disruption and regulatory response element disruption of all correlated SNPs at r(2) ≥ 0.88%. 88% of the 727 SNPs fall within putative enhancers, and many alter critical residues in the response elements of transcription factors known to be involved in prostate biology. We define as risk enhancers those regions with enhancer chromatin biofeatures in prostate-derived cell lines with prostate-cancer correlated SNPs. To aid the identification of these enhancers, we performed genomewide ChIP-seq for H3K27-acetylation, a mark of actively engaged enhancers, as well as the transcription factor TCF7L2. We analyzed in depth three variants in risk enhancers, two of which show significantly altered androgen sensitivity in LNCaP cells. This includes rs4907792, that is in linkage disequilibrium (r(2) = 0.91) with an eQTL for NUDT11 (on the X chromosome) in prostate tissue, and rs10486567, the index SNP in intron 3 of the JAZF1 gene on chromosome 7. Rs4907792 is within a critical residue of a strong consensus androgen response element that is interrupted in the protective allele, resulting in a 56% decrease in its androgen sensitivity, whereas rs10486567 affects both NKX3-1 and FOXA-AR motifs where the risk allele results in a 39% increase in basal activity and a 28% fold-increase in androgen stimulated enhancer activity. Identification of such enhancer variants and their potential target genes represents a preliminary step in connecting risk to disease process.

Genetic and genomic dissection of cardiogenesis in the Drosophila model

The linear heart tube of the fruit fly Drosophila has served as a very valuable model for studying the regulation of early heart development. In the past, regulatory genes of Drosophila cardiogenesis have been identified largely through candidate approaches. The vast genetic toolkit available in this organism has made it possible to determine their functions and build regulatory networks of transcription factors and signaling inputs that control heart development. In this review, we summarize the major findings from this study and present current approaches aiming to identify additional players in the specification, morphogenesis, and differentiation of the heart by forward genetic screens. We also discuss various genomic and bioinformatic approaches that are currently being developed to extend the known transcriptional networks more globally which, in combination with the genetic approaches, will provide a comprehensive picture of the regulatory circuits during cardiogenesis.