Search

The cardiac transcription factor (TF) gene NKX2-5 has been associated with electrocardiographic (EKG) traits through genome-wide association studies (GWASs), but the extent to which differential binding of NKX2-5 at common regulatory variants contributes to these traits has not yet been studied. We analyzed transcriptomic and epigenomic data from induced pluripotent stem cell-derived cardiomyocytes from seven related individuals, and identified ~2,000 single-nucleotide variants associated with allele-specific effects (ASE-SNVs) on NKX2-5 binding. NKX2-5 ASE-SNVs were enriched for altered TF motifs, for heart-specific expression quantitative trait loci and for EKG GWAS signals. Using fine-mapping combined with epigenomic data from induced pluripotent stem cell-derived cardiomyocytes, we prioritized candidate causal variants for EKG traits, many of which were NKX2-5 ASE-SNVs. Experimentally characterizing two NKX2-5 ASE-SNVs (rs3807989 and rs590041) showed that they modulate the expression of target genes via differential protein binding in cardiac cells, indicating that they are functional variants underlying EKG GWAS signals. Our results show that differential NKX2-5 binding at numerous regulatory variants across the genome contributes to EKG phenotypes.

Genetic variants affecting pancreatic islet enhancers are central to T2D risk, but the gene targets of islet enhancer activity are largely unknown. We generate a high-resolution map of islet chromatin loops using Hi-C assays in three islet samples and use loops to annotate target genes of islet enhancers defined using ATAC-seq and published ChIP-seq data. We identify candidate target genes for thousands of islet enhancers, and find that enhancer looping is correlated with islet-specific gene expression. We fine-map T2D risk variants affecting islet enhancers, and find that candidate target genes of these variants defined using chromatin looping and eQTL mapping are enriched in protein transport and secretion pathways. At IGF2BP2, a fine-mapped T2D variant reduces islet enhancer activity and IGF2BP2 expression, and conditional inactivation of IGF2BP2 in mouse islets impairs glucose-stimulated insulin secretion. Our findings provide a resource for studying islet enhancer function and identifying genes involved in T2D risk.

Efforts to identify driver mutations in cancer have largely focused on genes, whereas non-coding sequences remain relatively unexplored. Here we develop a statistical method based on characteristics known to influence local mutation rate and a series of enrichment filters in order to identify distal regulatory elements harboring putative driver mutations in breast cancer. We identify ten DNase I hypersensitive sites that are significantly mutated in breast cancers and associated with the aberrant expression of neighboring genes. A pan-cancer analysis shows that three of these elements are significantly mutated across multiple cancer types and have mutation densities similar to protein-coding driver genes. Functional characterization of the most highly mutated DNase I hypersensitive sites in breast cancer (using in silico and experimental approaches) confirms that they are regulatory elements and affect the expression of cancer genes. Our study suggests that mutations of regulatory elements in tumors likely play an important role in cancer development.Cancer driver mutations can occur within noncoding genomic sequences. Here, the authors develop a statistical approach to identify candidate noncoding driver mutations in DNase I hypersensitive sites in breast cancer and experimentally demonstrate they are regulatory elements of known cancer genes.

Large-scale collections of induced pluripotent stem cells (iPSCs) could serve as powerful model systems for examining how genetic variation affects biology and disease. Here we describe the iPSCORE resource: a collection of systematically derived and characterized iPSC lines from 222 ethnically diverse individuals that allows for both familial and association-based genetic studies. iPSCORE lines are pluripotent with high genomic integrity (no or low numbers of somatic copy-number variants) as determined using high-throughput RNA-sequencing and genotyping arrays, respectively. Using iPSCs from a family of individuals, we show that iPSC-derived cardiomyocytes demonstrate gene expression patterns that cluster by genetic background, and can be used to examine variants associated with physiological and disease phenotypes. The iPSCORE collection contains representative individuals for risk and non-risk alleles for 95% of SNPs associated with human phenotypes through genome-wide association studies. Our study demonstrates the utility of iPSCORE for examining how genetic variants influence molecular and physiological traits in iPSCs and derived cell lines.

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2005.09.020 Byline: Soichiro Yamada (1), Sabine Pokutta (1)(2), Frauke Drees (1), William I. Weis (1)(2), W. James Nelson (1) Abstract: Spatial and functional organization of cells in tissues is determined by cell-cell adhesion, thought to be initiated through trans-interactions between extracellular domains of the cadherin family of adhesion proteins, and strengthened by linkage to the actin cytoskeleton. Prevailing dogma is that cadherins are linked to the actin cytoskeleton through [beta]-catenin and [alpha]-catenin, although the quaternary complex has never been demonstrated. We test this hypothesis and find that [alpha]-catenin does not interact with actin filaments and the E-cadherin-[beta]-catenin complex simultaneously, even in the presence of the actin binding proteins vinculin and [alpha]-actinin, either in solution or on isolated cadherin-containing membranes. Direct analysis in polarized cells shows that mobilities of E-cadherin, [beta]-catenin, and [alpha]-catenin are similar, regardless of the dynamic state of actin assembly, whereas actin and several actin binding proteins have higher mobilities. These results suggest that the linkage between the cadherin-catenin complex and actin filaments is more dynamic than previously appreciated. Author Affiliation: (1) Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA (2) Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA Article History: Received 1 April 2005; Revised 28 July 2005; Accepted 12 September 2005 Article Note: (miscellaneous) Published: December 1, 2005

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2005.09.021 Byline: Frauke Drees (1), Sabine Pokutta (1)(2), Soichiro Yamada (1), W. James Nelson (1), William I. Weis (1)(2) Abstract: Epithelial cell-cell junctions, organized by adhesion proteins and the underlying actin cytoskeleton, are considered to be stable structures maintaining the structural integrity of tissues. Contrary to the idea that [alpha]-catenin links the adhesion protein E-cadherin through [beta]-catenin to the actin cytoskeleton, in the accompanying paper we report that [alpha]-catenin does not bind simultaneously to both E-cadherin-[beta]-catenin and actin filaments. Here we demonstrate that [alpha]-catenin exists as a monomer or a homodimer with different binding properties. Monomeric [alpha]-catenin binds more strongly to E-cadherin-[beta]-catenin, whereas the dimer preferentially binds actin filaments. Different molecular conformations are associated with these different binding states, indicating that [alpha]-catenin is an allosteric protein. Significantly, [alpha]-catenin directly regulates actin-filament organization by suppressing Arp2/3-mediated actin polymerization, likely by competing with the Arp2/3 complex for binding to actin filaments. These results indicate a new role for [alpha]-catenin in local regulation of actin assembly and organization at sites of cadherin-mediated cell-cell adhesion. Author Affiliation: (1) Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA (2) Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA Article History: Received 31 March 2005; Revised 28 July 2005; Accepted 12 September 2005 Article Note: (miscellaneous) Published: December 1, 2005

Cadherins are transmembrane adhesion molecules that mediate homotypic cell-cell contact. In adherens junctions, the cytoplasmic domain of cadherins is functionally linked to the actin cytoskeleton through a series of proteins known as catenins. E-cadherin binds to beta-catenin, which in turn binds to alpha-catenin to form a ternary complex. alpha-Catenin also binds to actin, and it was assumed previously that alpha-catenin links the cadherin-catenin complex to actin. However, biochemical, structural and live-cell imaging studies of the cadherin-catenin complex and its interaction with actin show that binding of beta-catenin to alpha-catenin prevents the latter from binding to actin. Biochemical and structural data indicate that alpha-catenin acts as an allosteric protein whose conformation and activity changes depending on whether or not it is bound to beta-catenin. Initial contacts between cells occur on dynamic lamellipodia formed by polymerization of branched actin networks, a process controlled by the Arp2/3 (actin-related protein 2/3) complex. alpha-Catenin can suppress the activity of Arp2/3 by competing for actin filaments. These findings lead to a model for adherens junction formation in which clustering of the cadherin-beta-catenin complex recruits high levels of alpha-catenin that can suppress the Arp2/3 complex, leading to cessation of lamellipodial movement and formation of a stable contact. Thus alpha-catenin appears to play a central role in cell-cell contact formation.

Cell adhesion between cells and with the extracellular matrix (ECM) results in dramatic changes in cell organization and, in particular, the cytoskeleton and plasma membrane domains involved in adhesion. However, current methods to analyze these changes are limited because of the small areas of membrane involved in adhesion, compared to the areas of membrane not adhering (a signal to noise problem), and the difficulty in accessing native protein complexes directly for imaging or reconstitution with purified proteins. The methods described here overcome these problems. Using a mammalian expression system, a chimeric protein comprising the extracellular domain of E-cadherin fused at its C-terminus to the Fc domain of human IgG1 (E-cadherin:Fc) is expressed and purified. A chemical bridge of biotin-NeutrAvidin-biotinylated Protein G bound to a silanized glass cover slip is fabricated to which the E-cadherin:Fc chimera binds in the correct orientation for adhesion by cells. After cell attachment, the basal membrane (a contact formed between cellular E-cadherin and the E-cadherin:Fc substratum) is isolated by sonication; a similar method is described to isolate basal membranes of cells attached to ECM. These membrane patches provide direct access to protein complexes formed on the membrane following cell-cell or cell-ECM adhesion.