my5c.umassmed.eduDekker Lab : Welcome

| welcome | about | my5C | collaborations | help | register | login | my5C. primers my5C. uploads my5C. heatmap my3C. primers my3C. uploads my3C. plot Welcome to 3DG We study how a genome is organized in three dimensions inside the nucleus. The spatial organization of a genome plays important roles in regulation of genes and maintenance of genome stability. Many diseases, including cancer, are characterized by alterations in the spatial organization of the genome. How genomes are organized in three dimensions, and how this affects gene expression is poorly understood. To address this issue we study the genomes of human and yeast, using a set of powerful molecular and genomic tools that we developed. In order to determine the spatial organization of chromosomes at high resolution we have developed the Chromosome Conformation Capture technology, commonly referred to as 3C (Dekker et al. (2002), Science, 295: 1306-1311). 3C is used to detect physical interactions between pairs of genomic loci. 3C is now widely used and has proven to be a very powerful tool to detect cis- and trans-interactions between genes and regulatory elements. In order to dramatically increase the throughput of the analysis of chromatin interactions we have developed the 3C-Carbon Copy (5C) technology that can be used to analyze millions of chromatin interactions in parallel (Dostie et al. (2006), Genome Research, 16(10): 1299-1309). 5C was the first method that combines 3C with microarray detection. 5C is highly versatile and can also be used in conjunction with ultra-high-throughput single molecule DNA sequencing. We are currently using 3C and 5C to map and study the networks of chromatin interactions that underlie long-range gene regulation in the human genome. To facilitate 5C experiment workflow, a full suite of web-based tools were developed for the design, analysis and data visualization of this new datatype. These tools allow users to design a 5C experiment for any given locus / species and ease them through the primer layout and filtering processes. Once designed a full spectrum of analysis, integration and visualizations tools become available. We call these tools...