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Nature Studies Include ENCODE Phase Three Papers, Method for Imaging the Human Genome

A collection of papers representing the third phase of the Encyclopedia of DNA Elements (ENCODE) project — which was launched in 2003 to identify all functional elements in the human genome — are presented in Nature, Nature Methods, and Nature Communications this week. In the lead report, ENCODE members describe the generation of nearly 6,000 new experiments that extend previous phases of ENCODE to define and annotate diverse classes of functional elements in the human and mouse genomes. "Whereas many experiments during earlier phases of ENCODE used model cell lines, a major goal of phase III was to broaden coverage of primary cells and tissues," and the encyclopedia now encompasses 503 biological cells or tissue types from more than 1,369 biological sample sources, the investigators write. 

Related papers describe new data set of RNA elements in the human genome that are recognized by RNA-binding proteins; the landscape of cohesin-mediated chromatin loops in the human genome; analyses of chromatin-associated proteins in a single human cell type; an atlas of dynamic chromatin landscapes in mouse fetal development; a study of spatiotemporal DNA methylome dynamics in the developing mouse fetus; changes in the mouse embryo transcriptome at whole-tissue and single-cell resolution; the mapping of human genomic footprints using high-density DNase I cleavage maps from 243 human cell types and states; a comprehensive and precise map of human DNase I hypersensitive sites; a custom annotation for using ENCODE data for cancer genomics; a genome-wide annotation of the pseudogenes in the mouse reference genome and inbred mouse strains; a tool for quantifying sample-relatedness and detecting incorrectly paired sequencing datasets from different donors; and a framework for accurately predicting active enhancers in a cell-type-specific manner.

"It is expected that many more elements in the human genome will be identified across a variety of cell types and conditions, their activities will be revealed (often at the single-cell level), and their biological functions will be inferred more accurately," ENCODE members write in an accompanying Perspectives piece. "The development of a systems-wide understanding of function and integration with genetic information associated with human traits will greatly enhance our understanding of human biology and disease."

GenomeWeb has more on these papers, here.

A series of strategies for super-resolution imaging of the human genome is reported by a team of Harvard Medical School researchers and collaborators in Nature Methods this week. Called OligoFISSEQ, the suite of methods uses fluorescence in situ sequencing of barcoded Oligopaint probes to enable the rapid visualization of many targeted genomic regions. OligoFISSEQ is also compatible with the single-molecule localization method OligoSTORM5, the scientists note, "laying the foundation for accelerated single-molecule super-resolution imaging of large swaths of, if not entire, human genomes."