Encode (original) (raw)

Threads

7 DNA methylation

ENCODE analysis identifies dynamic DNA methylation patterns and relationships to regulatory elements

ENCODE: The human encyclopaedia

First they sequenced it. Now they have surveyed its hinterlands. But no one knows how much more information the human genome holds, or when to stop looking for it.
News Feature5 Sep 2012 Nature

Lessons for big-data projects

To be successful, consortia need clear management, codes of conduct and participants who are committed to working for the common good, says ENCODE lead analysis coordinator Ewan Birney.

ENCODE explained

The Encyclopedia of DNA Elements (ENCODE) project dishes up a hearty banquet of data that illuminate the roles of the functional elements of the human genome. Here, six scientists describe the project and discuss how the data are influencing research directions across many fields. See Articles p.57, p.75, p.83, p.91, p.101 & Letter p.109

Research papers in Nature

An integrated encyclopedia of DNA elements in the human genome

This overview of the ENCODE project outlines the data accumulated so far, revealing that 80% of the human genome now has at least one biochemical function assigned to it; the newly identified functional elements should aid the interpretation of results of genome-wide association studies, as many correspond to sites of association with human disease.

Landscape of transcription in human cells

A description is given of the ENCODE effort to provide a complete catalogue of primary and processed RNAs found either in specific subcellular compartments or throughout the cell, revealing that three-quarters of the human genome can be transcribed, and providing a wealth of information on the range and levels of expression, localization, processing fates and modifications of known and previously unannotated RNAs.

The accessible chromatin landscape of the human genome

An extensive map of human DNase I hypersensitive sites, markers of regulatory DNA, in 125 diverse cell and tissue types is described; integration of this information with other ENCODE-generated data sets identifies new relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns.

Architecture of the human regulatory network derived from ENCODE data

A description is given of the ENCODE consortium’s efforts to examine the principles of human transcriptional regulatory networks; the results are integrated with other genomic information to form a hierarchical meta-network where different levels have distinct properties.

The long-range interaction landscape of gene promoters

Chromosome conformation capture carbon copy (5C) is used to look at the relationships between functional elements and distal target genes in 1% of the human genome in three dimensions; the study describes numerous long-range interactions between promoters and distal sites that include elements resembling enhancers, promoters and CTCF-bound sites, their genomic distribution and complex interactions.