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ENCODE 3

How cells, tissues and organisms interpret the information encoded in the genome has vital implications for our understanding of development, health and disease. Launched in 2003, the ENCyclopedia Of DNA Elements (ENCODE) project aims to map the functional elements in the human genome (later expanded to include model organisms).

This Collection showcases the main articles and related content resulting from the third phase of ENCODE, during which almost 6,000 new experiments were performed (4,834 involving human samples and 1,158 with mouse samples) and an online registry of more than one million human and mouse candidate cis-regulatory elements (cCREs) was curated. The Encyclopedia paper gives an overview of the various assays and describes the registry of cCREs, and in the companion articles, individual data types are analysed in more detail and the development of novel methodology is reported. This dedicated collection also contains a Perspective, News & Views articles and links to other resources

The Encyclopedia at a Glance

A collection of research articles and related content describing the Encyclopedia of DNA Elements, its datasets and tools.

Feature |

The authors summarize the history of the ENCODE Project, the achievements of ENCODE 1 and ENCODE 2, and how the new data generated and analysed in ENCODE 3 complement the previous phases.

Perspective | Open Access | | Nature

Mouse Epigenetics and Gene Expression

Human Gene Expression and RNA Regulation

ChIP–seq and CETCh–seq data are used to analyse binding maps for 208 transcription factors and other chromatin-associated proteins in a single human cell type, providing a comprehensive catalogue of the transcription factor landscape and gene regulatory networks in these cells.

Article | Open Access | | Nature

A map of cohesin-mediated chromatin loops in 24 types of human cells identifies loops that show cell-type-specific variation, indicating that chromatin loops may help to specify cell-specific gene expression programs and functions.

Article | Open Access | | Nature

ENCODE is a resource comprising thousands of functional genomic datasets. Here, the authors present custom annotation within ENCODE for cancer, highlighting a workflow that can help prioritise key elements in oncogenesis.

Article | Open Access | | Nature Communications

Giovanni Quinones-Valdez et al. examined the role of over 200 RNA-binding proteins in mediating A-to-I RNA editing. They identified several RNA-binding proteins that regulate ADAR1 expression, interaction, or binding with Alu elements in a cell type-specific manner.

Article | Open Access | | Communications Biology

Computational Analysis and Tools