An Integrated Encyclopedia of DNA Elements in the Human Genome

Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247.

Abstract

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.

Publication types

  • Research Support, American Recovery and Reinvestment Act
  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Alleles
  • Animals
  • Binding Sites / genetics
  • Chromatin / genetics
  • Chromatin / metabolism
  • Chromatin Immunoprecipitation
  • Chromosomes, Human / genetics
  • Chromosomes, Human / metabolism
  • DNA / genetics*
  • DNA Footprinting
  • DNA Methylation / genetics
  • DNA-Binding Proteins / metabolism
  • Deoxyribonuclease I / metabolism
  • Encyclopedias as Topic*
  • Exons / genetics
  • Genetic Predisposition to Disease / genetics
  • Genetic Variation / genetics
  • Genome, Human / genetics*
  • Genome-Wide Association Study
  • Genomics*
  • Histones / chemistry
  • Histones / metabolism
  • Humans
  • Mammals / genetics
  • Molecular Sequence Annotation*
  • Neoplasms / genetics
  • Polymorphism, Single Nucleotide / genetics
  • Promoter Regions, Genetic / genetics
  • Proteins / genetics
  • Regulatory Sequences, Nucleic Acid / genetics*
  • Sequence Analysis, RNA
  • Transcription Factors / metabolism
  • Transcription, Genetic / genetics

Substances

  • Chromatin
  • DNA-Binding Proteins
  • Histones
  • Proteins
  • Transcription Factors
  • DNA
  • Deoxyribonuclease I

Grant support