Scientific Understanding of Consciousness
Consciousness as an Emergent Property of Thalamocortical Activity

ENCODE encyclopedia of DNA elements in the human genome



Nature Volume: 489, 57–74, (06 September 2012)

An integrated encyclopedia of DNA elements in the human genome

ENCODE Project Consortium


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.

The human genome sequence provides the underlying code for human biology. Despite intensive study, especially in identifying protein-coding genes, our understanding of the genome is far from complete, particularly with regard to non-coding RNAs, alternatively spliced transcripts and regulatory sequences. Systematic analyses of transcripts and regulatory information are essential for the identification of genes and regulatory regions, and are an important resource for the study of human biology and disease. Such analyses can also provide comprehensive views of the organization and variability of genes and regulatory information across cellular contexts, species and individuals.

The Encyclopedia of DNA Elements (ENCODE) project aims to delineate all functional elements encoded in the human genome1, 2, 3. Operationally, we define a functional element as a discrete genome segment that encodes a defined product (for example, protein or non-coding RNA) or displays a reproducible biochemical signature (for example, protein binding, or a specific chromatin structure). Comparative genomic studies suggest that 3–8% of bases are under purifying (negative) selection and therefore may be functional, although other analyses have suggested much higher estimates. In a pilot phase covering 1% of the genome, the ENCODE project annotated 60% of mammalian evolutionarily constrained bases, but also identified many additional putative functional elements without evidence of constraint2. The advent of more powerful DNA sequencing technologies now enables whole-genome and more precise analyses with a broad repertoire of functional assays.

Here we describe the production and initial analysis of 1,640 data sets designed to annotate functional elements in the entire human genome. We integrate results from diverse experiments within cell types, related experiments involving 147 different cell types, and all ENCODE data with other resources, such as candidate regions from genome-wide association studies (GWAS) and evolutionarily constrained regions. Together, these efforts reveal important features about the organization and function of the human genome, summarized below.

The vast majority (80.4%) of the human genome participates in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type. Much of the genome lies close to a regulatory event: 95% of the genome lies within 8kilobases (kb) of a DNA–protein interaction (as assayed by bound ChIP-seq motifs or DNase I footprints), and 99% is within 1.7kb of at least one of the biochemical events measured by ENCODE.

Primate-specific elements as well as elements without detectable mammalian constraint show, in aggregate, evidence of negative selection; thus, some of them are expected to be functional.

Classifying the genome into seven chromatin states indicates an initial set of 399,124 regions with enhancer-like features and 70,292 regions with promoter-like features, as well as hundreds of thousands of quiescent regions. High-resolution analyses further subdivide the genome into thousands of narrow states with distinct functional properties.

It is possible to correlate quantitatively RNA sequence production and processing with both chromatin marks and transcription factor binding at promoters, indicating that promoter functionality can explain most of the variation in RNA expression.

Many non-coding variants in individual genome sequences lie in ENCODE-annotated functional regions; this number is at least as large as those that lie in protein-coding genes.

Single nucleotide polymorphisms (SNPs) associated with disease by GWAS are enriched within non-coding functional elements, with a majority residing in or near ENCODE-defined regions that are outside of protein-coding genes. In many cases, the disease phenotypes can be associated with a specific cell type or transcription factor.

ENCODE data production and initial analyses

Since 2007, ENCODE has developed methods and performed a large number of sequence-based studies to map functional elements across the human genome.

We used manual and automated annotation to produce a comprehensive catalogue of human protein-coding and non-coding RNAs as well as pseudogenes.

This includes 20,687 protein-coding genes (GENCODE annotation, v7) with, on average, 6.3 alternatively spliced transcripts (3.9 different protein-coding transcripts) per locus.

To identify regulatory regions directly, we mapped the binding locations of 119 different DNA-binding proteins and a number of RNA polymerase components in 72 cell types.

DNase I hypersensitive sites and footprints

Chromatin accessibility characterized by DNase I hypersensitivity is the hallmark of regulatory DNA regions. We mapped 2.89 million unique, non-overlapping DNase I hypersensitive sites (DHSs) by DNase-seq in 125 cell types, the overwhelming majority of which lie distal to TSSs.

DNA methylation

Methylation of cytosine, usually at CpG dinucleotides, is involved in epigenetic regulation of gene expression. Promoter methylation is typically associated with repression, whereas genic methylation correlates with transcriptional activity.

The most variably methylated CpGs are found more often in gene bodies and intergenic regions, rather than in promoters and upstream regulatory regions.

Chromosome-interacting regions

Physical interaction between distinct chromosome regions that can be separated by hundreds of kilobases is thought to be important in the regulation of gene expression.

Promoter-anchored integration

Many of the ENCODE assays directly or indirectly provide information about the action of promoters.

We observe two relatively distinct types of promoter: (1) broad, mainly (C+G)-rich, TATA-less promoters; and (2) narrow, TATA-box-containing promoters.

Transcription-factor-binding site-anchored integration

Transcription-factor-binding sites provide a natural focus around which to explore chromatin properties. Transcription factors are often multifunctional and can bind a variety of genomic loci with different combinations and patterns of chromatin marks and nucleosome organization.

All transcription-factor-binding data sets in all cell lines show predominantly asymmetric patterns (asymmetry ratio >0.6) for all chromatin marks but not for DNase I signal. This indicates that most transcription-factor-bound chromatin events correlate with structured, directional patterns of histone modifications, and that promoter directionality is not the only source of orientation at these sites.

We also examined nucleosome occupancy relative to the symmetry properties of chromatin marks around transcription-factor-binding sites.

Transcription factor co-associations

Transcription-factor-binding regions are nonrandomly distributed across the genome.

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