Collection |
Access the collected papers by exploring the thematic threads that run through them, with topics such as DNA methylation, RNA or machine learning.
ENCODE discovers many new transcription-factor-binding-site motifs and explores their properties
Both chromatin accessibility and histone modifications have different patterns around different transcription factor binding sites
The prevalence and analysis of ENCODE data are changing the definition and characterization of intergenic and genic regions
Patterns of gene expression can be modelled using histone modifications and transcription factor binding at promoters
Many novel and previously known non-coding RNA species are characterized in ENCODE
Many novel and previously known non-coding RNA species are characterized in ENCODE
ENCODE analysis identifies dynamic DNA methylation patterns and relationships to regulatory elements
ENCODE has developed methods to discover enhancers, and characterized them using comparisons with other data sets and by molecular biology experiments
ENCODE mapped long-range looping interactions between functional elements and genes, placing them in a three-dimensional context to reveal their functional relationships
ENCODE data analysis helps to describe the various types of regulatory "wiring" implicit in the genome
ENCODE has applied machine learning approaches to enable integration and exploration of large and diverse data
ENCODE provides an initial interpretation of many human variants and plausible leads for the role of many variants identified in genome-wide association studies
The imprint of evolutionary selection on ENCODE regulatory elements is manifested between species and within human populations.
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.
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.
The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription-factor association, chromatin structure and histone modification. In this overview, the Consortium guides the readers through the project itself, the data and their integrated analyses. Eighty per cent of the human genome now has at least one biochemical function assigned to it. In addition to expanding our understanding of how gene expression is regulated on a genome-wide scale, the newly identified functional elements should help researchers to interpret the results of genome-wide associated studies because many correspond to sites associated with human disease.
If they remain vigilant, early-career researchers can reap benefits from taking part in big international projects.
The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription-factor association, chromatin structure and histone modification. In this overview, the Consortium guides the readers through the project itself, the data and their integrated analyses. Eighty per cent of the human genome now has at least one biochemical function assigned to it. In addition to expanding our understanding of how gene expression is regulated on a genome-wide scale, the newly identified functional elements should help researchers to interpret the results of genome-wide associated studies because many correspond to sites associated with human disease.
These authors describe the ENCODE (Encyclopedia of DNA Elements) effort to provide a complete catalogue of primary and processed RNAs found either in specific sub-cellular compartments or throughout the cell. They show that three-quarters of the human genome can be transcribed, and provide a wealth of information about the range and levels of expression, localization, processing fates and modifications of both known and previously unannotated RNAs. Collectively, these observations suggest that the current concept of a gene should be revisited.
This paper describes the first extensive map of human DNaseI hypersensitive sites — markers of regulatory DNA — in 125 diverse cell and tissue types. Integration of this information with other data sets generated by ENCODE (Encyclopedia of DNA Elements) identified new relationships between chromatin accessibility, transcription, DNA methylation and regulatory-factor occupancy patterns. Evolutionary-conservation analysis revealed signatures of recent functional constraint within DNaseI hypersensitive sites.
DNaseI footprinting detects DNA sequences that are protected from cleavage by DNaseI because they are bound by regulatory factors. Studying these footprints in 41 diverse cell and tissue types, the authors describe millions of short sequence elements that are conserved recognition sequences for DNA-binding proteins. The effort nearly doubles the size of the human cis-regulatory lexicon and provides insight into chromatin states and levels of evolutionary conservation. A large collection of novel regulatory-factor recognition motifs that closely parallel major regulators of development, differentiation and pluripotency is also described.
This manuscript describes the effort of the ENCODE (Encyclopedia of DNA Elements) Consortium to examine the principles of human transcriptional regulatory networks, using a subset of 119 transcription factors. The results are integrated with other genomic information to form a multi-level meta-network in which different levels have distinct properties. The findings will aid future interpretations of human genomics and help us to understand the basic principles of human biology and disease.
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.
