Enciclopédia de DNA - ENCODE

Enciclopédia de DNA

20/4/2011

Agência FAPESP – O projeto “Encyclopedia of DNA Elements” (Encode) acaba de publicar um guia para auxiliar os cientistas a como utilizar os dados e recursos produzidos pelo projeto.

O Encode é um projeto internacional lançado em 2003 pelo National Human Genome Research Institute (NHGRI), dos Estados Unidos, com o objetivo de encontrar todos os elementos funcionais do genoma humano. Todos os dados gerados pelo projeto são publicados rapidamente em bancos de dados públicos.

O guia foi publicado nesta terça-feira (19/4) na revista PLoS Biology e, da mesma forma que os dados e softwares usados no projeto, estará disponível no site encodeproject.org.

Imagem: Darryl Leja (NHGRI), Ian Dunham (EBI) via PLoS Biology

“O projeto Encode exige a colaboração de muitas pessoas espalhadas pelo mundo que estão na vanguarda de suas áreas de pesquisa, para trabalhar de forma coordenada de modo a desvendar as funções do genoma humano”, disse Richard Myers, presidente do Instituto de Biotecnologia HudsonAlpha, um dos membros do projeto.

O guia explica como os dados podem ser úteis na interpretação de associações entre nucleotídeos únicos e doenças, usando exemplos como o da relação entre o gene c-Myc e o câncer.

Os dados permitem que pesquisas sejam feitas em milhares de variantes identificadas em estudos de associação genômica ampla, enfocando questões relacionadas aos mecanismos por trás das suscetibilidades a determinadas doenças.

Cientistas que integram o projeto Encode estão aplicando 20 testes diferentes a 108 linhas celulares usadas comumente. O guia explica como encontrar os dados resultantes desses testes e também a aplicá-los em interpretações do genoma humano.

O guia mostra onde o RNA é produzido a partir do DNA, onde as proteínas se grudam ao DNA e onde partes do código genético humano são modificadas por marcadores químicos adicionais. Essas adições, na forma de proteínas ou outras substâncias químicas, são fundamentais para compreender como as diferentes células no corpo humano interpretam a linguagem do DNA, destacam os autores.

Mais informações: encodeproject.org. 

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A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

The ENCODE Project Consortium

Abstract

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.

Author Summary 

The Encyclopedia of DNA Elements (ENCODE) Project was created to enable the scientific and medical communities to interpret the human genome sequence and to use it to understand human biology and improve health. The ENCODE Consortium, a large group of scientists from around the world, uses a variety of experimental methods to identify and describe the regions of the 3 billion base-pair human genome that are important for function. Using experimental, computational, and statistical analyses, we aimed to discover and describe genes, transcripts, and transcriptional regulatory regions, as well as DNA binding proteins that interact with regulatory regions in the genome, including transcription factors, different versions of histones and other markers, and DNA methylation patterns that define states of the genome in various cell types. The ENCODE Project has developed standards for each experiment type to ensure high-quality, reproducible data and novel algorithms to facilitate analysis. All data and derived results are made available through a freely accessible database. This article provides an overview of the complete project and the resources it is generating, as well as examples to illustrate the application of ENCODE data as a user's guide to facilitate the interpretation of the human genome.

Citation: The ENCODE Project Consortium (2011) A User's Guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biol 9(4): e1001046. doi:10.1371/journal.pbio.1001046

Academic Editor: Peter B. Becker, Adolf Butenandt Institute, Germany

Received: September 23, 2010; Accepted: March 10, 2011; Published: April 19, 2011

Copyright: © 2011 The ENCODE Project Consortium. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: Funded by the National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA. The role of the NIH Project Management Group in the preparation of this paper was limited to coordination and scientific management of the ENCODE Consortium.

Competing interests: The authors have declared that no competing interests exist.

Abbreviations: 3C, Chromosome Conformation Capture; API, application programming interface; CAGE, Cap-Analysis of Gene Expression; ChIP, chromatin immunoprecipitation; DCC, Data Coordination Center; DHS, DNaseI hypersensitive site; ENCODE, Encyclopedia of DNA Elements; EPO, Enredo, Pecan, Ortheus approach; FDR, false discovery rate; GEO, Gene Expression Omnibus; GWAS, genome-wide association studies; IDR, Irreproducible Discovery Rate; Methyl-seq, sequencing-based methylation determination assay; NHGRI, National Human Genome Research Institute; PASRs, promoter-associated short RNAs; PET, Paired-End diTag; RACE, Rapid Amplification of cDNA Ends; RNA Pol2, RNA polymerase 2; RBP, RNA-binding protein; RRBS, Reduced Representation Bisulfite Sequencing; SRA, Sequence Read Archive; TAS, trait/disease-associated SNP; TF, transcription factor; TSS, transcription start site

* E-mail: rmyers@hudsonalpha.org (RMM); jstam@u.washington.edu (JS); mpsnyder@stanford.edu (MS);dunham@ebi.ac.uk (ID); rch8@psu.edu (RCH); bernstein.bradley@mgh.harvard.edu (BEB);gingeras@cshl.edu (TRG); kent@soe.ucsc.edu (WJK); birney@ebi.ac.uk (EB); woldb@caltech.edu (BW);greg.crawford@duke.edu (GEC)

¶ Membership of the ENCODE Project Consortium is provided in the Acknowledgments.

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