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腾讯登录J Biol Chem：ENCODE计划揭示人类基因组调节和结构组织上的重大研究进展
| 导读 | 近日，国家人类基因组研究所公布了一项长达5年的关于人类基因组调节和结构组成的研究报告，这项计划名为ENCODE，其代表的意思是DNA元件百科全书（Encyclopedia of DNA Elements），刊登在近期国际杂志<em>Journal of Biological Chemistry</em>上的研究论文报告了研究发现的其中一些内容。
“ENCODE计划不仅... |
近日，国家人类基因组研究所公布了一项长达5年的关于人类基因组调节和结构组成的研究报告，这项计划名为ENCODE，其代表的意思是DNA元件百科全书（Encyclopedia of DNA Elements），刊登在近期国际杂志<em>Journal of Biological Chemistry</em>上的研究论文报告了研究发现的其中一些内容。
“ENCODE计划不仅仅产生了大量机体的基因组数据，而且其也分析了很多组织的信息以便我们更好地理解不同类型细胞中的基因组功能。这些综合型分析的结果揭示了机体的分子机器如何进行反应，以及解释了DNA如何工作产生蛋白质，以及RNAs为什么对于机体非常重要，”来自宾夕法尼亚大学的研究者Ross Hardison这样说，该研究者是该文章的第一作者。
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人类基因组包括了30亿个DNA碱基对，但是仅仅有很小一部分DNA来负责编码产生蛋白质。剩余的遗传信息的角色和功能目前并不清楚，这些剩余的DNA序列被称为无用的DNA序列。但是ENCODE研究计划的结果填补了这一信息空缺，这个计划的研究结果揭示了超过80%的人类基因组都和生物学功能直接相关。
本文的研究主要阐述了调节基因开关表达的蛋白质的相关信息，这些蛋白质可以在离目的基因一定的距离处对目的基因进行调节，而且其在与之反应的染色体上也确定了具体的位点，在特定位点上对DNA的修饰可以影响基因的表达，而且RNA的这种功能形式可以调节遗传信息的相关表达。
研究者Hardison表示，来自这项计划中关于基因调节的深入只是将会对未来医疗科学有正促进的影响，比如近日的遗传研究揭示了许多基因组位点，其可以影响一个人对于普通疾病的敏感性。这项计划也解释了涉及基因调节的许多区域，而且这些数据为理解这些区域的突变如何影响疾病的敏感性提供了相应的假设。
这项计划背后，研究者付出的努力非常之大，其中包括了美国、英国、西班牙、新加坡和日本的32个实验室超过440个科学家的努力，研究者在147个不同类型的组织中进行了超过1600次单独试验，研究结果于近日刊登在了国际主流杂志上，5篇刊登于Nature上，18篇刊登于Genome Research上，以及6篇刊登于Genome Biology上。
编译自：<a title="" href="http://www.sciencedaily.com/releases/2012/09/120905154613.htm" target="_blank">Major Advances in Understanding the Regulation and Organization of the Human Genome</a>
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<a title="" href="http://dx.doi.org/doi:10.1074/jbc.R112.365940" target="_blank">doi:10.1074/jbc.R112.365940</a>
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<br/><strong>Introduction to the Thematic Minireview Series on results from the ENCODE Project: Integrative global analyses of regulatory regions in the human genome </strong><br/>
Peggy J. Farnham
The Encyclopedia of DNA Elements (ENCODE) Project (www.encodeproject.org) is an international collaboration of research groups funded by the National Human Genome Research Institute, with the goal of delineating all functional elements encoded in the human genome. This project began in 2003 with a targeted analysis of a selected 1% of the human genome. The results from the pilot project were published in 2007 and a second phase of funding was then provided to scale the project to the entire human genome. Genome-scale projects in ENCODE involve the identification and quantification of RNA species in whole cells and subcellular compartments, mapping of protein-coding and non-coding genes by manual review and experimental methods, delineation of chromatin and DNA accessibility, mapping of histone modifications and transcription factor binding sites by chromatin immunoprecipitation (ChIP), and measurement of DNA methylation. More recently, ENCODE has adopted additional approaches that have not yet resulted in extensive datasets, including the examination of long-range chromatin interactions, the analysis of RNA binding proteins, and the validation of transcriptional enhancers and silencers. To date, more than 2000 datasets have been deposited for public use by the ENCODE Project at the University of California Santa Cruz (UCSC) Genome Browser; to encourage public use of the datasets, a “user’s guide” to the ENCODE datasets has been published. As the second phase of the ENCODE Project nears completion, the ENCODE Consortium has prepared a large, integrative manuscript that includes analyses of experiments from 147 cell types and provides a summary of their functional annotation of the human genome. Additionally, other more narrowly focused studies on subsets of ENCODE data have been or will soon be published; for a list of ENCODE publications, see <a href="http://genome-preview.ucsc.edu/ENCODE/pubs.html">http://genome-preview.ucsc.edu/ENCODE/pubs.html</a>).
<br/>来源：生物谷
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“ENCODE计划不仅仅产生了大量机体的基因组数据，而且其也分析了很多组织的信息以便我们更好地理解不同类型细胞中的基因组功能。这些综合型分析的结果揭示了机体的分子机器如何进行反应，以及解释了DNA如何工作产生蛋白质，以及RNAs为什么对于机体非常重要，”来自宾夕法尼亚大学的研究者Ross Hardison这样说，该研究者是该文章的第一作者。
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人类基因组包括了30亿个DNA碱基对，但是仅仅有很小一部分DNA来负责编码产生蛋白质。剩余的遗传信息的角色和功能目前并不清楚，这些剩余的DNA序列被称为无用的DNA序列。但是ENCODE研究计划的结果填补了这一信息空缺，这个计划的研究结果揭示了超过80%的人类基因组都和生物学功能直接相关。
本文的研究主要阐述了调节基因开关表达的蛋白质的相关信息，这些蛋白质可以在离目的基因一定的距离处对目的基因进行调节，而且其在与之反应的染色体上也确定了具体的位点，在特定位点上对DNA的修饰可以影响基因的表达，而且RNA的这种功能形式可以调节遗传信息的相关表达。
研究者Hardison表示，来自这项计划中关于基因调节的深入只是将会对未来医疗科学有正促进的影响，比如近日的遗传研究揭示了许多基因组位点，其可以影响一个人对于普通疾病的敏感性。这项计划也解释了涉及基因调节的许多区域，而且这些数据为理解这些区域的突变如何影响疾病的敏感性提供了相应的假设。
这项计划背后，研究者付出的努力非常之大，其中包括了美国、英国、西班牙、新加坡和日本的32个实验室超过440个科学家的努力，研究者在147个不同类型的组织中进行了超过1600次单独试验，研究结果于近日刊登在了国际主流杂志上，5篇刊登于Nature上，18篇刊登于Genome Research上，以及6篇刊登于Genome Biology上。
编译自：<a title="" href="http://www.sciencedaily.com/releases/2012/09/120905154613.htm" target="_blank">Major Advances in Understanding the Regulation and Organization of the Human Genome</a>
<div id="ztload">
<div>
<div>
<img src="http://www.bioon.com/biology/UploadFiles/201209/2012090622481731.jpg" alt="" width="113" height="149" border="0" />
<a title="" href="http://dx.doi.org/doi:10.1074/jbc.R112.365940" target="_blank">doi:10.1074/jbc.R112.365940</a>
PMC:
PMID:
</div>
<div>
<br/><strong>Introduction to the Thematic Minireview Series on results from the ENCODE Project: Integrative global analyses of regulatory regions in the human genome </strong><br/>
Peggy J. Farnham
The Encyclopedia of DNA Elements (ENCODE) Project (www.encodeproject.org) is an international collaboration of research groups funded by the National Human Genome Research Institute, with the goal of delineating all functional elements encoded in the human genome. This project began in 2003 with a targeted analysis of a selected 1% of the human genome. The results from the pilot project were published in 2007 and a second phase of funding was then provided to scale the project to the entire human genome. Genome-scale projects in ENCODE involve the identification and quantification of RNA species in whole cells and subcellular compartments, mapping of protein-coding and non-coding genes by manual review and experimental methods, delineation of chromatin and DNA accessibility, mapping of histone modifications and transcription factor binding sites by chromatin immunoprecipitation (ChIP), and measurement of DNA methylation. More recently, ENCODE has adopted additional approaches that have not yet resulted in extensive datasets, including the examination of long-range chromatin interactions, the analysis of RNA binding proteins, and the validation of transcriptional enhancers and silencers. To date, more than 2000 datasets have been deposited for public use by the ENCODE Project at the University of California Santa Cruz (UCSC) Genome Browser; to encourage public use of the datasets, a “user’s guide” to the ENCODE datasets has been published. As the second phase of the ENCODE Project nears completion, the ENCODE Consortium has prepared a large, integrative manuscript that includes analyses of experiments from 147 cell types and provides a summary of their functional annotation of the human genome. Additionally, other more narrowly focused studies on subsets of ENCODE data have been or will soon be published; for a list of ENCODE publications, see <a href="http://genome-preview.ucsc.edu/ENCODE/pubs.html">http://genome-preview.ucsc.edu/ENCODE/pubs.html</a>).
<br/>来源：生物谷
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