ARK-Genomics - UK centre for farm animal functional genomics

ARK-Genomics的主要目标是支持农场动物基因组学社区的研究需求。基因组学是科学家在全基因组（生物体中基因的集合）水平上研究基因的功能和作用的一个研究领域。随着包括鸡和牛在内的许多生物的基因组序列的公布，这一点尤为及时。英国农场动物基因组学中心ARK-Genomics （http://www.ark-genomics.org）是在BBSRC研究基因功能倡议的资助下建立的。ARK-Genomics与大多数来自研究机构和大学的科学家一起研究问题。目前，55份申请已获批准，28份仍在等待资助机构的决定。这些项目涵盖了广泛的需求，包括特定农场动物种群的基因与身体特征的关联（遗传联系）以及基因的功能，例如，在应对传染病方面的功能。遗传连锁研究需要追踪家族内的基因，这一过程被称为基因分型。ARK-Genomics已经建立了可以追踪数千种动物的100种DNA变异的方法。然而，随着农场动物基因组序列的公布，数以百万计的DNA变体正在被识别出来。这些个体或单核苷酸多态性（snp）之间DNA序列的差异催生了对数千种动物的大量snp进行快速廉价基因分型的新技术。ARK-Genomics提供这些技术。与我们的合作者一起，我们已经描述了鸡、猪和牛的数千个基因。这些技术已被用于制造DNA芯片（在玻片上标记每个基因的特定DNA），这种芯片可用于检测任何组织中的基因表达。这些阵列将进一步发展，以增加阵列上基因的代表性，同时降低其生产和使用的成本。随着寡核苷酸（合成DNA序列）价格的降低，将生产基于20,000个寡核苷酸的新阵列。这将使标准基因阵列的成本降低50%。最初，将与一个对发育、疾病和行为感兴趣的科学家联盟合作生产鸡20K基因阵列。随后，类似的阵列将用于牛、猪和其他农场动物。每个阵列的细节将与英国剑桥的ENSEMBL团队创建的基因组数据库相匹配，该团队是人类基因组序列的发源地。近年来，通过在细胞系和整个生物体中应用抑制rna （siRNA分子）来操纵基因表达的方法的发展为研究基因在细胞中的作用及其功能提供了有力的工具。ARK-Genomics将与谢菲尔德大学合作，提供针对1000多种鸡基因的siRNA。我们期望这些将是巨大的价值发育生物学家希望了解关键基因的功能在鸡胚胎的发展。这些研究还将得到1.8万个鸡基因中近50%的全长基因拷贝（cDNA）的帮助。这个基因组学设施的最初发展已经为农场动物基因组学创造了一个核心的专业知识，在这个应用程序中，这些将得到扩展。将开发新的技术和资源，包括用于比较相关生物体基因组的基因组阵列，以及确定基因何时何地起作用的控制区和位点的图谱。这项申请是为了以最具成本效益和最及时的方式维护和发展ARK-Genomics提供的基因组设施和资源，以满足农场动物研究界的需求。ARK-Genomics的建立使英国处于农场动物科学的前沿，这些资金需要保持在那里。

The primary aim of ARK-Genomics is to support the research needs of the Farm Animal Genomics Community. Genomics is a research field in which scientists study the function and role of genes at the whole genome (the collection of genes in a living organism) level. This is particularly timely with the release of the genome sequences of many organisms, including the chicken and soon the cow. The UK Centre for Farm Animal Genomics, ARK-Genomics (http://www.ark-genomics.org), was established with funds from the BBSRC Investigating Gene Function initiative. ARK-Genomics works together with scientists, mostly from research institutes and universities, on research problems. Currently, 55 applications have been successful and 28 are still awaiting a decision from funding bodies. These projects cover a wide range of needs, including the association of genes with physical characteristics (genetic linkage) in specific populations of farm animals and the function of genes, for example, in response to infectious diseases. Genetic linkage studies require the tracking of genes within families, a process known as genotyping. ARK-Genomics has established methods that can track 100s of DNA variants in 1000s of animals. However with the release of the genome sequences of farm animals, millions of DNA variants are being recognised. These differences in DNA sequences between individual or single nucleotide polymorphisms (SNPs) have spawned new technologies for rapid and cheap genotyping of large numbers of SNPs on 1000s of animals. ARK-Genomics provides access to these technologies. Working together with our collaborators we have characterised thousands of genes from chickens, pigs and cattle. These have been used to create DNA chips (DNA specific for each gene spotted onto glass slides) that can be used to detect the expression of genes in any tissue. These arrays will be developed further increasing the representation of genes on the arrays whilst decreasing the costs of their production and use. With the reduction in oligonucleotide (synthetic DNA sequences) prices new arrays based on 20,000 oligonucleotides will be produced. These will reduce the cost of the standard gene arrays by 50 percent. Initially a chicken 20K gene array will be produced in collaboration with a consortium of scientists with interests in development, disease and behaviour. Later similar arrays will be made for cattle, pigs and other farm animals. The details of each array will be matched to the genome databases being created by the ENSEMBL team in Cambridge, the UK home for the human genome sequence. The recent development of methods to manipulate the expression of genes through the application of inhibitory RNAs (siRNA molecules) in cell lines and whole organisms provides a powerful tool to examine the role of genes and their function in the cell. In collaboration with the University of Sheffield ARK-Genomics will provide siRNA specific to over 1000 chicken genes. We expect these will be of immense value to developmental biologists wishing to understand the function of key genes in the development of the chick embryo. These studies will also be aided by the full length copies of the genes (cDNA) available for almost 50 percent of the 18,000 chicken genes. The original development of this genomics facility has created a core of expertise for farm animal genomics and in this application these will be extended. New technologies and resources will be developed, including genomic arrays to compare the genomes of related organisms and the mapping of control regions, sites that determine when and where genes work. This application is for funds to maintain and develop the genomic facilities and resources provided by ARK-Genomics for the needs of the farm animal research community in the most cost effective and timely manner. The establishment of ARK-Genomics has enable d the UK to be at the leading edge of farm animal science, these funds are needed to remain there.