Copy number variation and gene expression

拷贝数变异和基因表达

• 批准号: BB/I006370/1
• 负责人: John Armour
• 金额: $ 52.42万
• 依托单位: University of Nottingham
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2011
• 资助国家: 英国
• 起止时间: 2011 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FI006370%2F1
• 关键词: Copy; number; variation; gene; expression

In many animals and plants, the structure of the genome appears to be very wasteful, with large amounts of DNA apparently having no function, and many sequences being highly repeated. In addition to this complexity in genome structure, there is variation in the gene content of the genome. There have been rapid advances recently in our understanding of such variation in gene copy number, particularly in the study of the human genome. For most human genes, all of us have two copies - one from each parent. For some genes, however, different people can have different numbers of copies, and it is clear that the number of copies can matter. People who are Rhesus-negative have no copies at all of the corresponding gene, while Rhesus-positive individuals have one or two copies. These differences underlie the mother-child mismatch that can lead to a 'Rhesus baby' . Similarly, reduced numbers of the alpha-globin gene (usually four copies per person) are the basis of the globally common blood disease alpha-thalassaemia. Although natural selection generally ensures that variants do not get to be very common if they have negative effects on their carriers, it is clear that in humans and many other species, there are some important genes that show extensive variation, with many different gene copy numbers in the population. For example, the gene encoding the salivary amylase enzyme, responsible for digestion of starch in food, is present in variable numbers - some people have as few as two copies of this gene, while others can have as many as 12. It has been suggested that this variation leads to corresponding variation in the production of amylase in saliva, and so to variation in ability to digest starch. This is an attractive idea, but is it really true? More generally, does variation in gene number really lead to variation in gene function - and if so, how? In reality, the situation is complicated. Having twice as many genes does not necessarily mean that twice as much of the relevant protein is made - there are examples in which extra copies of a gene may or may not be used, or be only partially active, depending on its precise position, or on the number of other copies in the same cell. This project examines directly whether copy number variation leads to changes in gene expression - and if so in what patterns. To do this we will measure protein levels in cells and secretions, and ask how they relate to the copy number of variable genes. Surprisingly, counting copies of DNA in a genome is technically difficult - indeed, sequencing DNA is much more straightforward than knowing exactly how many copies have been sequenced. Clearly, if copy number is not being measured accurately, deductions about the effect on gene expression will also be inaccurate. It is therefore a real challenge in this project to type copy number variation accurately, so that (for example) a test can clearly distinguish whether an individual has 6 or 7 copies of a variable gene. One particular advantage our group has in undertaking this work is experience in the accurate measurement of gene copy number. The project examines three examples of variable-number genes from the human genome that show wide variation in number; the alpha-defensins (involved, as their name implies, in defence against infection) vary commonly between 4 and 11 copies per person; the salivary amylase gene, varying 2-12 copies per person; and finally, the beta-defensin DEFB109 varies independently of the alpha-defensins (between 2 and 7 copies in most people) but also has some copies that are inactivated by an internal mutation - in this case it is likely that gene expression will relate not just to the total number of copies, but the number of copies capable of making an active protein.

在许多动物和植物中，基因组的结构似乎非常浪费，大量的DNA显然没有功能，许多序列高度重复。除了基因组结构的复杂性之外，基因组的基因内容也存在变异。最近，我们对基因拷贝数变异的理解有了迅速的进展，特别是在人类基因组的研究中。对于大多数人类基因，我们所有人都有两个副本-每个来自父母。然而，对于某些基因，不同的人可能有不同数量的拷贝，很明显，拷贝的数量可能很重要。恒河猴阴性的人没有相应基因的拷贝，而恒河猴阳性的人有一个或两个拷贝。这些差异是导致“恒河猴宝宝”的母子不匹配的基础。同样，α-珠蛋白基因数量的减少（通常每人四个拷贝）是全球常见血液疾病α-地中海贫血的基础。虽然自然选择通常确保变异不会变得非常普遍，如果它们对它们的载体产生负面影响，但很明显，在人类和许多其他物种中，有一些重要的基因显示出广泛的变异，在人群中有许多不同的基因拷贝数。例如，负责消化食物中淀粉的唾液淀粉酶的编码基因以不同的数量存在-有些人只有两个这种基因的拷贝，而另一些人可能有多达12个。有人认为，这种变化导致唾液中淀粉酶产生的相应变化，从而导致消化淀粉能力的变化。这是一个很吸引人的想法，但这真的是真的吗？更一般地说，基因数量的变化真的会导致基因功能的变化吗？如果是的话，又是如何导致的呢？实际上，情况是复杂的。拥有两倍多的基因并不一定意味着两倍多的相关蛋白质被制造出来--有一些例子表明，一个基因的额外拷贝可能被使用，也可能不被使用，或者只是部分活跃，这取决于它的精确位置，或者取决于同一细胞中其他拷贝的数量。该项目直接研究拷贝数的变化是否会导致基因表达的变化，如果是的话，是什么样的模式。为了做到这一点，我们将测量细胞和分泌物中的蛋白质水平，并询问它们与可变基因拷贝数的关系。令人惊讶的是，计算基因组中DNA的拷贝数在技术上是困难的--事实上，对DNA进行测序比确切知道有多少拷贝被测序要简单得多。显然，如果拷贝数没有被准确测量，那么关于对基因表达的影响的推断也将是不准确的。因此，准确地对拷贝数变异进行分型是该项目中的真实的挑战，以便（例如）测试可以清楚地区分个体是否具有可变基因的6个或7个拷贝。我们小组在进行这项工作中的一个特别优势是在精确测量基因拷贝数方面的经验。该项目研究了人类基因组中的三个可变数量基因的例子，这些基因在数量上表现出很大的差异;（涉及，顾名思义，在防御感染）变化通常在4和11个拷贝之间每人;唾液淀粉酶基因，变化2-12个拷贝每人;最后，β-防御素DEFB 109的变化独立于α-防御素（大多数人有2到7个拷贝），但也有一些拷贝因内部突变而失活-在这种情况下，基因表达可能不仅与总拷贝数有关，而且与能够产生活性蛋白质的拷贝数有关。

项目成果

Copy number variation of human AMY1 is a minor contributor to variation in salivary amylase expression and activity.

• DOI: 10.1186/s40246-017-0097-3
• 发表时间: 2017-02-20
• 期刊: Human genomics
• 影响因子: 4.5
• 作者: Carpenter D;Mitchell LM;Armour JA
• 通讯作者: Armour JA

Inferring mechanisms of copy number change from haplotype structures at the human DEFA1A3 locus.

• DOI: 10.1186/1471-2164-15-614
• 发表时间: 2014-07-21
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Black HA;Khan FF;Tyson J;Al Armour J
• 通讯作者: Al Armour J

Obesity, starch digestion and amylase: association between copy number variants at human salivary (AMY1) and pancreatic (AMY2) amylase genes.

• DOI: 10.1093/hmg/ddv098
• 发表时间: 2015-06-15
• 期刊: Human molecular genetics
• 影响因子: 3.5
• 作者: Carpenter D;Dhar S;Mitchell LM;Fu B;Tyson J;Shwan NA;Yang F;Thomas MG;Armour JA
• 通讯作者: Armour JA

Accurate measurement of gene copy number for human alpha-defensin DEFA1A3.

• DOI: 10.1186/1471-2164-14-719
• 发表时间: 2013-10-20
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Khan FF;Carpenter D;Mitchell L;Mansouri O;Black HA;Tyson J;Armour JA
• 通讯作者: Armour JA