Novel genomic effects of Y-linked polymorphisms

描述（由申请人提供）：我们提出的研究是新颖的，假设驱动的，变革性的，与NIH使命相关的。我们最近发现，果蝇的Y染色体是多态性的序列，差异影响数百个常染色体和X-连锁基因的表达的新颖性出现。不同Y染色体对基因表达的数量效应称为Y连锁调控变异（Y-linked regulatory variation，YRV）。该实验为研究YRV的发病机制提供了第一个分子途径。受YRV影响的基因包括所有类型的基因：性别间表达无偏倚，女性偏倚和男性偏倚。许多受YRV影响的基因与适应性性状有关（例如，例如，在一个实施例中，热耐受性）或性选择（e.例如，在一个实施例中，信息素接收）。YRV的发现可能具有重要意义，因为它表明包括人类在内的所有生物体中的Y染色体在通过其大量非编码DNA的互补介导基因表达的主要基因组效应方面非常特殊。拟议的实验将测试的假设，YRV的结果从Y-连锁序列的拷贝数的变化，竞争与限制量的染色质相关蛋白质的结合，影响基因表达水平的常染色体和X-连锁基因。所提出的实验还将检验YRV由与位置效应杂色（PEV）和/或重复相关小干扰RNA（rasiRNA）相关的调节途径介导的假设。因此，拟议的研究是变革性的，因为它可能从根本上改变我们对Y染色体非编码序列通过其对基因调控的影响来解释表型变异的作用的理解。通过调控作用的选择可能会驱动Y染色体中非编码序列的快速进化，这些序列在进化上比单拷贝序列更具动态性。这种观点挑战了目前的范式，即这种序列仅仅是中性进化的“垃圾”DNA。拟议的实验还将确定一组与精子发生的耐热性相关的受YRV影响的候选基因，这是限制许多昆虫（包括传播疟疾的蚊子）生态范围的关键生物因素。我们还将开发与YRV相关的多态性Y染色体的群体动态的理论模型，以确定是否有可能与现实的参数值的竞争性结合的模型为基础。与NIH的使命相关的是，我们关于果蝇Y染色体的发现可能在异染色质丰富的基因组（包括人类基因组）中相当普遍。因此，我们预测，影响人类健康和疾病的重要表型变异最终将追溯到人类染色体中异染色质的变异。这项研究的长期目标是了解Y染色体在遗传变异和进化中的调节作用。最终，X染色体和常染色体的近着丝粒异染色质也必须进行研究，但果蝇Y染色体是研究的起点，因为它的编码序列含量低，非编码重复序列含量高，遗传操作相对容易，而且遗传资源丰富。相关性这项研究的相关性在于它调查了Y染色体对基因表达的新发现影响的分子机制和适应意义，这可能对Y染色体在人类和其他生物体中的作用产生广泛影响。公共卫生相关性：Y染色体被广泛认为是基因贫乏的，缓慢退化的基因组DNA荒地，其唯一的功能是作为X染色体的配对伴侣，并携带不同物种中的雄性或雄性生育力基因。我们的初步研究结果强烈表明，这种观点是错误的。我们的新发现是，Y染色体多态性差异影响基因组中数百个基因的表达水平。我们相信这些效应是由快速进化的，很少了解的Y染色体区域介导的，该区域含有非编码DNA的重复序列。提出的实验在挑战Y染色体影响其他基因表达以及Y染色体如何随时间变化的当前观点方面具有变革性。我们预测，影响人类健康和疾病的重要表型变异最终将追溯到人类Y染色体非编码DNA序列重复的变异。

DESCRIPTION (provided by applicant): We propose research which is novel, hypothesis driven, transformative, and relevant to the NIH mission. The novelty emerges from our recent discovery that the Y chromosome of Drosophila melanogaster is polymorphic for sequences that differentially affect the expression of many hundreds of autosomal and X-linked genes. The quantitative effects of different Y chromosome on gene expression are termed YRV (Y-linked regulatory variation). The proposed experiments provide the first molecular approach to study the mechanism of YRV. The genes affected by YRV include all classes of genes: unbiased in expression between the sexes, female-biased, and male-biased. Many of the genes affected by YRV are related to adaptive traits (e. g., thermal tolerance) or sexual selection (e. g., pheromone reception). The discovery of YRV is potentially of great significance because it suggests that the Y chromosome in all organisms, including humans, is very special in mediating major genomic effects on gene expression through its large complement of noncoding DNA. The proposed experiments will test the hypothesis that YRV results from variation in the copy number of Y-linked sequences that compete with the autosomal and X-linked genes for binding with limiting amounts of chromatin-associated proteins that affect levels of gene expression. The proposed experiments will also test the hypothesis that YRV is mediated by regulatory pathways associated with position-effect variegation (PEV) and/or repeat- associated small interfering RNA (rasiRNA). The proposed research is therefore transformative because it may radically change our understanding of the role of Y chromosome noncoding sequences in accounting for phenotypic variation through its effects on gene regulation. Selection acting through regulatory effects may drive the rapid evolution of noncoding sequences in the Y chromosome, which are evolutionarily much more dynamic than single-copy sequences. This view challenges the current paradigm that such sequences are mere "junk" DNA evolving neutrally. The proposed experiments will also identify a set of YRV-affected candidate genes associated with thermal tolerance of spermatogenesis, a key biological factor in limiting the ecological range of many insects including the mosquitoes that transmit malaria. We will also develop theoretical models for the population dynamics of polymorphic Y chromosomes associated with YRV to determine whether a model based on competitive binding is possible with realistic values of the parameters. The relevance to the NIH mission is that our findings about the Drosophila Y chromosome are likely to be quite general among organisms with genomes rich in heterochromatin including the human genome. Hence we predict that important phenotypic variation affecting human health and disease will ultimately be traced to variation in heterochromatin in human chromosomes. The long-range goal of this research is to understand the regulatory role of the Y chromosome in genetic variation and evolution. Eventually the pericentromeric heterochromatin of the X chromosome and autosomes must also be studied, but the Drosophila Y chromosome is the place to start because of its low content of coding sequences, its high content of noncoding repetitive sequences, its relative ease of genetic manipulation, and the genetic resources available. Relevance The relevance of this research is that it investigates the molecular mechanisms and adaptive significance of newly discovered effects of the Y chromosome on gene expression, which may have widespread implications for the role of the Y chromosome in humans and other organisms. Public Health Relevance: The Y chromosome is widely considered as a gene-poor, slowly degenerating wasteland of genomic DNA whose only functions are to serve as a pairing partner for the X and to carry genes for maleness or male fertility in different species. Our preliminary findings strongly suggest that this view is false. Our novel finding is that Y chromosome polymorphisms differentially affect the level of expression of many hundreds of genes across the genome. We believe that these effects are mediated by rapidly evolving, little understood regions of the Y chromosome containing sequence repeats of noncoding DNA. The experiments proposed are transformative in challenging the current view of Y-chromosome affects on the expression of other genes, and of how the Y chromosome changes through time. We predict that important phenotypic variation affecting human health and disease will ultimately be traced to variation in sequence repeats of noncoding DNA in the human Y chromosome.