Novel genomic effects of Y-linked polymorphisms

描述(由申请者提供)：我们提出的研究是新颖的、假设驱动的、具有变革性的、与NIH的任务相关的。我们最近发现，果蝇的Y染色体是多态的，这些序列对数百个常染色体和X连锁基因的表达产生了不同的影响。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(YRV)。这些实验为研究YRV的致病机理提供了第一个分子途径。受YRV影响的基因包括所有类别的基因：在性别之间表达无偏见、女性偏见和男性偏见。受YRV影响的许多基因与适应性特征(如耐热性)或性选择(如信息素接收)有关。YRV的发现具有潜在的重大意义，因为它表明Y染色体在包括人类在内的所有生物中都非常特殊，它通过其大量的非编码DNA来调节对基因表达的主要基因组效应。拟议的实验将检验这样一种假设，即YRV是由Y连锁序列的拷贝数变化引起的，这些Y连锁序列与常染色体和X连锁基因竞争结合有限数量的染色质相关蛋白，从而影响基因表达水平。拟议的实验还将检验YRV是由与位置效应变异(PEV)和/或重复相关小干扰RNA(RasiRNA)相关的调控通路介导的假说。因此，这项拟议的研究具有变革性，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而在解释表型变异中所起作用的理解。通过调控效应进行的选择可能会推动Y染色体上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化。这一观点挑战了当前的范式，即这样的序列只是中性进化的“垃圾”DNA。拟议的实验还将确定一组受YRV影响的候选基因，这些基因与精子发生的热耐受有关，这是限制许多昆虫生态范围的关键生物学因素，包括传播疟疾的蚊子。我们还将开发与YRV相关的多态Y染色体群体动力学的理论模型，以确定基于竞争结合的模型是否可能与参数的真实值相关联。与NIH任务相关的是，我们关于果蝇Y染色体的发现在包括人类基因组在内的富含异染色质的基因组中很可能是相当普遍的。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，还必须研究X染色体和常染色体的着丝粒周围异染色质，但果蝇Y染色体是一个起点，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，以及可用的遗传资源。相关性这项研究的相关性在于，它研究了新发现的Y染色体对基因表达的影响的分子机制和适应性意义，这可能对Y染色体在人类和其他生物中的作用具有广泛的影响。公共卫生相关性：Y染色体被广泛认为是一片基因匮乏、缓慢退化的基因组DNA荒地，其唯一功能是充当X染色体的配对伙伴，并在不同物种中携带雄性或雄性生育基因。我们的初步发现强烈表明，这种观点是错误的。我们的新发现是，Y染色体的多态对基因组中数百个基因的表达水平产生了不同的影响。我们认为，这些效应是由Y染色体上快速进化的、鲜为人知的区域介导的，这些区域包含非编码DNA的序列重复。提出的实验对当前Y染色体影响其他基因表达的观点以及Y染色体如何随时间变化的观点提出了革命性的挑战。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.