Novel genomic effects of Y-linked polymorphisms

描述（由申请人提供）：我们建议的研究是新颖的，假设驱动的，变革性的，并且与NIH的使命相关。我们最近发现，黑腹果蝇的Y染色体是多态性的，其序列对数百种常染色体和x连锁基因的表达有不同的影响。不同Y染色体对基因表达的定量影响被称为Y连锁调控变异（YRV）。本实验为研究YRV的机制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：在性别之间的表达无偏倚，女性偏倚和男性偏倚。许多受YRV影响的基因与适应性性状（如耐热性）或性选择（如信息素接受）有关。YRV的发现具有潜在的重大意义，因为它表明，包括人类在内的所有生物中的Y染色体通过其大量的非编码DNA补体介导基因表达的主要基因组效应是非常特殊的。拟议的实验将验证这样的假设，即YRV是由y连锁序列拷贝数的变化引起的，y连锁序列与常染色体和x连锁基因竞争，与影响基因表达水平的有限数量的染色质相关蛋白结合。该实验还将验证YRV是由位置效应变异（PEV）和/或重复相关小干扰RNA （rasiRNA）相关的调控途径介导的假设。因此，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染色体非编码序列的快速进化，这比单拷贝序列在进化上更具动态性。这一观点挑战了当前的范式，即这些序列仅仅是中性进化的“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耐热性有关，这是限制包括传播疟疾的蚊子在内的许多昆虫的生态范围的一个关键生物学因素。我们还将开发与YRV相关的多态Y染色体种群动力学的理论模型，以确定基于竞争结合的模型是否可能与参数的实际值相匹配。与NIH任务相关的是，我们关于果蝇Y染色体的发现可能在具有丰富异染色质基因组的生物体（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。本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，我们还必须研究X染色体和常染色体的近中心异染色质，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，基因操作相对容易，遗传资源可用。本研究的意义在于探讨了新发现的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意义。公共卫生相关性：Y染色体被广泛认为是一个基因贫乏，缓慢退化的基因组DNA的荒地，其唯一功能是作为X的配对伙伴，并在不同物种中携带男性或男性生育能力的基因。我们的初步调查结果强烈表明，这种观点是错误的。我们的新发现是，Y染色体多态性对基因组中数百个基因的表达水平有不同的影响。我们认为，这些影响是由快速进化的、鲜为人知的Y染色体区域介导的，该区域包含非编码DNA的序列重复。提出的实验在挑战当前关于Y染色体对其他基因表达的影响以及Y染色体如何随时间变化的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染色体中非编码DNA序列重复序列的变异。

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.