Evolutionary Genomics of Functional Chromatin Domains

项目摘要/摘要 着丝粒和伪常染色体区域(PARs)是高度特化的染色质结构域，它们是 对于正确的染色体分离是必不可少的。着丝粒提供了染色体的连接点 细胞分离机制，将染色体连接到蛋白质，在这两个过程中将染色体拉到细胞极点 体细胞和生殖细胞分裂。PAR是X和Y之间具有保守序列同一性的区域 染色体上展开配对、联会和重组的减数分裂程序，以确保 正确的性染色体分离。破坏着丝粒完整性或降低着丝粒之间同源性的突变 X和Y连锁的PARS可导致染色体分离错误，并构成重要的遗传 癌症、细胞衰老和不孕不育的机制。尽管它们的根本意义在于 染色体传递和基因组稳定性，对遗传的水平和模式知之甚少。 着丝粒的多样性和这种变异的PAR或生物学影响。重复序列 这些区域的含量构成了其分子分析的主要障碍，而PAR和着丝粒 在许多最高质量的参考基因组上保持未组装或不完全组装。我的小组 最近开发了实验和生物信息学工具，使我们能够对整个 PAR和着丝粒，为后续研究 这些基因座的遗传变异。在接下来的五年里，我们将把这些分析工具与各种 小鼠模型，染色体的细胞遗传学研究和进化分析，以解决三个关键的 问题。首先，这些染色质结构域之间的DNA序列变异程度如何？我们 将结合有针对性的长时间测序，重新分析公共档案中的基因组数据，以及分析 在对PAR和PAR进行编目的枪击测序读物集合中特定核苷酸“词”的频率 哺乳动物模型系统中的着丝粒多样性，包括大小、基因组结构、 核苷酸序列，以及重复内容。第二，PAR和着丝粒的等位基因差异是怎样的？ 序列在染色体分离中影响其固有的染色质依赖功能 生育能力？我们将测试关于PAR和着丝粒变异如何影响生育率的明确假设 并对染色体传递进行偏向，以量化DNA序列多样性和功能之间的关系。 第三，是什么机制保障了这些基因座基于染色质的功能？ 快速的序列级进化？我们将通过澄清来探索这种令人困惑的二元性的可能解决方案 天真DNA序列如何获得染色质依赖的功能 平价扩张。总体而言，该项目的成功将极大地促进我们对多样性的理解， 在染色体分离中具有关键生物学作用的两个基因座上的进化和功能 它们的DNA序列的产物，而不是它们染色质的固有属性。

PROJECT SUMMARY/ABSTRACT Centromeres and pseudoautosomal regions (PARs) are highly specialized chromatin domains that are essential for proper chromosome segregation. Centromeres provide chromosomal points of attachment to the cellular segregation machinery, linking chromosomes to the proteins that pull them to the cell poles during both somatic and germline cell divisions. The PAR is a region of conserved sequence identity between the X and Y chromosomes over which the meiotic program of pairing, synapsis, and recombination unfolds to ensure correct sex chromosome segregation. Mutations that disrupt centromere integrity or reduce homology between X- and Y-linked PARs can lead to chromosome segregation errors and constitute important genetic mechanisms for cancer, cellular senescence, and infertility. Despite their fundamental significance for chromosome transmission and genome stability, little is known about the levels and patterns of genetic diversity across centromeres and the PAR or the biological impacts of this variation. The repetitive sequence content of these regions poses a major barrier to their molecular analysis, and the PAR and centromeres remain unassembled or incompletely assembled on many of the highest quality reference genomes. My group has recently developed experimental and bioinformatic tools that will allow us to catalog variation across the PAR and centromeres, setting the stage for subsequent investigations into the functional consequences of genetic variation across these loci. Over the next five years, we will combine these analytical tools with diverse mouse models, cytogenetic investigations of chromosomes, and evolutionary analyses to address three critical questions. First, what it is the extent of DNA sequence variation across these chromatin domains? We will combine targeted long-read sequencing, re-analysis of genomic data in public archives, and analyses of the frequency of specific nucleotide “words” in collections of shot-gun sequenced reads to catalog PAR and centromere diversity in a mammalian model system, including variation in size, genomic architecture, nucleotide sequence, and repeat content. Second, how do allelic differences in PAR and centromere sequences impact their intrinsic chromatin-dependent functions in chromosome segregation and fertility? We will test explicit hypotheses about how variation at the PAR and centromeres influences fertility and biases chromosome transmission to quantify relationships between DNA sequence diversity and function. Third, what mechanisms safeguard the chromatin-based functions of these loci in the face of their rapid sequence-level evolution? We will explore possible resolutions to this perplexing duality by elucidating how naïve DNA sequence acquires chromatin-dependent functions using mouse models with spontaneous PAR expansions. Overall, the success of this project will significantly advance our understanding of diversity, evolution, and function at two loci with critical biological roles in chromosome segregation that arise not from products of their DNA sequence, but rather the intrinsic properties of their chromatin.