Evolutionary Genomics of Functional Chromatin Domains

项目总结/摘要 着丝粒和假常染色体区域（PAR）是高度特化的染色质结构域， 对染色体分离至关重要。着丝粒提供染色体的附着点， 细胞分离机制，将染色体与蛋白质连接起来，在两个过程中将它们拉到细胞两极。 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 染色体上的配对，联会和重组的减数分裂程序展开，以确保 正确的性染色体分离。破坏着丝粒完整性或降低同源性的突变 X和Y连锁的PAR可导致染色体分离错误，并构成重要的遗传学基础。 癌症、细胞衰老和不育的机制。尽管它们对人类具有重要意义， 染色体传递和基因组的稳定性，很少有人知道的水平和模式的遗传 着丝粒和PAR之间的多样性或这种变化的生物学影响。重复序列 这些区域的含量构成了它们的分子分析的主要障碍，并且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 最近开发出了实验和生物信息学工具，使我们能够对整个基因组的变异进行编目。 PAR和着丝粒，为随后的研究奠定了基础， 这些基因座的遗传变异。在接下来的五年里，我们将联合收割机与各种分析工具相结合， 小鼠模型，染色体的细胞遗传学研究和进化分析，以解决三个关键问题 问题.首先，DNA序列在这些染色质结构域中的变异程度如何？我们将 联合收割机结合靶向长读序测序，重新分析公共档案中的基因组数据， 特定核苷酸“词”在猎枪测序读数集合中的频率以分类PAR， 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， 核苷酸序列和重复内容。第二，PAR和着丝粒的等位基因差异 序列影响其内在的染色质依赖的功能，染色体分离和生育力？我们 将测试关于PAR和着丝粒的变化如何影响生育力和偏差的明确假设 染色体传递来量化DNA序列多样性和功能之间的关系。第三，什么 机制保障这些基因座的染色质为基础的功能，在面对他们的快速序列水平 进化？我们将探讨可能的解决方案，这个令人困惑的二元性，阐明如何天真的DNA 序列使用具有自发PAR扩增的小鼠模型获得染色质依赖性功能。 总的来说，这个项目的成功将极大地促进我们对多样性，进化， 在染色体分离中具有关键生物学作用的两个基因座上起作用，而不是由它们的产物产生。 DNA序列，而是其染色质的内在属性。

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.