Cancer, speciation, and chromosomes: how somatic chromosome pairing influences gene expression

项目摘要 同源染色体配对，同源染色体的物理匹配，是一种 染色体力学的基本方面。在大多数生物中，配对只能发生在减数分裂到 允许重组。在其他时候偶然配对可能会导致许多问题，包括非整倍体 以及多种癌症。了解控制这种体细胞配对的机制将提供洞察力 研究染色体生物学的基本方面。 为了研究体细胞中的同源染色体配对，我们需要一种系统，在那里我们可以执行 控制整个基因组配对状态的操纵。与大多数其他生物不同，果蝇 苍蝇总是将它们所有的体细胞染色体配对；然而，一只果蝇的后代 黑腹果蝇和一只拟态果蝇失去了在少数可复制区域的配对 基因组。这一现象是我们可以利用来广泛理解体细胞配对的机会。 果蝇丰富的遗传工具，在正常果蝇中存在体细胞配对，在杂交中存在异常配对 苍蝇为理解配对的机制基础提供了一个强大的系统。 我计划通过使用Hi-C测序来测量正常个体和物种间杂交的配对 技术。这种方法将首次在全基因组范围内描述正常配对和异常配对。 种间杂交种的基因组区域。然后，我将使用D.Blackogaster的基因组注释来识别 基因组特征，如基因和重复的DNA基序，在非配对区域中过度表达。 在配对丢失的地方持续发现的DNA特征将提供对支配因素的洞察 配对。我将通过上调或下调配对相关基因，改变 在染色体上配对，并复制物种间杂交的结果。因为配对 是已知通过转基因现象影响基因表达的，我将使用等位基因特异性 在配对和不配对的情况下测量每个基因的顺式和反式调节的表达，展示效果 基因表达上的配对。总而言之，这些实验将表征构成 染色体配对的基本过程。这一新知识将告诉我们对配对的理解 与细胞功能、疾病和进化有关。

Project Summary Homologous chromosome pairing, the physical matching up of homologous chromosomes, is a fundamental aspect of chromosome mechanics. In most organisms, pairing must occur only during meiosis to allow for recombination. Accidental pairing at other times can lead to numerous problems, including aneuploidy and many types of cancer. Understanding the mechanisms that control such somatic pairing will provide insight into fundamental aspects of chromosome biology. To study homologous chromosome pairing in somatic cells, we require a system where we can perform controlled manipulations of the state of pairing across the genome. Unlike most other organisms, Drosophila flies pair all of their somatic chromosomes all of the time; however, the offspring of one Drosophila melanogaster fly and one Drosophila simulans fly lose pairing in a small number of replicable regions of the genome. This phenomenon is an opening that we can exploit to understand somatic pairing broadly. Drosophila's wealth of genetic tools, presence of somatic pairing in normal flies, and aberrant pairing in hybrid flies provide a powerful system to understand the mechanistic basis of pairing. I plan to measure pairing in normal individuals and interspecies hybrids by using the Hi-C sequencing technique. This approach will provide the first genome-wide description of properly and aberrantly paired genome regions in interspecies hybrids. I will then use the D. melanogaster genome annotation to identify genome features such as genes and repeated DNA motifs that are overrepresented in non-pairing regions. DNA features that are consistently found where pairing is lost will provide insight into the factors that govern pairing. I will confirm these features by up- or down-regulating pairing-related genes, changing the rate of pairing across the chromosomes and replicating the results of the interspecies hybridization. Because pairing is known to influence gene expression through the phenomenon of transvection, I will use allele-specific expression to measure each gene's cis- and trans- regulation with and without pairing, demonstrating the effect of pairing on gene expression. Together, these experiments will characterize the mechanisms that underlie the fundamental process of chromosome pairing. This new knowledge will inform our understanding of pairing as it relates to cell function, disease, and evolution.