The formation of Heterochromatin on evolving Y chromosomes

描述（由申请人提供）：真核生物基因组的重要部分，包括Y染色体，是异色的，主要由重复序列组成，具有与基因沉默相关的独特染色质结构。异染色质区域具有高重复含量，并以特定的组蛋白修饰为特征，但定义特定染色体结构域作为异染色质组装首选位点的一级序列元件尚不清楚。最近的研究表明，可能来自转座因子（te）的小rna有助于异染色质靶向。果蝇albomicans和D. miranda新近形成的新y染色体正处于染色质结构改变的进化过程中：在D. miranda新y染色体上，大约1个小时前形成的大片段已经获得了异色外观，te显示出惊人的积累。大约一半的neo-Y基因座已经失去功能，大多数基因（<80%）从neo-Y下调。这支持了异染色质形成和重复DNA之间的联系，以及它对基因表达的抑制作用。更年轻的D. albomicans neo-Y （<0.1 MY old）大部分是正染色的，大多数基因在neo-Y上起作用（<2%的假基因）。然而，近30%的neo-Y基因是下调的，原位杂交实验揭示了D. albomicans的neo-Y上异染色质积累的一些早期迹象。因此，miranda博士和albomicans博士为研究异染色质形成的机制和进化提供了独特的系统。结合比较序列分析、基因表达研究、小RNA分析和ChIP-seq实验来绘制与异染色质相关的组蛋白修饰和基因组相互作用图，我们将解决以下问题：用于靶向异染色质的主要序列元件是什么？小rna参与异染色质靶向吗？异染色质形成对基因表达水平的影响是什么？异染色质以顺式或三维方式扩散多远？高重复序列是异染色质扩散所必需的吗？在neo-Y染色体上是否进化出染色质边界元件来限制扩散？它们的分子性质是什么？组蛋白修饰与活性转录是否会抑制异染色质的扩散？我们能识别出其他的DNA序列元素作为新y染色体的边界元素吗？某些类型的基因更可能是异色的吗？这将使我们能够研究异染色质的分子基础以及它是如何进化的。

DESCRIPTION (provided by applicant): Significant portions of eukaryotic genomes, including the Y chromosome, are heterochromatic, made up largely of repetitive sequences and possessing a distinctive chromatin structure associated with gene silencing. Heterochromatic regions have a high repeat content and are characterized by specific histone modifications, but the primary sequence elements that define specific chromosomal domains as preferred sites of heterochromatin assembly are not well understood. Recent studies suggest that small RNAs -- possibly derived from transposable elements (TEs) -- contribute to heterochromatin targeting. The recently formed neo-Y chromosomes of Drosophila albomicans and D. miranda are in the process of evolving altered chromatin structure: On the D. miranda neo-Y - which was formed about 1 MY ago - large segments have already acquired a heterochromatic appearance and TEs show a striking accumulation. About half of the neo-Y-loci have become non-functional, and most genes (<80%) are down-regulated from the neo-Y. This is supporting a link between heterochromatin formation and repetitive DNA, and its repressive effect on gene expression. The much younger D. albomicans neo-Y (<0.1 MY old) is mostly euchromatic, and most genes are functional on the neo-Y (<2% pseudogenes). However, almost 30% of neo-Y genes are down-regulated and in situ hybridization experiments reveal some early signs of accumulation of heterochromatin on the neo-Y of D. albomicans. D. miranda and D. albomicans therefore provide unique systems to study the mechanisms and evolution of heterochromatin formation in action using evolutionary approaches. Using a combination of comparative sequence analysis, gene expression studies, small RNA profiling and ChIP-seq experiments to map histone modifications associated with heterochromatin and genome interaction maps, we will address the following questions: What are the primary sequence elements used for targeting heterochromatin? Are small RNAs involved in heterochromatin targeting? What is the influence of heterochromatin formation on levels of gene expression? How far does heterochromatin spread in cis or in 3D? Is a high repeat content necessary for spreading of heterochromatin? Have chromatin boundary elements evolved on the neo-Y to limit spreading, and what is their molecular nature? Are histone modifications associated with active transcription counteracting the spread of heterochromatin? Can we identify other DNA sequence elements functioning as boundary elements on the neo-Y? Are certain categories of genes more likely to be heterochromatic? It will allow us to study the molecular basis of heterochromatin and how it evolves.