The formation of Heterochromatin on evolving Y chromosomes

描述（由申请人提供）：真核基因组的大部分，包括Y染色体，是异染色质的，主要由重复序列组成，并具有与基因沉默相关的独特染色质结构。异染色质区具有高重复含量，其特征在于特定的组蛋白修饰，但将特定染色体结构域定义为异染色质组装的优选位点的一级序列元件还不清楚。最近的研究表明，小RNA-可能来自转座因子（TE）-有助于异染色质靶向。本文报道了银额果蝇（Drosophila albomicans）和果蝇（D. miranda在进化过程中改变了染色质结构：在D.米兰达neo-Y-这是形成约1百万年前-大片段已经获得了异染色质的外观和TE显示出惊人的积累。大约一半的neo-Y基因座已经变得无功能，并且大多数基因（<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）大部分是常染色体的，并且大多数基因在neo-Y上是功能性的（<2%假基因）。然而，近30%的neo-Y基因被下调，原位杂交实验揭示了异染色质在D.阿尔伯米坎人D. miranda和D.因此，Albomicans提供了独特的系统来研究异染色质形成的机制和进化。使用比较序列分析，基因表达研究，小RNA分析和ChIP-seq实验相结合，以映射与异染色质和基因组相互作用图相关的组蛋白修饰，我们将解决以下问题：什么是用于靶向异染色质的主要序列元素？小RNA参与异染色质靶向吗？异染色质的形成对基因表达水平有什么影响？异染色质在顺式或3D中扩散多远？异染色质的扩散是否需要高的重复序列含量？染色质边界元件是否在新Y染色体上进化以限制扩散，它们的分子本质是什么？组蛋白修饰是否与主动转录有关，从而抵消异染色质的扩散？我们能识别出其他DNA序列元件作为neo-Y的边界元件吗？某些类别的基因更可能是异染色质的吗？它将使我们能够研究异染色质的分子基础及其如何进化。

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.