The formation of Heterochromatin on evolving Y chromosomes

描述(申请人提供)：真核基因组的很大一部分，包括Y染色体，是异染色质，主要由重复序列组成，并具有与基因沉默相关的独特的染色质结构。异染色质区域具有很高的重复含量，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的首选位置的初级序列元件尚未被很好地理解。最近的研究表明，小RNA--可能来自转座元件(TES)--有助于异染色质靶向。白腹果蝇和米兰达果蝇新近形成的neo-Y染色体正在进化改变染色质结构的过程中：在米兰达果蝇的neo-Y染色体上--大约形成于1my之前--大片段已经获得了异染色质的外观，并且TES显示出惊人的积累。大约一半的neo-Y基因座已经变得不起作用，大多数基因(80%)比neo-Y基因座下调。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。年轻得多的白纹伊氏菌neo-Y(&lt；0.1my old)大多是常染色质的，并且大多数基因在neo-Y(&lt；2%的伪基因)上是功能的。然而，几乎30%的neo-Y基因表达下调，原位杂交实验显示，一些异染色质在白纹伊蚊的neo-Y上积累的早期迹象。因此，米兰达和白纹伊蚊提供了独特的系统，利用进化方法研究异染色质形成的作用机制和进化。使用比较序列分析、基因表达研究、小RNA图谱和芯片序列实验相结合的方法来定位与异染色质相关的组蛋白修饰和基因组相互作用图谱，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是否参与异染色质靶向？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中的扩散距离有多大？高重复含量是异染色质扩散的必要条件吗？染色质边界元素是否在neo-Y上进化以限制扩散，它们的分子性质是什么？组蛋白修饰是否与主动转录有关，以对抗异染色质的扩散？我们能识别出在neo-Y上起边界作用的其他DNA序列元件吗？是不是某些类别的基因更有可能是异色的？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.