Mechanisms of epigenetic gene regulation by the Drosophila COMPASS-like complex

每个生物体的遗传密码都包含在染色体中，统称为基因组。在所有真核生物中，基因组通过形成称为染色质的浓缩分子而被压缩到细胞核中。最小的单个致密单元被称为核小体，其由147个碱基对的DNA包裹在小的碱性组蛋白的八聚体周围组成。为了使调节因子和酶能够获得遗传密码并适当调节正常发育和细胞存活所必需的过程，核小体需要在称为染色质重塑的过程中被移到一边或直接修饰特定的氨基酸残基。进行染色质重塑的酶和其他蛋白质是古老的，并且非常保守，从单细胞生物到脊椎动物，其复杂性不断增加。该项目的总体影响将是更好地理解染色质重塑如何控制基因组内编码的信息的表达。此外，高中，本科和研究生将参加指导研究。妇女和少数民族将有很高的代表性。多学科的培训和教育对于为不同的科学职业做准备至关重要，该项目采用了目前可用于果蝇研究的独特工具。学生将接受分子和发育遗传学，生物化学，分子生物学和生物信息学，结构和发育生物学的培训。该项目将加强机构内的教师科学家之间的互动，并与学生在多个本科院校探索生物信息学的快速新兴领域。本科生将学习新的信息学工具和方法，使用来自这个项目的实验数据的任务。为了确定Cmi和相关哺乳动物结构域的组蛋白识别和结合特性，并阐明COMPASS样复合物靶向基因增强子的潜在机制，将采用包括组蛋白识别结构域的X射线晶体学和核磁共振以及结合亲和力和体内染色质缔合的体外测量的靶向诱变的合作结构研究。该项目还使用下一代高通量染色质和RNA分析（ChIP-Seq，RNA-Seq）和靶基因研究。使用来自cmi突变动物的染色质的ChIP-Seq将使表观遗传标记与Cmi功能相关，并将RNA-Seq基因表达数据与染色质结合进行比对，以解决关键的发育功能。使用为这些研究开发的独特遗传工具，组织特异性靶向去除cmi和trr以及过表达cmi，将允许直接测试靶基因上的COMPASS样功能。前沿的染色质技术，检查遥远的基因区域之间的物理连接，将阐明新的调节作用，果蝇COMPASS样复合物，促进适当的基因控制所必需的增强子-启动子通信。这些研究将有助于揭示染色质重塑和修饰复合物的基本性质，并为发育基因调控机制提供重要的见解。

The genetic code of every living organism is contained within chromosomes, referred to collectively as the genome. In all eukaryotes, the genome is compacted into the nucleus through the formation of condensed molecules known as chromatin. The smallest individual units of compaction are known as nucleosomes that are comprised of 147 base pairs of DNA wrapped around an octamer of small basic histone proteins. In order for regulatory factors and enzymes to access the genetic code and properly regulate processes essential for normal development and cell survival, the nucleosomes need to be moved aside or directly modified on specific amino acid residues in a process termed chromatin remodeling. The enzymes and other proteins that carry out chromatin remodeling are ancient and remarkably conserved, with increasing complexity from single celled organisms up through vertebrates. The overall impact of this project will be a better understanding of how chromatin remodeling controls expression of the information that is encoded within the genome. In addition, high school, undergraduate and graduate students will participate in mentored research. Women and minorities will be highly represented. Multidisciplinary training and education are vital to prepare for diverse science careers and this project employs the unique tools currently available for Drosophila studies. Students will be trained in molecular and developmental genetics, biochemistry, molecular biology and bioinformatics, structural and developmental biology. The project will enhance interactions among faculty scientists within the institution and with students at multiple undergraduate institutions to explore the rapidly emerging field of bioinformatics. Undergraduate students will be tasked with learning new informatics tools and approaches using experimental data derived from this project. In order to define the histone recognition and binding properties of Cmi and related mammalian domains and elucidate the potential mechanism of COMPASS-like complex targeting to gene enhancers, collaborative structural studies that include X-ray crystallography and nuclear magnetic resonance of the histone recognition domains and targeted mutagenesis combined with in vitro measurements of binding affinities and in vivo chromatin association will be employed. The project also uses next-generation high throughput chromatin and RNA analyses (ChIP-Seq, RNA-Seq) and target gene studies. ChIP-Seq using chromatin from cmi mutant animals will enable correlation of epigenetic marks with Cmi function and align the RNA-Seq gene expression data with chromatin binding to address key developmental functions. Tissue-specific targeted removal of both cmi and trr and overexpression of cmi using unique genetic tools developed for these studies will allow for direct testing of COMPASS-like functions on target genes. Leading edge chromatin technologies that examine physical connections between distant gene regions will elucidate novel regulatory roles for the Drosophila COMPASS-like complex in facilitating enhancer-promoter communication necessary for proper gene control. These studies will help to reveal essential and foundational properties of chromatin remodeling and modifying complexes and provide critical insight into the mechanisms of developmental gene regulation.