Genomic Analysis of Nucleic Acid Transactions

大多数真核生物的前mRNAs，特别是在后生动物中，被交替剪接以产生多个 核糖核酸和蛋白质。鉴于选择性剪接在调节基因表达和增强 蛋白质组的多样性，了解剪接的机制和如何替代是至关重要的 拼接是受监管的。在这个项目中，我们将研究RNA结合蛋白在选择性剪接中的作用， 强调RNA结合蛋白如何自动和交叉调节自己和其他RNA的剪接 结合蛋白基因。这项工作将为RNA加工的机制以及如何 这些蛋白质相互调节以实现同质凝集。 许多原核生物编码CRISPR-CAS系统，这是RNA引导的适应性免疫系统， 保护原核生物免受病毒和质粒等入侵者的侵袭。免疫记忆是 编码为短DNA序列，称为“间隔区”，与入侵者基因组相匹配，并存储为 短重复数组(CRISPR数组)中散布的元素。CRISPR阵列被转录 并加工成与CaS核酸酶配对的引导RNA，识别和降解目标核酸 (干扰)。新的免疫记忆在“适应”期间形成，当入侵者DNA片段 获得并整合到CRISPR阵列中，以用于未来的目标。虽然已知的数量巨大 关于入侵核酸的靶向和降解，人们对其过程知之甚少 适应。我们计划进一步表征原核生物CRISPR-CAS系统中的适应过程。这 这项工作还将深入了解原核生物免疫系统的适应机制。在……里面 除了加强我们对原核生物免疫系统基础科学的了解外，还有 这项工作可能导致开发可用于基因组的新工具的巨大潜力 编辑应用程序。 所有这些项目都将使用我们开发的一般方法来解决 作为剪接记者、单细胞RNA-Seq、纳米孔测序、RNAi或CRISPR筛选，以及 计算基因组学。我们还将继续开发更多的创新方法来解决这些问题 在需要时或由于该领域的技术进步而出现机会时的问题。

Most eukaryotic pre-mRNAs, especially in metazoans, are alternatively spliced to generate multiple mRNAs and proteins. Given the importance of alternative splicing in regulating gene expression and enhancing the diversity of the proteome, it is essential to understand the mechanisms of splicing and how alternative splicing is regulated. In this project, we will study the roles of RNA binding proteins in alternative splicing, with an emphasis on how RNA binding proteins auto- and cross-regulate the splicing their own and other RNA binding protein genes. This work will provide new insight into the mechanisms of RNA processing and how these proteins regulate one another to achieve homoestasis. Many prokaryotes encode CRISPR-Cas systems which are RNA-guided adaptive immune systems that protects prokaryotic organisms against invaders such as viruses and plasmids. Immune memories are encoded as short DNA sequences, called “spacers”, that match invader genomes and are stored as interspersed elements in an array of short repeats (the CRISPR array). The CRISPR arrays are transcribed and processed into guide RNAs which pair with Cas nucleases to recognize and degrade target nucleic acid (interference). New immune memories are formed during “adaptation” when fragments of invader DNA are acquired and integrated into CRISPR arrays for use in future targeting. While a tremendous amount is known about the targeting and degradation of invading nucleic acids, much less is known about the process of adaptation. We plan to further characterize the adaptation process in prokaryotic CRISPR-Cas systems. This work will also provide insight into the mechanisms of adaptation in the immune systems of prokaryotes. In addition to enhancing our understanding of the basic science of prokaryotic immune systems, there is tremendous potential that this work could lead to the development of new tools that can be used for genome editing applications. All of these projects will be addressed using the types of general approaches we have developed such as splicing reporters, single cell RNA-Seq, nanopore sequencing, RNAi or CRISPR screens, and computational genomics. We will also continue to develop additional innovative approaches to address these issues as needed or as opportunities arise due to technical advances in the field.