Genomic Analysis of Nucleic Acid Transactions

大多数真核生物的前体 mRNA，尤其是后生动物中的前体 mRNA，会被选择性剪接以产生多个 mRNA 和蛋白质。鉴于选择性剪接在调节基因表达和增强基因表达方面的重要性 由于蛋白质组的多样性，了解剪接机制以及替代方法至关重要 拼接受到监管。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，其中 强调 RNA 结合蛋白如何自动和交叉调节自身和其他 RNA 的剪接 结合蛋白基因。这项工作将为 RNA 加工机制以及如何进行提供新的见解。 这些蛋白质相互调节以实现稳态。 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害。免疫记忆是 编码为短 DNA 序列，称为“间隔序列”，与入侵者基因组相匹配并存储为 散布在一系列短重复序列中的元素（CRISPR 阵列）。 CRISPR 阵列被转录 并加工成引导RNA，与Cas核酸酶配对以识别和降解目标核酸 （干扰）。当入侵者 DNA 片段被破坏时，新的免疫记忆就会在“适应”过程中形成。 获得并整合到 CRISPR 阵列中以用于未来的靶向。虽然已知数量巨大 关于入侵核酸的靶向和降解，人们对入侵核酸的过程知之甚少。 适应。我们计划进一步表征原核 CRISPR-Cas 系统的适应过程。这个 这项工作还将深入了解原核生物免疫系统的适应机制。在 除了增强我们对原核免疫系统基础科学的理解之外，还有 这项工作具有巨大的潜力，可能会导致可用于基因组的新工具的开发 编辑应用程序。 所有这些项目都将使用我们开发的通用方法类型来解决 作为剪接报告基因、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创新方法来解决这些问题 由于该领域的技术进步而需要或出现机会时出现的问题。

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.