Genome architecture dynamics and expression

基因组结构动态和表达

• 批准号: RGPIN-2014-06018
• 负责人: Chen, Nansheng
• 金额: $ 3.42万
• 依托单位: Simon Fraser University
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2015
• 资助国家: 加拿大
• 起止时间: 2015-01-01 至 2016-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=588757
• 关键词: Genome; architecture; dynamics; expression

Accelerating advances in DNA sequencing technologies is driving the creation of an unprecedented genome resource for a wide range of organisms, presenting golden opportunities for mining the genome information that instructs the generation of biological processes including development, aging, metabolism, and learning and memory. The long-term goal of my research program is to understand genome structural changes (i.e., architecture dynamics) and how this affects genome expression. The strength of this program builds on our combined experience in nematode molecular biology and in developing and applying innovative bioinformatics tools. We work with the genomes of nematodes because this phylum contains both the well-studied model organism C. elegans, and many pathogens including deadly animal (including human) and plant parasites. The proposed research will address two complementary short-term objectives over the next 5 years, aiming to understand genome expression from both the whole-genome level and a single-gene level. Our first objective is to investigate genome architecture dynamics and how such dynamics define genomic novelty and affect gene expression. We hypothesize that the formation of novel genes and isoforms is the driving force in shaping genomic and phenotypic diversity. Novel genes can form through a variety of mechanisms including duplication, extension or truncation of genes, fusion between full or partial genes, and de novo formation. In order to identify novel genes, we will analyze genomic differences between C. elegans strains (including the reference N2 strain and strains collected worldwide), as well as between C. elegans and C. briggsae (the most extensively studied sister species) and other related nematode species, followed by examining how they contribute to the formation of novel genes. Candidate novel genes will be validated through transcriptome sequencing and analysis (RNA-seq), as well as full-length cDNA analysis. In contrast, the formation of novel isoforms of a gene is not well understood. Our recent quantitative comparison RNA-seq results of C. elegans and C. briggsae revealed that orthologs in these two species can have drastically different splicing, suggesting the formation of novel isoforms. Novel isoforms (as well as de novo genes) will be uncovered via direct RNA-seq analysis of various strains and species. We will evaluate the function of the predicted novel genes through computational and experimental approaches. The second objective is to study gene expression regulation at the level of transcription, focusing on the transcriptional regulation of the ciliary gene MAK/dyf-5 in C. elegans that we have cloned and identified previously. dyf-5 is a conserved gene found in a wide range of organisms including the green algae Chlamydomonas reinhardtii and humans. Loss-of-function of dyf-5 leads to defective cilia development and function. We will carry out genetic screening to identify mutants that affect the expression of dyf-5 that is tagged with fluorescence protein tdTomato. These mutated genes will be identified through genetic mapping, genome sequencing, and bioinformatics analysis, followed by molecular studies of their functional contribution to the precise expression of dyf-5. We expect to identify co-transcription factors that function together with RFX/DAF-19, a transcription factor that is required for the expression of essentially all ciliary genes. Collectively, research of these objectives will reveal mechanisms underlying the creation of genomic novelty and phenotypic diversity, which contribute to the initiation of speciation. Bioinformatics tools developed in the course of this proposed research will greatly facilitate the field of comparative genomics.

DNA测序技术的加速进步正在推动为广泛的生物体创造前所未有的基因组资源，为挖掘基因组信息提供了黄金机会，这些信息指导生物过程的产生，包括发育、衰老、新陈代谢、学习和记忆。我的研究计划的长期目标是了解基因组结构变化（即结构动力学）以及这如何影响基因组表达。这个项目的优势建立在我们在线虫分子生物学和开发和应用创新生物信息学工具方面的综合经验之上。我们研究的是线虫的基因组，因为这一门既包含被充分研究的模式生物秀丽隐杆线虫，也包含许多病原体，包括致命的动物（包括人类）和植物寄生虫。拟议的研究将在未来5年内实现两个互补的短期目标，旨在从全基因组水平和单基因水平了解基因组表达。