Integrative genomics: the biological impacts of DNA content diversity

整合基因组学：DNA 内容多样性的生物学影响

• 批准号: 327315-2011
• 负责人: Gregory, Ryan
• 金额: $ 2.33万
• 依托单位: University of Guelph
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2011
• 资助国家: 加拿大
• 起止时间: 2011-01-01 至 2012-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=481679
• 关键词: Integrative; genomics; biological; impacts; DNA

Protein coding genes in the human genome number only ~25,000 and constitute less than 2% of the total DNA sequence. Whereas classical genetics and comparative genomics have generated major insights into the roles of individual genes, the biological significance of the vast non-coding majority of the genome has remained enigmatic. Major initiatives involving sequence comparisons (e.g., ENCODE) are underway to determine whether and in what way portions of the non-genic majority of a typical mammalian genome may be functional in regulatory or other capacities. It is also possible that non-coding DNA plays important roles in a manner independent of nucleotide sequence, for example in maintaining or modifying the physical structure of chromosomes or the spatial arrangement of genes. These investigations are important, but it must be borne in mind that regulatory or other functions are very unlikely to account for the enormous diversity in DNA content observed across species - in animals, the smallest and larger genomes differ in size by a factor of 7,000. Of course, the DNA in a given genome need not have a specific function to exert important biological impacts. For example, there is strong evidence that DNA amount per nucleus is tightly linked to cell size and cell division rate, and that this may result in organism-level relationships with metabolic rate, developmental rate, body size, and other biological properties of fundamental significance. The research proposed here will focus on the patterns and biological significance of DNA content diversity from three perspectives. In the first project, my students and I will investigate the patterns and biological impacts of genome size diversity among several key groups of animals. This will be accomplished using both Feulgen image analysis densitometry and flow cytometry to estimate nuclear DNA content, and will be linked to morphological, developmental, and physiological parameters and analyzed within a phylogenetic context. The groups of animals to be analyzed have all been very poorly studied from the perspective of genome size to date, but are of particular interest for their theoretical and/or practical importance. These include i) the early-branching metazoan phyla (Porifera, Cnidaria, Ctenophora, and Placozoa), which are of particular phylogenetic interest in addition to providing opportunities to test possible links between genome size and devolpmental lifestyle, ii) crustaceans, which are very diverse both taxonomically and ecologically and provide an opportunity to investigate many aspects of genome evolution, and iii) parasitic helminths including flatworms and nematodes, which allows a test of the hypothesis that parasitism constrains body size/developmental rate and thus genome size. In the second project, we will investigate the prevalence and distributions of very large genomes (>5x human genome size) and use modern genomics tools to investigate the quantity and distribution of transposable elements in genomes that are currently far too large to be subject to complete genome sequencing. In the third project, we will investigate the biological significance of endopolyploidy, in which the genome is replicated up to thousands of times within individual cells. Endopolyploidy appears to be a very widespread phenomenon, and is particularly common in tissues involved in intensive protein excretion, and we intend to examine the degree and timing of endopolyploidization in tissues of particular interest such as insect ovaries with and without nutritive trophocytes ("nurse cells"), in the silk glands of domesticated silkworms, and in the venom and silk glands of spiders with varying feeding habits.

人类基因组中的蛋白质编码基因数量仅约 25,000 个，仅占总 DNA 序列的不到 2%。 尽管经典遗传学和比较基因组学已经对单个基因的作用产生了重要的见解，但基因组中绝大多数非编码部分的生物学意义仍然是个谜。 涉及序列比较（例如，ENCODE）的重大举措正在进行中，以确定典型哺乳动物基因组的非基因大部分部分是否以及以何种方式在调节或其他能力方面发挥作用。 非编码DNA也可能以独立于核苷酸序列的方式发挥重要作用，例如在维持或改变染色体的物理结构或基因的空间排列方面。这些研究很重要，但必须记住，监管或其他功能不太可能解释在不同物种中观察到的 DNA 含量的巨大多样性——在动物中，最小和较大的基因组大小相差 7,000 倍。当然，特定基因组中的 DNA 不需要具有特定的功能来发挥重要的生物学影响。例如，有强有力的证据表明，每个核的 DNA 量与细胞大小和细胞分裂率密切相关，这可能会导致生物体水平与代谢率、发育率、身体大小和其他具有根本意义的生物学特性之间的关系。这里提出的研究将从三个角度关注DNA内容多样性的模式和生物学意义。 在第一个项目中，我和我的学生将研究几个关键动物群体的基因组大小多样性的模式和生物学影响。 这将使用 Feulgen 图像分析密度测定法和流式细胞术来估计核 DNA 含量，并将与形态学、发育和生理参数联系起来，并在系统发育背景下进行分析。 迄今为止，从基因组大小的角度来看，待分析的动物群体的研究都非常少，但因其理论和/或实际重要性而特别令人感兴趣。 其中包括 i) 早期分支的后生动物门（多孔动物门、刺胞动物门、栉水母动物门和扁动物门），它们除了提供测试基因组大小和发育生活方式之间可能联系的机会外，还具有特别的系统发育意义；ii) 甲壳动物，它们在分类学和生态学上都非常多样化，为研究基因组进化的许多方面提供了机会；以及 iii) 寄生动物 包括扁形虫和线虫在内的蠕虫，这可以检验寄生限制身体大小/发育速率以及基因组大小的假设。 在第二个项目中，我们将研究非常大的基因组（> 5倍人类基因组大小）的普遍性和分布，并使用现代基因组学工具来研究目前太大而无法进行完整基因组测序的基因组中转座元件的数量和分布。 在第三个项目中，我们将研究内多倍体的生物学意义，其中基因组在单个细胞内复制数千次。 内多倍化似乎是一种非常普遍的现象，在涉及密集蛋白质排泄的组织中尤其常见，我们打算检查特别感兴趣的组织中内多倍化的程度和时间，例如有或没有营养性滋养细胞（“护士细胞”）的昆虫卵巢，家蚕的丝腺，以及蜘蛛的毒液和丝腺 不同的饮食习惯。