Integrative genomics: the biological impacts of DNA content diversity

人类基因组中的蛋白质编码基因数量仅约25，000个，占总DNA序列的不到2%。 虽然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大的见解，但基因组中绝大多数非编码的生物学意义仍然是个谜。 涉及序列比较的主要举措（例如，ENCODE）正在进行中，以确定典型哺乳动物基因组的非基因大部分是否以及以何种方式在调节或其他能力中起作用。 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，例如在维持或修饰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，调节或其他功能不太可能解释跨物种观察到的DNA含量的巨大差异-在动物中，最小和较大的基因组大小相差7，000倍。当然，给定基因组中的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，每个细胞核的DNA量与细胞大小和细胞分裂速率密切相关，这可能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的关系。本文拟从三个方面探讨DNA内容多样性的模式及其生物学意义。 在第一个项目中，我和我的学生将研究几个关键动物群体中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，发育和生理参数相关联，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，待分析的动物组都研究得很差，但由于其理论和/或实际重要性而特别感兴趣。 这些包括i）早期分支的后生动物门（多孔动物门、刺胞动物门、栉水母门和扁平动物门），它们除了提供测试基因组大小和发育生活方式之间的可能联系的机会之外，还具有特别的系统发育兴趣，ii）甲壳类动物，它们在分类学和生态学上都非常多样，并提供研究基因组进化的许多方面的机会，和iii）寄生蠕虫，包括扁形虫和线虫，这允许检验寄生作用限制了身体大小/发育速率并因此限制了基因组大小的假设。 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）的流行和分布，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因子的数量和分布。 在第三个项目中，我们将研究内多倍性的生物学意义，其中基因组在单个细胞内复制高达数千次。 内多倍体似乎是一个非常普遍的现象，是特别常见的组织中涉及密集的蛋白质分泌，我们打算检查的程度和时间内多倍体化的组织特别感兴趣的，如昆虫卵巢营养滋养细胞（“护士细胞”），在家蚕丝腺的家蚕，并在毒液和丝腺的蜘蛛与不同的食性。

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.