Comparative DNA sequence analysis of the yeast genome

我们建议确定四种Saccharomyces物种的基因组序列（Aim 1），以确定其DNA序列中保守的，因此可能的功能特征。而不是关注蛋白质和蛋白质编码DNA（这类研究的共同重点），我们寻求在非编码序列中发现隐藏的功能特征（Aim 2），例如调节基因表达、染色体维持和编码非蛋白质编码rna的序列。由于这类序列的进化速度很快，因此需要比较关系相对密切的物种的序列。我们已经得出结论，酿酒酵母的DNA序列与至少3种其他Saccharomyces物种的DNA序列比对（即4-way比对）将是必要的，以观察具有重要意义的保守序列块。4个不同物种的全基因组散弹枪测序（2-3倍覆盖），然后在4向比对中有限地填补空白，似乎是获得必要数据的最有效和最经济的方法。我们将通过测试一些保守序列的功能（目标3）来评估我们基于其保守性识别功能序列元件的能力，这些保守序列设计用于识别转录调控序列及其结合蛋白，以及非蛋白编码rna。酵母是这些研究的优秀生物，因为1)它们相对较小的基因组使项目具有成本效益，2)关于酵母的丰富信息可用于评估保守序列的意义，3)可以设计敏锐的实验来测试保守序列的生物学功能，4)数据将使研究这一重要模式生物的大量科学家受益。我们希望为比较DNA序列分析作为基因组注释方法的发展做出贡献，并学习如何有效地使用它。

We propose to determine the genome sequences of four Saccharomyces species (Aim 1), for the purpose of identifying conserved, and therefore likely functional features in their DNA sequences. Rather than focusing on proteins and protein-coding DNA (a common emphasis of such studies), we seek instead to find hidden functional features in non-coding sequence (Aim 2), such as sequences regulating gene expression, chromosome maintenance, and encoding non-protein coding RNAs. Because these kinds of sequences evolve rapidly, sequences of relatively closely related species need to be compared. We have come to the conclusion that alignment of S. cerevisiae DNA sequence to that of at least 3 other Saccharomyces species (i.e., 4-way alignments) will be necessary to observe conserved blocks of sequence that are significant. Whole genome shotgun sequencing (2-3-fold coverage) of the genomes of 4 different species, followed by limited filling of gaps in the 4-way alignments, seems like the most efficient and economical way to acquire the necessary data. We will assess our ability to recognize functional sequence elements based on their conservation by testing the function of some of the conserved sequences (Aim 3) with experiments designed to identify transcriptional regulatory sequences and the proteins that bind to them, as well as non-protein coding RNAs. Yeasts are excellent organisms for these studies because 1) their relatively small genomes makes the project cost effective, 2) a wealth of information on yeast is available for assessing the significance of conserved sequences, 3) incisive experiments can be designed to test the biological function of conserved sequences, and 4) the data will benefit the large community of scientists studying this important model organism. We hope to contribute to the development of comparative DNA sequence analysis as an approach to annotating genomes, and learn how to use it effectively.