Comparative DNA sequence analysis of the yeast genome

我们建议确定的基因组序列的四个酵母属物种（目的1），以确定保守的，因此可能在其DNA序列的功能特征。 而不是专注于蛋白质和蛋白质编码DNA（这类研究的共同重点），我们试图找到隐藏在非编码序列（目标2）的功能特征，如调节基因表达，染色体维护和编码非蛋白质编码RNA的序列。 由于这类序列进化迅速，因此需要比较相对密切相关的物种的序列。 我们得出结论，S。酿酒酵母DNA序列与至少3种其它酵母属物种的DNA序列相同（即，4-方式比对）对于观察重要的保守序列块是必要的。 对4个不同物种的基因组进行全基因组鸟枪测序（2-3倍覆盖率），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式。 我们将评估我们的能力，识别功能序列元件的基础上，他们的保守性测试的功能，一些保守的序列（目的3）与实验设计，以确定转录调控序列和蛋白质结合到他们，以及非蛋白质编码RNA。 酵母是这些研究的优秀生物体，因为1）它们相对较小的基因组使该项目具有成本效益，2）关于酵母的丰富信息可用于评估保守序列的意义，3）可以设计深入的实验来测试保守序列的生物学功能，以及4）数据将有利于研究这种重要模式生物的科学家的大社区。 我们希望有助于比较DNA序列分析的发展，作为一种注释基因组的方法，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.