UNDERSTANDING GENOMES BY THEIR REPEATED SEQUENCES

本提案概述了对若干问题的注释和说明工作， 细菌的基因组，包括红细菌的基因组， 在芝加哥大学的实验室里 罗伯特·哈塞尔科恩博士这项工作的总体目标是创造一个 基因功能的字典，将用于商业上寻找 致病性和工业上重要的基因组中的重要基因 并尝试在人类基因组中进行功能分配。不寻常 DNA序列的对称性，通常与调节 转录，复制和重组，将被映射为一个 全局注释工作。这些序列，包括倒置、镜像和 直接重复序列在统计学上被排除在编码区之外， 用于消除虚假的开放阅读框架（ORF）， 重要的监管区域。这些退化序列的注释 将包括在一个自动注释系统，称为MAGPIE， 是在芝加哥大学发展起来的。将确认ORF边界 通过直接转录测定。重要的调节元件可以是 通过破坏这些序列中的对称性来测试功能， 体外测定转录异常。平行测序 其他R. capsulatus将允许 简并序列基序和重组点的比较。 将检测提示性简并序列的重组活性 直接在涉及恢复抗生素的简单体内系统中 抗性标记深入了解ORF确定和预测 重组可能与复杂得多的类似任务有关， 比如人类基因组。

This proposal outlines work on the annotation and elucidation of several bacterial genomes, including that of Rhodobacter capsulatus, now being sequenced at the University of Chicago in the laboratory in the laboratory of Dr. Robert Hasselkorn. The general aim of this work is to create a dictionary of gene functions that will be used to find commercially important genes in the genomes of pathogenic and industrially important organisms and attempt functional assignments in the human genome. Unusual DNA sequence symmetries, often implicated in the regulation of transcription, replication and recombination, will be mapped as part of a global annotation effort. These sequences, including inverted, mirror, and direct repeats, are statistically excluded from coding regions and will be used to eliminate spurious open reading frames (ORFs) and to identify important regulatory regions. Annotation of these degenerate sequences will be included in an automatic annotation system, called MAGPIE, being developed at the University of Chicago. ORF boundaries will be confirmed by direct transcriptional assays. Important regulatory elements can be tested for function by destroying the symmetries in these sequences and assaying for transcriptional anomalies in vitro. Parallel sequencing of the genomes of other strains of R. capsulatus will allow for the comparison of degenerate sequence motifs and recombination points. Suggestive degenerate sequences will be tested for recombinagenic activity directly in a simple in vivo system involving restoration of an antibiotic resistance marker. Insights into ORF determination and predicting recombination may be relevant to similar tasks in much more complicated sequences like the human genome.