Detecting Human Functional Sequences with Microarrays

用微阵列检测人类功能序列

• 批准号: 7096139
• 负责人: Ian Dunham
• 金额: $ 27.21万
• 依托单位: SANGER INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-09-30 至 2007-09-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7096139
• 关键词: DNA methylation; DNA replication origin; biotechnology; chromatin; clinical research; cooperative study; genetic mapping; high throughput technology; histones; human genetic material tag; microarray technology; nucleic acid sequence; technology /technique development; transcription factor

DESCRIPTION (provided by applicant): With the recent completion of the DNA sequence of the euchromatic portion of the human genome, the inherited information that determines cellular and organismal function is available. The next challenge lies in understanding how to connect the information in the genome sequence with the functions it encodes. This project aims to refine and implement efficient high throughput experimental methods to identify the sequence features that encode regulatory and maintenance functions of the human genome. Specifically the project will aim to design and construct micorarrays consisting of 1.5kb PCR products covering the entire unique genomic sequence of the 30 Mb targeted by the ENCODE project. In parallel a collection of BAC and other sequencing tilepath clones will be establish to cover the targeted regions in a tile-path BAC subarray. At the same time we will optimize assays to provide DNA fractions enriched for specific functional elements from three actively dividing cell lines representing B cells, T cells and fibroblasts. These DNA fractions will be assayed using the genomic microarrays to identify DNA fragments containing functional elements. This will establish a map of various functional properties for 1% of the physical genome, specifically replication timing, location of replication origins, chromatin modification, and common transcription factor binding sites. These maps will be analyzed in comparison to other properties of the genome sequence including G+C content, gene content, repeat content, and sequence conservation. All data will be deposited with the ENCODE consortium as soon as it is shown to be reliable by replication and preliminary analysis.

描述(申请人提供)：随着最近人类基因组常染色质部分的DNA序列的完成，决定细胞和器官功能的遗传信息可用。下一个挑战在于理解如何将基因组序列中的信息与其编码的功能联系起来。该项目旨在改进和实施高效的高通量实验方法，以确定编码人类基因组调节和维护功能的序列特征。具体地说，该项目的目标是设计和构建由1.5kb的聚合酶链式反应产物组成的微阵列，覆盖ENCODE项目所针对的30Mb的整个独特的基因组序列。同时，将建立BAC和其他测序块路径克隆的集合，以覆盖块路径BAC子阵列中的目标区域。与此同时，我们将优化分析，从代表B细胞、T细胞和成纤维细胞的三个活跃分裂细胞系中提供富含特定功能元素的DNA组分。这些DNA组分将使用基因组微阵列进行分析，以识别包含功能元件的DNA片段。这将为1%的物理基因组建立一张各种功能属性的图谱，特别是复制时机、复制起点的位置、染色质修饰和共同的转录因子结合位点。这些图谱将与基因组序列的其他属性进行比较，包括G+C含量、基因含量、重复含量和序列保守性。一旦经复制和初步分析证明是可靠的，所有数据将立即存入ENCODE财团。