INFERRING CHROMOSOME ARCHITECTURE FROM GENOMIC SEQUENCE

从基因组序列推断染色体结构

• 批准号: 6536467
• 负责人: CRAIG J. BENHAM
• 金额: $ 22.26万
• 依托单位: UNIVERSITY OF CALIFORNIA AT DAVIS
• 依托单位国家: 美国
• 财政年份: 2000
• 资助国家: 美国
• 起止时间: 2000-04-17 至 2004-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6536467
• 关键词: DNA binding protein; DNA replication origin; binding sites; biotechnology; chemical stability; chromosomes; eukaryote; gene therapy; genome; mathematical model; method development; nuclear matrix; nucleic acid sequence; statistics /biometry; transfection /expression vector

Eukaryotic chromosomal DNA is partitioned into domains by periodic attachment to a protein scaffold. The sites on the DNA where attachment occurs, called scaffold (or matrix) attachment regions (S/MARs), strongly influence many regulatory events including transcriptional augmentation and enhancement, initiation of DNA replication, retroviral integration, and apoptosis. Progress in understanding the mechanisms underlying scaffold attachment and its regulatory effects has been hampered by the fact that S/MARs have no consensus sequence associated with them. Recent work by this research group and our experimentalist collaborators implicates stress-induced DNA duplex destabilization (SIDD) in eukaryotic scaffold binding. When this investigator uses his theoretical method to calculate destabilization profiles of superhelical DNA sequences containing known S/MARs, the S/MAR sites coincide with regions of extensive destabilization. Our experimentalist collaborators have shown that these sites actually undergo base unpairing, both in vitro and in vivo. Moreover, the extent of SIDD is highly correlated with strength of binding. This collaborative research program will extend our investigation of the role of duplex destabilization in scaffold attachment and ancillary regulatory events. We will investigate in detail the associations between strength of SAR binding and SIDD characteristics. We will completely characterize the SIDD properties of SARs, and use this information to design artificial SAR elements based on our understanding of their required attributes. These will be constructed by our collaborators from prokaryotic DNA, and their scaffold binding properties will be assessed. We will develop computational search strategies to detect SAR elements in genomic DNA sequences by their SIDD properties. This will provide the first method for inferring chromosomal architecture and nuclear organization directly from the DNA sequence. It will enable a host of important studies to be performed regarding the organization and regulation of genomic DNA. It will be used to develop a new generation of precisely targeted and regulated transfection vectors for gene therapy.

真核染色体DNA通过周期性附着在蛋白质支架上分配到结构域中。 DNA上发生附着的位点，称为支架（或矩阵）附着区域（S/MARS），强烈影响许多调节事件，包括转录增强和增强，DNA复制的启动，逆转录病毒整合，逆转录病毒和凋亡。了解S/MARS没有与之相关的共识序列，理解脚手架附着及其调节作用的机制及其调节作用的进展受到了阻碍。该研究小组和我们的实验主义合作者的最新工作暗示了在真核支架结合中应激诱导的DNA双链稳定（SIDD）。当该研究者使用他的理论方法计算包含已知S/MARS的超螺旋DNA序列的不稳定谱时，S/MAR位点与广泛的不稳定区域一致。我们的实验主义合作者表明，这些站点实际上在体外和体内都经历了基础不足。此外，SIDD的程度与结合强度高度相关。该协作研究计划将扩展我们对双工不稳定在脚手架依恋和辅助监管事件中的作用的研究。我们将详细研究SAR结合和SIDD特征的强度之间的关联。我们将完全表征SARS的SIDD属性，并根据我们对其所需属性的理解来设计人工SAR元素。这些将由我们的核DNA合作者构建，并评估它们的脚手架结合特性。我们将开发计算搜索策略，以通过其SIDD特性检测基因组DNA序列中的SAR元素。这将为直接从DNA序列直接推断染色体体系结构和核组织的第一种方法。这将使有关基因组DNA的组织和调节进行大量重要研究。它将用于开发新一代的精确靶向和受调节的转染载体，以进行基因治疗。