Global Predictions and Tests of Erythroid Regulation

红细胞调节的全球预测和测试

• 批准号: 8046378
• 负责人: Gerd A Blobel
• 金额: $ 57.58万
• 依托单位: PENNSYLVANIA STATE UNIVERSITY, THE
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-02-01 至 2014-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8046378
• 关键词: Affinity; Algorithms; Anemia; Binding; Binding Sites; Biochemical; Bioinformatics; Biological; Biological Assay; Biological Models; Biological Preservation; Biological Process; Biological Testing; Cell model; Cells; Characteristics; Chromatin; Code; Complement; Complex; Computer software; Critical Pathways; DNA; DNA Resequencing; DNA Sequence; Data; Data Analyses; Data Set; Development; Developmental Biology; Disease; Distal; Enhancers; Erythrocytes; Erythroid; Erythroid Cells; Erythroid Progenitor Cells; Erythropoiesis; Evolution; Gene Activation; Gene Expression; Gene Expression Regulation; Genes; Genome; Genomics; Goals; Health; Hereditary Disease; Histones; Inherited; Investigation; Location; Machine Learning; Maps; Measurement; Methods; Mining; Modeling; Modification; Molecular; Mus; Mutagenesis; Nucleosomes; Organism; Pattern; Phenotype; Phylogenetic Analysis; Predisposition; Process; Property; Proteins; Recording of previous events; Regulation; Reporter Genes; Research; Resolution; Reverse Transcriptase Polymerase Chain Reaction; Role; Sensitivity and Specificity; Sequence Alignment; Signal Transduction; Site; Stream; Structure; Techniques; Technology; Testing; Therapeutic Intervention; Tissues; Transcript; Transfection; analytical tool; chromatin immunoprecipitation; computerized data processing; data acquisition; data mining; density; gain of function; gene repression; genome-wide; histone modification; human GATA1 protein; improved; in vivo; insight; novel; promoter; public health relevance; research study; restoration; software development; success; tool; transcription factor

DESCRIPTION (provided by applicant): Proper regulation of gene expression is essential to the normal development and health of organisms, whereas aberrant gene regulation is known to cause many genetic diseases, including some inherited anemias, and it is thought to be a major contributor to complex phenotypes such as susceptibility to common diseases. Understanding the molecular mechanisms of gene regulation may provide novel candidates for therapeutic interventions. Our studies aim for a deeper molecular understanding of global aspects of gene regulation in an important biological process, the maturation of erythroid precursor cells to become red blood cells. Building on our progress using patterns in sequence alignments to predict cis-regulatory modules for erythroid genes and deciphering functional correlations of their evolutionary history, we propose to acquire genome-wide information on biochemical features associated with regulation to reach a more complete understanding of gene regulation in erythroid cells. Specifically, we propose to use high throughput biochemical assays such as chromatin immunoprecipitation followed by hybridization to microarrays and deep re-sequencing to acquire data on genomic DNA sequences (Aim 1) occupied in vivo by critical tissue-specific transcription factors, (Aim 2) bound by histones with modifications associated with gene activation or repression, (Aim 3) in chromatin with an altered structure, and (Aim 4) transcribed in a mouse erythroid cell model that undergoes maturation upon restoration of the critical transcription factor GATA-1. Then we will (Aim 5) apply existing software and develop new data-processing algorithms to determine peaks of signals that are likely to represent the locations of the features targeted in aims 1-4. Aim 6 will mine the peak-calling results, along with raw data, multiple sequence alignments and other information to investigate their covariation structure and integrate them to predict cis-regulatory modules, classify the modules by function, identify motifs associated with specific protein occupancy, and deduce the phylogenetic depth of preservation of critical motifs in the regulatory modules. Aim 7 will experimentally test biological hypotheses that arise from the analyses in Aims 6 and 7, determining the extent to which we can validate the locations of protein occupancy and transcripts, the predictions of both positive and negative cis-regulatory modules by gain-of-function cell transfection assays, and the role of motifs implicated in occupancy by directed mutagenesis and in vivo binding assays. We will test whether the motif- constraint hypothesis for protein-occupied DNA segments involved in enhancement applies to transcription factors in addition to GATA-1, and we will conduct additional experiments probing deeper biological issues. This research will provide not only global insights into mechanisms and effects of gene regulation during erythroid maturation, but the techniques and analytical tools developed here can be applied to better understand the development and differentiation of any tissue. PUBLIC HEALTH RELEVANCE: Proper regulation of gene expression is essential to the normal development and health of organisms, whereas aberrant gene regulation can cause genetic diseases, and it appears to be a major contributor to susceptibility to common diseases. Understanding the molecular mechanisms of gene regulation may provide novel candidates for therapeutic interventions. Our studies collecting genome-wide data on many biochemical features associated with gene regulation, mining the data deeply to predict functional DNA sequences, and experimentally testing those bioinformatic predictions will provide global insights into mechanisms and effects of gene regulation during erythroid maturation and provide techniques and analytical tools to better understand the development and differentiation of any tissue.

描述（由申请人提供）：基因表达的适当调节对于生物体的正常发育和健康至关重要，而异常基因调节已知会引起许多遗传疾病，包括一些遗传性贫血，并且被认为是对常见疾病易感性的复杂表征的主要因素。了解基因调节的分子机制可能会为治疗干预提供新的候选。我们的研究旨在在重要的生物学过程中更深入地了解基因调节的全球方面，即红细胞细胞的成熟成为红细胞。在我们的进步基础上，使用序列对准模式预测红斑基因的顺式调节模块以及其进化史的解密功能相关性，我们建议获取有关与调节相关的生化特征的全基因组知识信息，以使对毛细血管细胞中基因调节的基因调节更完整。具体而言，我们建议使用高吞吐物生化测定，例如染色质免疫沉淀，然后将杂交与微阵列杂交，并进行深层重新介绍，以获取基因组DNA序列的数据（AIM 1）（目标1）通过关键组织特异性转录因子（AIM 2）与基因和基因相关（AIM 2）的结合（AIM 2），（AIM 2）与基因的变化（AIM 2）相关联（AIM 2），（AIM 2）与Gene Artistation（AIM）相关联（AIM 2）（AIM 2），将其与结构（AIM）相关联（AIM 2），以Crysection（AIM）进行反应（AIM 2）。 （AIM 4）在恢复关键转录因子GATA-1后经历成熟的小鼠红细胞模型中转录。然后，我们（AIM 5）应用现有软件并开发新的数据处理算法来确定可能代表目标1-4中针对特征位置的信号峰。 AIM 6将挖掘峰值的结果，以及原始数据，多个序列比对和其他信息，以研究其协变结构并整合它们以预测顺式调节模块，通过功能对模块进行分类，识别与特定蛋白质占有率相关的基序，并推导在调节模块中关键基序的系统发育深度。 AIM 7将通过实验测试目标6和7中的分析产生的生物学假设，确定我们可以验证蛋白质占用和转录的位置的程度，阳性和负CIS调节模块的预测通过功能官方的转化分析获得的阳性和负面调节模块的预测，以及通过构图的作用，与无数的疾病构成的作用，并在Diredsississ中涉及viveSiss和vivageSeiss viv and viviv。我们将测试涉及增强蛋白的DNA片段的基序约束假设是否适用于GATA-1之外的转录因子，我们还将进行其他实验，以探测更深入的生物学问题。这项研究不仅将提供对红系成熟过程中基因调节的机制和影响的全球见解，而且此处开发的技术和分析工具可用于更好地了解任何组织的发展和分化。 公共卫生相关性：适当的基因表达调节对于生物的正常发育和健康至关重要，而异常的基因调节可能会导致遗传疾病，并且似乎是对常见疾病易感性的主要因素。了解基因调节的分子机制可能会为治疗干预提供新的候选。我们的研究收集了与基因调节相关的许多生物化学特征，深入挖掘数据以预测功能性DNA序列的研究，并且在实验测试这些生物信息学预测的研究中，将提供全球洞察力和基因调节效果的全球见解，并在促进和分析工具和分析工具和分析工具过程中更好地了解任何开发和分化的开发和分化。