Determining the developmental progression of PTF1 targets by ChIP-seq

通过 ChIP-seq 确定 PTF1 靶标的发育进程

• 批准号: 7572766
• 负责人: RAYMOND J. MACDONALD
• 金额: $ 23.55万
• 依托单位: UT SOUTHWESTERN MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-01-15 至 2010-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7572766
• 关键词: Acinar Cell; Adult; Area; Binding; Binding Sites; Bioinformatics; Cancer Cell Growth; Cell Line; Cell Lineage; Cells; Chromatin; Complex; Consensus; DNA Binding; Development; Diabetes Mellitus; Disease; Ductal; Embryo; Embryonic Development; Enzyme Gene; Enzymes; Epithelium; Exocrine pancreas; Exploratory/Developmental Grant; Funding; Gene Expression; Gene Targeting; Genetic Transcription; Growth; Growth and Development function; Insulin; Malignant Neoplasms; Modeling; Molecular; Morphogenesis; Natural regeneration; Organogenesis; Pancreas; Pancreatitis; Process; Proteins; Protocols documentation; Regulation; Role; Sequence Analysis; Signal Transduction; Site; Staging; Technology; Tissues; Validation; Yeasts; chromatin immunoprecipitation; genome wide association study; high risk; in vivo; insight; islet; neuronal cell body; notch protein; novel; pancreas development; paralogous gene; progenitor; programs; public health relevance; reconstitution; transcription factor

DESCRIPTION (provided by applicant): We request R21 funding for a high risk, exploratory project for the genome-wide identification of target genes of PTF1a, a key bHLH transcriptional regulator of pancreatic organogenesis. During development, PTF1a functions in two temporally distinct trimeric complexes. It is required for early growth and morphogenesis in one complex bound to RBPJ, in a novel Notch-independent role. At the onset of islet, ductal and acinar lineage specification, it becomes restricted to nascent acinar cells and exchanges RBPJ for RBPJL, a constitutively active, vertebrate-specific and Notch-indifferent paralogue, and directs the acinar differentiation program. Comprehensive identification of direct targets of transcription factors that control embryonic development has proven extraordinarily difficult, due largely to the difficulty of recognizing functional binding sites in chromatin. Consequently, only limited advances in this area have been made, mostly through candidate, target-by-target strategies. The availability of only very small quantities of embryonic chromatin requires special technical considerations and refinements of current protocols. Here we propose an aggressive approach using cutting edge technologies to make a more substantial advance in highly inclusive target-identification during embryonic development using PTF1a in the pancreas as our model. Aim 1 will establish conditions to prepare sufficient ChIP-enriched embryonic chromatin for massive parallel sequencing using the Illumina platform, identify and validate PTF1a-target sites, and compare targets for the early growth, lineage-decision, and differentiation stages of pancreatic development. Aim 2 will compare and contrast the targets of the trimeric PTF1 complexes with those for RBPJL alone and for RBPJ in its distinct function for Notch-signaling. For reasons of high risk and the potential for high impact, we believe that the project outlined in this application is an appropriate candidate for the R21 mechanism. PUBLIC HEALTH RELEVANCE: Diabetes, pancreatitis and cancer are common diseases of the pancreas. By better understanding the control of normal development of the pancreas, we hope to contribute to therapies that may help reconstitute insulin producing cells, regenerate a pancreas badly damaged by pancreatitis, or identify ways to stop the growth of cancer cells derived from the exocrine pancreas without damaging other cells of the body.

描述（由申请人提供）：我们请求R21资助一个高风险的探索性项目，用于全基因组鉴定PTF1a的靶基因，PTF1a是胰腺器官发生的关键bHLH转录调节因子。在发育过程中，PTF1a在两个时间上不同的三聚体复合物中发挥作用。它是所需的早期生长和形态发生在一个复杂的结合RBPJ，在一个新的缺口独立的作用。在胰岛、导管和腺泡谱系特化开始时，它变得限于新生腺泡细胞，并将RBPJ交换为RBPJL，RBPJL是一种组成型活性的、脊椎动物特异性的和Notch无关的paradox，并指导腺泡分化程序。控制胚胎发育的转录因子的直接靶标的全面鉴定已被证明是非常困难的，这主要是由于识别染色质中的功能结合位点的困难。因此，在这一领域只取得了有限的进展，主要是通过候选的逐个目标的战略。只有非常少量的胚胎染色质的可用性需要特殊的技术考虑和当前协议的改进。在这里，我们提出了一种积极的方法，使用尖端技术，在胚胎发育过程中，使用胰腺中的PTF1a作为我们的模型，在高度包容性的靶点识别方面取得了更大的进展。目标1将建立条件，以制备足够的ChIP富集的胚胎染色质，用于使用Illumina平台进行大规模平行测序，鉴定和验证PTF1a靶位点，并比较胰腺发育早期生长，谱系决定和分化阶段的靶点。目的2将比较和对比三聚体PTF 1复合物的靶点与单独的RBPJL和RBPJ在Notch信号传导中的独特功能。由于高风险和可能产生高影响的原因，我们认为本申请中概述的项目是R21机制的适当候选项目。公共卫生相关性：糖尿病、胰腺炎和癌症是胰腺的常见疾病。通过更好地了解胰腺正常发育的控制，我们希望有助于重建胰岛素产生细胞的治疗，再生胰腺炎严重受损的胰腺，或确定阻止来自外分泌胰腺的癌细胞生长的方法。