Assessing parent-of-origin transcriptional effects in Xenopus laevis

评估非洲爪蟾的亲本转录效应

• 批准号: 8911356
• 负责人: Alexander Gimelbrant
• 金额: $ 20.84万
• 依托单位: DANA-FARBER CANCER INST
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-08-15 至 2017-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8911356
• 关键词: Affect; African; Alleles; Allelic Imbalance; Amphibia; Angelman Syndrome; Angiosperms; Animals; Beckwith-Wiedemann Syndrome; Biochemistry; Biological Assay; Biological Models; Biology; Candidate Disease Gene; Cellular biology; Collaborations; Complement; Complex; Data; Development; Developmental Biology; Diploidy; Disease; Embryo; Employee Strikes; Epigenetic Process; Exhibits; Gene Expression; Gene Expression Profile; Generations; Genes; Genetic Polymorphism; Genomic Imprinting; Genotype; Goals; Health; Heterozygote; Human; Inbreeding; Individual; Inherited; Lead; Link; Live Birth; Mammals; Molecular Biology; Mothers; Nucleotides; Parents; Phenotype; Placenta; Play; Post-Translational Protein Processing; Proteomics; RNA Sequences; Regulator Genes; Resources; Role; Seeds; Study models; Surveys; Tadpoles; Technology; Vertebrates; Xenopus; Xenopus laevis; Xenopus sp.; base; deep sequencing; design; developmental disease; gene function; imprint; in vivo; infancy; mouse model; research study; tool; trait; transcriptome sequencing; transcriptomics; treatment strategy

DESCRIPTION (provided by applicant): Parent-of-origin effects are epigenetic phenomena that appear as phenotypic differences between heterozygotes depending on the allelic parent of origin. The primary epigenetic phenomenon that can lead to the parent-of-origin effects is genomic imprinting. Some imprinted loci are expressed from the maternal copy only, while others from the paternal copy. Imprinted genes play an important part in a number of complex traits, notably in early development. Though the taxonomic distribution of gene imprinting remains uncertain, a widely-accepted view holds that among animals it is limited to mammals, and most studies had been performed in mouse models. There are significant technical challenges in assessment of imprinting in a wider variety of species. A major limiting factor is lack of multiple inbred lines with significant nucleotide-level differences between them, since the most direct way to identify imprinting involves generation of reciprocal crosses between such lines. In addition, transcriptome-wide surveys of allele-specific expression have only recently become feasible, and the analytical and statistical tools for analysis of such data are still in thir infancy. We have pioneered several technologies for the analysis of allele-specific expression. In collaboration with experts in the biology of the African clawed frog, Xenopus laevis, we have performed preliminary RNA sequencing experiments on mixed crosses between inbred lines that strongly suggest that there are genes in X. laevis that exhibit parent-of-origin imprinting. The goal of this project is to carefully and thoroughly assess this striking hypothesis. In order t do that, we will execute a "zoom in sequencing" approach which consists of a "wide but shallow" round where we screen for candidate genes, complemented by a "deep but narrow" round where we focus in detail on the allelic bias of a set of candidate genes. Identification of parent of-origin imprinting in an amphibian would represent a significant conceptual advance in understanding the evolutionary origins of that epigenetic mechanism and its role in development. Moreover, Xenopus has long been an important tool for in vivo studies in molecular, cell, and developmental biology of vertebrate animals. It is the only vertebrate model system that allows for high-throughput in vivo analyses of gene function and biochemistry. Xenopus as a model for the study of imprinting would allow for the development of screens to identify new targets important for disease and for the design of new therapies involving imprinted genes.

描述（由申请方提供）：起源亲本效应是表观遗传现象，表现为杂合子之间的表型差异，取决于起源的等位亲本。基因组印记是导致亲本效应的主要表观遗传现象。一些印记基因座仅从母本拷贝表达，而另一些则从父本拷贝表达。印记基因在许多复杂的性状中起着重要作用，特别是在早期发育中。 虽然基因印迹的分类学分布仍不确定，但一种被广泛接受的观点认为，在动物中，它仅限于哺乳动物，并且大多数研究都是在小鼠模型中进行的。在更广泛的物种中评估印记存在重大的技术挑战。一个主要的限制因素是缺乏多个自交系，它们之间具有显着的核苷酸水平差异，因为 鉴定印记的最直接的方法包括在这些品系之间产生相互杂交。此外，等位基因特异性表达的全转录组调查最近才变得可行，并且用于分析这些数据的分析和统计工具仍处于婴儿期。 我们已经开创了几种分析等位基因特异性表达的技术。在与非洲爪蟾（Xenopus laevis）生物学专家的合作中，我们对近交系之间的混合杂交进行了初步的RNA测序实验，这些实验强烈表明X中存在基因。表现出原始印记母体的光滑组织。 这个项目的目标是仔细和彻底地评估这个惊人的假设。为了做到这一点，我们将执行一个“放大测序”的方法，它包括一个“宽而浅”的回合，我们在其中筛选候选基因，辅之以一个“深而窄”的回合，我们在其中详细关注一组候选基因的等位基因偏好。 父母的身份 两栖动物的起源印记将代表理解表观遗传机制的进化起源及其在发育中的作用的重要概念进展。此外，非洲爪蟾长期以来一直是脊椎动物分子、细胞和发育生物学体内研究的重要工具。它是唯一的脊椎动物模型系统，允许高通量的基因功能和生物化学的体内分析。非洲爪蟾作为研究印迹的模型，将允许屏幕的发展，以确定新的目标，重要的疾病和设计新的治疗方法涉及印迹基因。