Single molecule detection of L1 insertions and intermediates

L1 插入和中间体的单分子检测

基本信息

批准号：
10662586
负责人：
BRADLEY Evan BERNSTEIN
金额：
$ 45.05万
依托单位：
DANA-FARBER CANCER INST
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-04-01 至 2025-03-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10662586
关键词：
3&apos Flanking Region Admixture Benchmarking Biological Assay Biology Cataloging Catalogs Cell Nucleus Cells Cellular Assay Code Complement Complementary DNA Coupled DNA DNA Insertion Elements DNA Transposable Elements Data Data Analyses Detection Development Disease Elements Epigenetic Process Event Gene Frequency Genetic Variation Genome Genomic DNA Genomics Goals Heritability High-Throughput Nucleotide Sequencing Human Human Genetics Hybrids In Situ Inherited Laboratories Long Interspersed Elements Malignant Neoplasms Maps Methods Methylation Molecular Biology Molecular Computations Mosaicism Normal tissue morphology Phase Population Procedures Production Proteins Quality Control RNA Reaction Repression Research Personnel Retrotransposition Retrotransposon Reverse Transcription Sensitivity and Specificity Single Nucleotide Polymorphism Site Somatic Mutation Sorting Source Standardization Technology Tissues Validation Variant computational pipelines data analysis pipeline experience genetic variant genome-wide genomic locus genomic tools human tissue innovation instrument method development multidisciplinary nanopore promoter scale up single cell technology single molecule technology development tool tool development transposon sequencing variant detection whole genome

3&apos Flanking Region Admixture Benchmarking Biological Assay Biology Cataloging Catalogs Cell Nucleus Cells Cellular Assay Code Complement Complementary DNA Coupled DNA DNA Insertion Elements DNA Transposable Elements Data Data Analyses Detection Development Disease Elements Epigenetic Process Event Gene Frequency Genetic Variation Genome Genomic DNA Genomics Goals Heritability High-Throughput Nucleotide Sequencing Human Human Genetics Hybrids In Situ Inherited Laboratories Long Interspersed Elements Malignant Neoplasms Maps Methods Methylation Molecular Biology Molecular Computations Mosaicism Normal tissue morphology Phase Population Procedures Production Proteins Quality Control RNA Reaction Repression Research Personnel Retrotransposition Retrotransposon Reverse Transcription Sensitivity and Specificity Single Nucleotide Polymorphism Site Somatic Mutation Sorting Source Standardization Technology Tissues Validation Variant computational pipelines data analysis pipeline experience genetic variant genome-wide genomic locus genomic tools human tissue innovation instrument method development multidisciplinary nanopore promoter scale up single cell technology single molecule technology development tool tool development transposon sequencing variant detection whole genome

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项目摘要

Project Summary Transposable elements are major sources of heritable human genetic variation and can contribute to disease by causing somatic mutations. This application focuses on the development of genomic tools and technologies to assess the contributions of these transposons to somatic mosaicism in normal tissues. Specifically, we will develop tools and technologies to detect variants in long interspersed element-1 (LINE-1, L1) sequences. L1 is the only active self-propagating protein-coding transposon in humans. We each inherit a distinct complement of active L1 loci, each of which is typically repressed through methylation of its internal promoter. Here, we propose to develop single cell mapping approaches to detect de novo L1 insertions and integrate these with long-read sequencing approaches to reveal the epigenetic status of source elements. We will also pioneer highly innovative approaches to detect intermediates of the target primed reverse transcription (TPRT) reaction that gives rise to L1 insertion events. Our multidisciplinary team brings together investigators with expertise in retrotransposon biology and genetic variation; innovation in the field of epigenetics; and experience with molecular biology and computational genomics methods development. Our shared goal in this UG3/UH3 project is to provide enabling tools and technologies to the Somatic Mosaicism across Human Tissues (SMaHT) Network.

项目摘要转座元素是可遗传人类遗传变异的主要来源，可以通过引起躯体突变。该应用的重点是开发基因组工具和技术评估这些转座子对正常组织中体细胞镶嵌的贡献。具体来说，我们会的开发工具和技术，以检测长期插入的元素-1（LINE-1，L1）序列中的变体。 L1是人类中唯一活跃的自传播蛋白质编码转座子。我们每个人都继承了一个独特的补充活性L1基因座，每个基因座通常都通过其内部启动子的甲基化来抑制。在这里，我们建议开发单细胞映射方法以检测从头l1插入，并将其与长阅读集成在一起测序方法揭示了源元素的表观遗传状态。我们还将开拓高度创新性检测目标引发逆转录（TPRT）反应的中间体的方法，该反应引起 L1插入事件。我们的跨学科团队将逆转汇率专业知识的调查员聚集在一起生物学和遗传变异；表观遗传学领域的创新；以及分子生物学的经验和计算基因组学方法的发展。我们在这个UG3/UH3项目中的共同目标是提供启用人类组织（SMAHT）网络的体细胞镶嵌的工具和技术。