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Determining the influence of 3D chromatin structure on human evolution

确定 3D 染色质结构对人类进化的影响

基本信息

批准号：
10473729
负责人：
Lana Harshman
金额：
$ 2.39万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-09-16 至 2022-11-18
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10473729
关键词：
3-Dimensional Affect Binding Binding Sites CCCTC-binding factor CRISPR/Cas technology Categories Cell Line Cell Survival Cells Chromatin Chromatin Loop Chromatin Structure Clustered Regularly Interspaced Short Palindromic Repeats Consensus DNA Data Data Set Ensure Eukaryota Evolution Gene Expression Gene Expression Profile Gene Expression Regulation Genes Genome Genomic Segment Genomics Haploid Cells Haploidy Hi-C Hominidae Human Human Cell Line Human Genome Hylobates Genus Individual Lead Lentivirus Libraries Limb structure Location Mammals Measures Methods Modernization Molecular Conformation Morphology Neighborhoods Organism Pan Genus Phenotype Play Positioning Attribute Prevalence Recording of previous events Regulatory Element Repression Research Personnel Role Scanning Site Structure Time Untranslated RNA Work base computerized tools driving force experimental study fascinate genomic data in silico nonhuman primate novel organizational structure three dimensional structure trait transcription factor trend

项目摘要

PROJECT SUMMARY/ABSTRACT The importance of 3D genome structure on the evolution of human specific gene regulation, phenotypes, and speciation remains largely unknown. Here, I plan to characterize in a high- throughput manner the impact of topologically associated domains (TADs), which are genomic neighborhoods of self-interacting DNA, and CCCTC binding factor (CTCF) binding motifs, which help facilitate DNA looping, on cell viability and evolution. I hypothesize that a subset of TAD boundaries are critical for maintaining important gene regulation throughout evolution and that derived CTCF binding sites in the human lineage may have led to gene expression changes. I will interrogate this hypothesis by first performing a high-throughput CRISPR-deletion screen in which I will delete a set of over 300 evolutionarily conserved and human specific TAD boundaries in a human haploid cell line to determine if any of these boundaries are essential for cell viability (Aim 1). Second, I will identify human specific CTCF binding motifs that are gained or lost in humans or have orientation changes by comparing genome sequences from human, chimpanzee, and two extinct archaic hominids: Neanderthal and Denisovan. I will further interrogate the importance of a subset of these novel CTCF sites by CRISPR/Cas9 editing human cells to mimic that of an extinct genome and phenotype them for changes in gene expression changes and chromatin conformation. It will then be possible to determine if these changes caused differences in gene regulation and genome looping (Aim 2). Combined, this proposal will take a crucial step in further understanding how 3D chromatin structure can affect phenotypes especially as it relates to human evolution.

项目总结/文摘