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Editing CG and non-CG DNA methylation to identify genomic elements that regulate gene expression

编辑 CG 和非 CG DNA 甲基化以识别调节基因表达的基因组元件

基本信息

批准号：
10487529
负责人：
Hani Goodarzi
金额：
$ 40.38万
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：
2021
资助国家：
美国
起止时间：
2021-09-10 至 2025-06-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10487529
关键词：
Address Biology Brain CRISPR screen Cell division Cells Chimeric Proteins Chromosomes Clustered Regularly Interspaced Short Palindromic Repeats Code Communities Correlative Study CpG Islands DNA DNA Methylation DNA Methylation Regulation DNA Sequence Deposition Development Disease Elements Enhancers Epigenetic Process Gene Expression Gene Expression Profile Gene Expression Regulation Gene Silencing Genes Genetic Enhancer Element Genetic Transcription Genome Genomic approach Genomics Genotype Goals Histones Human Human Biology Human Chromosomes Human Genome Human Genome Project Maps Measures Methods Methylation Modeling Names Neurons Nucleic Acid Regulatory Sequences Outcome Measure Phenotype Pluripotent Stem Cells Proteins Regulation Regulator Genes Regulatory Element Research Resolution Resources Sequence-Specific DNA Binding Protein Specific qualifier value Technology Testing Tissue-Specific Gene Expression Untranslated RNA Writing base biomedical scientist cell type combinatorial epigenetic memory epigenome editing experimental study functional genomics gene repression genetic regulatory protein histone modification human disease human pluripotent stem cell induced pluripotent stem cell programs promoter stem cell differentiation stem cells tool transcription factor transcriptome

项目摘要

PROJECT SUMMARY / ABSTRACT A long-standing goal in biology is to define the relationship between genotype and phenotype. A major surprise of the human genome project was that the human genome encodes so few genes despite the complexity of cell types that compose for example, the human brain. As such it is assumed that combinatorial gene expression programs are key for specifying the function of specialized cell types such as neurons. Cell type specific gene expression programs therefore must be encoded by cis- and trans- non-coding regulatory DNA elements whose function is regulated by the epigenetic code and key proteins such as transcription factors. Elucidating how non-coding regulatory elements function to program cells will transform our understanding of human biology, development and disease. CRISPR/dCas9 technologies enable us to move beyond correlative studies, by editing the epigenome and determining the direct effect of epigenetic alterations on gene expression. We have created a new epigenetic editing functional genomics approach that we have named CRISPRoff. CRISPRoff robustly and specifically writes CpG DNA methylation (5mC) and repressive histone modifications to target loci. We are proposing to use CRISPRoff to map all genomic regulatory elements that are regulated by 5mC across an entire human chromosome. In the proposed experiments we will use perturb-seq, which combines pooled CRISPR screens with a single cell transcriptome readout, to directly measure how deposition of 5mC by CRISPRoff across an entire chromosome modulates gene expression. This approach will identify genetic regulatory elements key for induced pluripotent stem cells and neurons, a key step to understanding how tissue-specific gene expression is controlled. Our proposed research will serve to demonstrate the utility of this approach and motivate extending this approach to map gene regulatory elements across the entire human genome. The results of the proposed research will serve as a fundamental resource and roadmap for a broad community of biomedical scientists and greatly inform our understanding of human biology and disease.

项目摘要/摘要