High-throughput systematic characterization of regulatory element function

调控元件功能的高通量系统表征

• 批准号: 10238366
• 负责人: MICHAEL C BASSIK
• 金额: $ 103.26万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-01 至 2022-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10238366
• 关键词: Administrative Supplement; CRISPR screen; Cell Line; Chromatin Structure; Collection; Coupled; Data; Elements; Gene Expression; Generations; Genes; Genomics; Maps; Methods; Regulatory Element; Resolution; Technology; Testing; Tissues; Validation; genome-wide; large datasets; transcription factor

Project Summary This application is an administrative supplement request for 5UM1HG009436. The ENCODE project has produced high-resolution, high-quality maps of components of the `regulome' in a set of tissues and cell lines, identifying a collection of putative regulatory elements. Our proposal aims to generate and release data that test the functional relevance of these putative elements with high-throughput, pooled CRISPR screens, as well as a number of other methods that are aimed to understand the relationship between transcription factor levels, global accessibility at regulatory elements, an the effects on gene expression.

项目摘要 本申请是5UM1HG 009436的管理补充申请。ENCODE项目 在一组组织和细胞系中产生了“调节组”组分的高分辨率、高质量图谱， 鉴定推定的调控元件的集合。我们的建议旨在生成和发布数据， 用高通量、合并的CRISPR筛选来测试这些推定元件的功能相关性， 与其他一些旨在了解转录因子之间关系的方法一样， 水平，调控元件的全局可及性，以及对基因表达的影响。

项目成果

A genome-wide atlas of co-essential modules assigns function to uncharacterized genes.

• DOI: 10.1038/s41588-021-00840-z
• 发表时间: 2021-05
• 期刊: Nature genetics
• 影响因子: 30.8
• 作者: Wainberg M;Kamber RA;Balsubramani A;Meyers RM;Sinnott-Armstrong N;Hornburg D;Jiang L;Chan J;Jian R;Gu M;Shcherbina A;Dubreuil MM;Spees K;Meuleman W;Snyder MP;Bassik MC;Kundaje A
• 通讯作者: Kundaje A

Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators.

全基因组筛选对L1调节剂的选择性沉默对圣体的L1s的选择性沉默。

• DOI: 10.1038/nature25179
• 发表时间: 2018-01-11
• 期刊: Nature
• 影响因子: 64.8
• 作者: Liu N;Lee CH;Swigut T;Grow E;Gu B;Bassik MC;Wysocka J
• 通讯作者: Wysocka J

Single-Molecule Multikilobase-Scale Profiling of Chromatin Accessibility Using m6A-SMAC-Seq and m6A-CpG-GpC-SMAC-Seq.

• DOI: 10.1007/978-1-0716-2140-0_15
• 发表时间: 2022
• 期刊: Methods in molecular biology (Clifton, N.J.)

Genome-Wide Mapping of Active Regulatory Elements Using ATAC-seq.

使用 ATAC-seq 进行活性调控元件的全基因组图谱。

• DOI: 10.1007/978-1-0716-2899-7_1
• 发表时间: 2023
• 期刊: Methods in molecular biology (Clifton, N.J.)
• 作者: Marinov,GeorgiK;Shipony,Zohar;Kundaje,Anshul;Greenleaf,WilliamJ
• 通讯作者: Greenleaf,WilliamJ