对非编码CRISPRi屏幕的多中心综合分析
David Yao1, Josh Tycko2,3, Jin Woo Oh4
1Department of Genetics, Stanford University, Stanford, CA, USA.
Nature methods
|March 20, 2024
概括
在ENCODE4的功能性特征中心中,使用集成的CRISPR屏幕来系统地研究cis-regulatory元素 (CREs). 制定了指导方针和数据资源,以加速非编码基因组的功能基因组学.
科学领域:
- 基因组学就是基因组学.
- 分子生物学分子生物学
- 功能性基因组学 功能性基因组学
背景情况:
- 恩科德联盟 (ENCODE Consortium) 标注了非编码的Cis调节元件 (CREs),以了解基因调节.
- 聚合,非编码的CRISPR屏幕提供了一种系统的方法来研究cis-regulatory机制.
研究的目的:
- 建立使用CRISPR干扰 (CRISPRi) 选内源非编码元素的指导方针.
- 为非编码基因组的功能性特征提供可访问的数据资源和工具.
主要方法:
- 在人类细胞系中进行了108个合并的非编码CRISPR查 (>54万个扰动).
- 在K562细胞中利用332个功能确认的CRE基因链接来制定指导方针.
- 基准测试了五种CRISPR屏幕分析工具,确定CASA是强大的和保守的.
主要成果:
- 建立了对内源性非编码元素的CRISPRi查的指导方针,包括检测低效CREs.
- 在转录的区域中确定了CRISPRi的DNA链偏差,影响了屏幕设计.
- 开发了一个数据资源,为3,275,697个ENCODE SCREEN候选CREs预定单一导向RNA.
结论:
- 该研究提供了实用的指导方针和一个有价值的数据资源,以推进非编码基因组的功能基因组学.
- 这些资源将加快使用CRISPRi屏幕对cis-regulatory元素的系统功能表征.
相关概念视频
02:53CRISPR and crRNAs
Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...
02:46Genetic Screens
Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
01:05Single Nucleotide Polymorphisms-SNPs
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...