合成细胞类型特定的cis-监管元素的机器引导设计
S J Gosai1,2,3,4, R I Castro5, N Fuentes5,6
1Broad Institute of MIT and Harvard, Cambridge, MA, USA.
bioRxiv : the preprint server for biology
|August 23, 2023
概括
科学家们设计了合成的Cis-regulatory元素 (CREs),其性能优于自然元素. 这些新型CREs为特定细胞类型的基因表达提供了精确的控制,推动了生物技术和治疗应用.
科学领域:
- 基因组学就是基因组学.
- 分子生物学分子生物学
- 合成生物学 合成生物学
背景情况:
- 细胞调节元件 (CREs) 对于控制基因表达,决定细胞身份和反应至关重要.
- 对于特定的治疗或生物技术需求,天然CREs可能不是最佳的.
- 设计具有编程细胞类型特异性的定制CREs是一个重大挑战.
研究的目的:
- 开发一个平台,用于设计和验证具有编程细胞类型特异性的合成CREs.
- 创建新的调节元件,以精确控制目标细胞中的基因表达.
- 为了证明合成CREs可以在驱动细胞特异性表达方面超越自然的人类序列.
主要方法:
- 利用深度神经网络建模来预测多种细胞类型的CRE活动.
- 使用高效的in silico优化来设计合成CRE序列.
- 利用大规模并行报告员测试 (MPRA) 来对数千个CREs进行高通量实证测试.
- 对工程CREs进行了体外和体内验证.
主要成果:
- 合成CREs成功地被设计为驱动具有编程细胞类型特异性的基因表达.
- 经过验证的合成序列与自然人体CREs相比,表现优越.
- 工程CREs表现出独特的序列语法,用于增强目标活动和减少目标之外的表达.
- 在脊椎动物模型中证明了合成CREs的体内疗效.
结论:
- 开发的平台为前性工程功能CREs提供了一个可概括的框架.
- 合成CREs为生物技术和治疗应用中精确基因调节提供了强大的工具.
- 这项工作建立了为适合目的 in vivo 应用程序设计监管代码的能力.
相关概念视频
02:02Cis-regulatory Sequences
9.9K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
9.9K
02:53Conservative Site-specific Recombination and Phase Variation
6.0K
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
The recognition sites for Cre recombinase called LoxP...
6.0K
02:23Master Transcription Regulators
6.9K
Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...
6.9K
01:58Cell Specific Gene Expression
4.7K
4.7K
02:33Combinatorial Gene Control
8.4K
Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
8.4K