转录尺度的长距离调节与基因组距离以基因特定的方式
bioRxiv : the preprint server for biology
|July 29, 2024
概括
卡戈-VPR直接招募激活剂以准基因,绕过转录因子. 基因表达取决于激活器和促进器之间的距离,揭示了对基因调节的新见解.
科学领域:
- 分子生物学分子生物学
- 遗传学 遗传学 是一个
- 表观遗传学 在表观遗传学中,表观遗传学是指表观遗传学.
背景情况:
- 增强剂-促进剂通信对于基因转录至关重要,但仍然不太了解.
- 目前的方法通常依赖于特定序列的转录因子来实现向基因激活.
研究的目的:
- 开发和验证一种新的方法,CARGO-VPR,用于在任意基因组位点直接招募激活剂.
- 为了研究激活剂招募部位位置和转录输出之间的关系,独立于转录因子.
主要方法:
- 开发了CARGO-VPR (基于CRISPR的激活器招募使用指导RNA组织阵列 - VPR激活域) 用于多重dCas9-VPR向.
- 将CARGO-VPR应用于小鼠胚胎干细胞 (mESCs) 中的Prdm8-Fgf5位点.
- 分析了转录诱导及其与基因组距离的相关性,3D染色质接触,DNA序列和压制标记.
主要成果:
- CARGO-VPR成功地将激活器招募到目标基因组位置,包括以前无法访问的网站.
- 在激活剂招募时观察到Prdm8和Fgf5的转录诱导.
- 基因表达水平强烈依赖于招募地点和促进者之间的基因组距离.
- 这种取决于距离的表达关系在基因之间有明显的差异,并不能通过3D接触,DNA序列或染色质标记来解释.
结论:
- CARGO-VPR提供了一种多功能工具,可以在没有特定序列的转录因子的情况下进行向基因激活.
- 基因组距离在调节转录方面发挥着关键的,基因特异性的作用,独立于其他已知的调节因素.
- 这项研究为基因表达和增强功能的空间控制提供了新的视角.
相关概念视频
Cis-regulatory Sequences
9.8K
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...
9.8K
Chromatin Position Affects Gene Expression
23.3K
Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area.
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the...
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the...
23.3K
Regulation of Expression Occurs at Multiple Steps
22.6K
Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
22.6K
Regulation of Expression at Multiple Steps
880
The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
880
RNA Polymerase II Accessory Proteins
9.1K
Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
9.1K
Cooperative Binding of Transcription Regulators
6.4K
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
6.4K


