在miRNA基因的促进区域中识别Cis-regulatory绑定位点:一步一步的协议
Judith Jazmin Bernal-Gallardo1, Stefan de Folter2
1Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Guanajuato, México.
Methods in molecular biology (Clifton, N.J.)
|May 16, 2025
概括
这项研究提出了一个易于使用的协议,用于识别植物微RNA (miRNA) 促进体中的转录因子 (TF) 结合位. 该方法通过分析调节区域的TF-DNA相互作用来增强对基因调节的理解.
科学领域:
- 植物分子生物学 植物分子生物学
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- 植物微RNA (miRNA) 在基因调节中起着至关重要的作用.
- 转录因子 (TFs) 通过与促进子区域结合来控制miRNA的表达.
- 识别这些TF结合位点对于理解基因调节网络至关重要.
研究的目的:
- 提供一个用户友好的协议,用于识别植物miRNA促进体中的TF结合位.
- 为了使研究人员具有有限的编程经验来分析miRNA基因调节.
- 为了方便有效地发现控制miRNA表达的cis-regulatory元素.
主要方法:
- 利用MEME套件在miRNA促进子序列中发现动机.
- 使用TOMTOM将发现的动机与TF绑定网站数据库进行比较.
- 为序列检索和分析提供手动和自动化方法.
- 将TF结合点分析集成到一个简化协议中.
主要成果:
- 成功开发了一种用于识别miRNA促进体中TF结合位点的协议.
- 证明了协议对具有最小计算专业知识的用户的可访问性.
- 为有效分析miRNA调节元件提供了一个框架.
- 促进了对植物基因调节机制的更深入的了解.
结论:
- 开发的协议提供了一种高效且易于使用的方法,用于分析植物miRNA促进体中的TF结合位.
- 这种方法通过阐明TFs在控制miRNA表达中的作用来增强对基因调节的理解.
- 该协议使研究人员能够更轻松,更准确地研究miRNA介导的基因沉默.
相关概念视频
01:22MicroRNAs
MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...
02:02Cis-regulatory Sequences
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...
02:13Cooperative Binding of Transcription Regulators
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 dimers that...
02:02Cis-regulatory Sequences
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...
01:22MicroRNAs
MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
01:23Regulation of Expression at Multiple Steps
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 addition of a...