预测RNA聚合酶II转录延长暂停和相关的基因素代码
Lixin Ren1, Wanbiao Ma1, Yong Wang2,3,4,5
1School of Mathematics and Physics, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
Briefings in bioinformatics
|May 24, 2024
概括
研究人员开发了一种机器学习工具RP3,用于预测RNA聚合酶II (Pol II) 暂停. 这种方法有助于理解基因转录调节及其在生物过程和疾病中的作用.
科学领域:
- 分子生物学分子生物学
- 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:
- RNA聚合酶II (Pol II) 转录延长暂停对于多细胞生物的基因调节至关重要.
- 波尔二暂停会影响重要的生物过程和疾病的发展.
- 对全基因组Pol II暂停的实验测量是困难的,其调节机制仍然不清楚.
研究的目的:
- 开发一种用于预测Pol II暂停事件的计算方法.
- 整合多样化的基因组和表观基因组数据,以提高预测准确度.
- 确定与Pol II暂停相关的关键调节因素,包括转录因子和基因组修饰.
主要方法:
- 开发了RP3 (RNA聚合酶II暂停预测),这是一个网络规范化的逻辑回归机器学习模型.
- 来自基因组序列,基因组修饰,基因表达,染色质可访问性和蛋白质与蛋白质相互作用的综合数据.
- 采用前特征选择框架来识别显著的基因组修饰信号.
主要成果:
- RP3准确地预测了Pol II在各种细胞环境中的暂停.
- 该方法成功地识别了参与Pol II暂停机制的转录因子.
- 系统地确定了与Pol II暂停相关的关键质子修饰信号.
结论:
- RP3提供了一个强大的工具,用于预测和分析全基因组的Pol II暂停事件.
- 这项研究增强了对控制转录暂停的分子机制的理解.
- RP3促进了对Pol II暂停在基因调节,发育和疾病中的作用的研究.
相关概念视频
02:35Transcription Elongation Factors
10.8K
Transcription elongation is a dynamic process that alters depending upon the sequence heterogeneity of the DNA being transcribed. Hence, it is not surprising that the elongation complex's composition also varies along the way while transcribing a gene.
The transcription elongation is regulated via pausing of RNA polymerase on several occasions during transcription. In bacteria, these halts are necessary because the transcription of DNA into mRNA is coupled to the translation of that mRNA...
The transcription elongation is regulated via pausing of RNA polymerase on several occasions during transcription. In bacteria, these halts are necessary because the transcription of DNA into mRNA is coupled to the translation of that mRNA...
10.8K
02:36RNA Polymerase II Accessory Proteins
9.2K
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...
9.2K
01:47Transcription Initiation
16.4K
Initiation is the first step of transcription in eukaryotes. Prokaryotic RNA Polymerase (RNAP) can bind to the template DNA and start transcribing. On the other hand, transcription in eukaryotes requires additional proteins, called transcription factors, to first bind to the promoter region in the DNA template. This binding helps recruit the specific RNAP that can assemble on the DNA and start transcription.
The promoters and enhancers and their accessory proteins allow tight regulation of...
The promoters and enhancers and their accessory proteins allow tight regulation of...
16.4K
02:41Chromatin Structure Regulates pre-mRNA Processing
7.0K
In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...
The chromatin structure, especially...
7.0K
01:53Bacterial Transcription
28.1K
RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
28.1K
00:58Eukaryotic RNA Polymerases
24.1K
RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...
All three eukaryotic RNAPs require specific transcription factors, of which the...
24.1K