构建动态转录监管网络,以确定特定表型的转录监管器
1School of Information Science and Engineering, Lanzhou University, Lanzhou 730000, China.
Briefings in bioinformatics
|October 25, 2024
概括
本研究介绍了DTGN,这是通过构建动态转录调节网络来识别表型特异的转录因子和途径的新框架. DTGN有效地捕捉了基因调节的动态性质,优于现有的方法.
科学领域:
- 生物信息学是一种生物信息学.
- 系统生物学 系统生物学
- 基因组学就是基因组学.
背景情况:
- 转录调节网络 (TRNs) 模型基因调节,但静态模型忽略了动态特征.
- 鉴定表型特异性调节剂对于理解特定条件下的基因功能至关重要.
- 现有的方法往往无法捕捉转录调节者的动态性质,限制了它们阐明表型相关作用的能力.
研究的目的:
- 引入一种新的框架,即动态转录图网络 (DTGN),用于识别表型特定的转录因子 (TF) 和途径.
- 通过结合转录调节器的动态特征来解决静态TRN的局限性.
- 提供一种新的方法来探索与特定表型相关的转录调节者的功能作用.
主要方法:
- 设计了一个图形自编码模型,以整合表型时间序列基因表达数据与静态TRN,学习时间基因表示.
- 开发了一种基于学习时间基因表征的统计方法来构建动态TRN,这反映了表型的发展.
- 使用构建的动态TRN识别了特定于表型的TF和路径.
主要成果:
- DTGN框架成功地确定了表型特定的转录因子和途径.
- 结果表明,DTGN在识别多个表型数据集中的表型特异性TF和途径方面优于现有方法.
- 动态方法捕获了关键的监管信息,这些信息通常被静态模型遗漏.
结论:
- DTGN框架在理解表型特异性转录调节方面取得了重大进展.
- 通过结合动态TRN,DTGN提供了更全面的方法来识别关键的监管要素.
- 这种新的框架增强了与特定表型相关的转录调节者的功能作用的探索.
更多相关视频
11:32Identification of Transcription Factor Regulators using Medium-Throughput Screening of Arrayed Libraries and a Dual-Luciferase-Based Reporter
Published on: March 27, 2020
6.7K
09:22Rapid Synthesis and Screening of Chemically Activated Transcription Factors with GFP-based Reporters
Published on: November 26, 2013
14.5K
相关概念视频
Master 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
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
General Transcription Factors
5.2K
Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
5.2K
Combinatorial Gene Control
8.3K
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...
8.3K
Transcription Factors
75.7K
Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
75.7K
Co-activators and Co-repressors
7.3K
Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
7.3K
