CR-deal:用于circRNA-RBP结合位点识别和解释的可解释的神经网络
Yuxiao Wei1, Zhebin Tan1, Liwei Liu2
1College of Software, Dalian Jiaotong University, Dalian, 116028, China.
Interdisciplinary sciences, computational life sciences
|March 27, 2025
概括
一个新的深度学习网络CR-deal准确地预测了循环RNA (circRNA) 和RNA结合蛋白 (RBP) 的相互作用. 该工具通过提供可解释的预测和识别关键结合区域,增强对circRNA功能和疾病作用的理解.
科学领域:
- 计算生物学 计算生物学
- 基因组学就是基因组学.
- 分子生物学分子生物学
背景情况:
- 循环RNAs (circRNAs) 是具有独特封闭结构的非编码RNA分子.
- 环RNA和RNA结合蛋白 (RBPs) 之间的相互作用对于生物功能和转录后调节至关重要.
- 预测circRNA-RBP相互作用的现有计算模型缺乏准确性和可解释性.
研究的目的:
- 开发一个可解释的联合深度学习网络,CR-deal,用于预测circRNA-RBP结合位点.
- 通过整合序列和结构特征来提高circRNA-RBP相互作用预测的准确性.
- 通过可解释的预测,提供关于circRNA-RBP相互作用的功能机制的见解.
主要方法:
- CR-deal使用图表注意网络来统一序列和结构特征.
- 该模型利用集成梯度特征解释来推断标记基因和功能区域.
- 全基因组 circRNA 结合事件数据被用于模型训练和验证.
主要成果:
- 在37个circRNA和7个lncRNA数据集中,CR-deal在预测circRNA-RBP结合位点方面表现出更好的准确性.
- 该模型成功提供了可解释的预测,识别了结合部位内的关键标记基因.
- 使用5个circRNA数据集发现了参与circRNA-RBP相互作用的功能结构区域.
结论:
- CR-deal为预测circRNA-RBP相互作用提供了一个强大而可解释的工具.
- 这些发现增强了对circRNA功能,调节机制及其在疾病中的作用的理解.
- CR-deal促进了对circRNA生物学和疾病发病的更深入的生物学见解.
相关概念视频
lncRNA - Long Non-coding RNAs
8.4K
In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA...
8.4K
Riboswitches
8.0K
Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
8.0K
RNA Interference
25.7K
RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
25.7K
Leaky Scanning
5.0K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.0K
Cis-regulatory Sequences
9.5K
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...
9.5K


