从单细胞转录基因数据预测蛋白质-RNA相互作用
Jonathan Fiorentino1, Alexandros Armaos2, Alessio Colantoni1,3
1Center for Life Nano- and Neuro-Science, RNA Systems Biology Lab, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy.
Nucleic acids research
|February 16, 2024
概括
我们开发了scRAPID,这是一个计算管道,用于使用单细胞转录基因数据预测RNA结合蛋白 (RBP) 和RNA相互作用. 这种方法准确地识别了RBP-RNA相互作用,包括那些具有长非编码RNA的相互作用.
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:
- 了解蛋白质-RNA相互作用对于破译RNA生物学至关重要,但目前的实验方法范围有限.
- 现有的计算方法往往忽略了细胞类型特异性和基因调控网络 (GRN) 背景.
研究的目的:
- 评估GRN推断算法,从单细胞转录基因数据中预测蛋白质-RNA相互作用.
- 引入 scRAPID,一个将GRN方法与catRAPID集成的管道,用于增强RBP-RNA相互作用预测.
主要方法:
- 在单细胞RNA测序数据上评估GRN推断算法.
- 集成选定的GRN算法与catRAPID物理相互作用预测工具.
- 开发了用于RBP-RNA相互作用检测的scrapid管道.
主要成果:
- scRAPID从单细胞数据准确地预测RBP-RNA相互作用,超越或匹配转录因子-目标相互作用推断.
- 整合catRAPID显著提高了预测准确性,特别是对于长非编码RNA.
- 根据共享的RNA目标确定了关键的枢纽RBP,RNA和潜在的RBP-RBP相互作用.
结论:
- 单细胞转录组学与GRN推断和物理相互作用预测相结合,是研究RBP-RNA相互作用的强大方法.
- scRAPID提供了一个强大的计算框架,用于发现特定于细胞类型的RBP-RNA调节网络.
- 开发的管道有助于确定RBPs和RNA在细胞过程中的新型调节作用.
相关概念视频
02:24Ribosome Profiling
3.5K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.5K
03:21RNA-seq
10.0K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.0K
02:43Nucleic Acids
44.2K
Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
44.2K