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Ribosome Profiling

Ribosome Profiling

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...

Leaky Scanning

Leaky Scanning

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...

Regulation of Expression Occurs at Multiple Steps

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...

Nonsense-mediated mRNA Decay

Nonsense-mediated mRNA Decay

The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...

RNA-seq

RNA-seq

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...

pre-mRNA Processing

pre-mRNA Processing

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl...

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相关实验视频

Updated: Jun 7, 2025

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Published on: March 7, 2018

整合生物化学和计算方法解读RNA处理代码.

Chen Du¹, Weiliang Fan¹, Yu Zhou^1,2,3

¹College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Wuhan University, Wuhan, China.

Wiley interdisciplinary reviews. RNA

|November 11, 2024

概括

此摘要是机器生成的。

本综述详细介绍了了解RNA代码的生物化学和计算方法,这些代码控制着RNA处理. 这些RNA代码对于预测RNA产物和理解疾病变异影响至关重要.

关键词:

编码的RNA是RNA的代码处理RNA处理RNA的过程调节RNA的调节深度学习是一种深度学习.机器学习是机器学习.

更多相关视频

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

Published on: July 10, 2019

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

Published on: April 30, 2011

相关实验视频

Last Updated: Jun 7, 2025

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Published on: March 7, 2018

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

Published on: July 10, 2019

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

Published on: April 30, 2011

科学领域:

分子生物学分子生物学
生物信息学是一种生物信息学.
基因组学就是基因组学.

背景情况:

RNA处理包括关键步骤,如拼接和多化,对于基因表达和RNA多样性至关重要.
高通量测序技术产生大量的RNA数据,需要先进的计算方法.
机器学习和深度学习越来越多地用于解释复杂的"RNA代码",这些代码决定了RNA序列与功能之间的关系.

研究的目的:

系统地审查生物化学和计算方法来破译关键RNA代码.
突出实验数据生成,计算模型特征和研究RNA代码的工具.
讨论挑战,并提出对计算RNA代码分析的改进.

主要方法:

对生化和计算方法的系统文献综述.
对生成RNA处理数据的实验技术的分析.
机器学习和深度学习模型用于RNA代码预测的评估.

主要成果:

五个主要RNA代码的方法的综合摘要:替代拼接,替代多化,RNA定位,RNA修饰和RNA结合蛋白 (RBP) 结合.
详细概述现有计算工具的功能,模型架构和性能.
识别预测建模方面的挑战,包括数据集成和领域知识整合.

结论:

准确的RNA代码对于预测RNA产品,理解分子机制和评估疾病变异效应至关重要.
持续开发计算工具,利用大型语言模型和领域知识,对于推进RNA代码研究至关重要.
改进的计算方法将提高我们解读RNA生物学及其在健康和疾病中的作用的能力.