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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...

Transcription Attenuation in Prokaryotes

Transcription Attenuation in Prokaryotes

Transcriptional attenuation occurs when RNA transcription is prematurely terminated due to the formation of a terminator mRNA hairpin structure. Bacteria use these hairpins to regulate the transcription process and control the synthesis of several amino acids including histidine, lysine, threonine, and phenylalanine. Transcription attenuation takes place in the non-coding regions of mRNA.
There are several different mechanisms used to attenuate transcription. In ribosome mediated...

Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....

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Updated: Jul 9, 2025

Analysis of Termination of Transcription Using BrUTP-strand-specific Transcription Run-on TRO Approach

Analysis of Termination of Transcription Using BrUTP-strand-specific Transcription Run-on TRO Approach

Published on: March 12, 2017

TRS:一种用于从RNAtag-seq测序数据中确定转录端子的方法.

Amir Bar¹, Liron Argaman¹, Michal Eldar¹

¹Department of Microbiology and Molecular Genetics IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112102, Israel.

Nature communications

|November 29, 2023

概括

此摘要是机器生成的。

我们开发了TRS,一种计算方法,可以从RNA-seq数据中识别细菌转录3'终端. 这种方法增强了对不同细菌和条件的基因表达调节的研究.

更多相关视频

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells

Published on: January 30, 2019

3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

相关实验视频

Last Updated: Jul 9, 2025

Analysis of Termination of Transcription Using BrUTP-strand-specific Transcription Run-on TRO Approach

Analysis of Termination of Transcription Using BrUTP-strand-specific Transcription Run-on TRO Approach

Published on: March 12, 2017

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells

Published on: January 30, 2019

3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

科学领域:

微生物学微生物学
分子生物学分子生物学
生物信息学是一种生物信息学.

背景情况:

转录3'端的确定对于细菌基因表达调节至关重要,影响转录的稳定性和功能.
目前用于识别转录3'终端的实验方法范围有限,适用于少数细菌物种和生长条件.
RNA测序 (RNA-seq) 数据为研究转录终止提供了潜在的资源,但需要特定的分析方法.

研究的目的:

使用现有的RNA-seq数据,提出一种简单的计算方法来识别细菌转录3'终端.
为了利用RNAtag-seq协议生成的特定读数分布模式,以准确识别终端.
为了能够对各种物种和实验条件的细菌转录终止进行大规模分析.

主要方法:

开发TRS (Termini by Read Starts),一个设计用于分析RNAtag-seq数据的计算管道.
利用观察到的阅读映射的过剩来转录RNAtag-seq数据集中的3'终端.
通过计算分析验证识别的3' termini的可靠性.

主要成果:

该TRS管道成功地从RNAtag-seq数据中识别了细菌转录3'终端.
已识别的3'终端显示出高可靠性,通过计算方法验证.
该方法不需要额外的实验程序超出标准RNA-seq.

结论:

TRS提供了一种强大且易于使用的计算工具,用于确定细菌转录3' termini.
由于RNAtag-seq数据的广泛可用性,这种方法适合进行大规模的研究.
这种方法显著推进了对细菌转录终止的研究,提供了前所未有的范围和细节.