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Related Experiment Video

Updated: Sep 19, 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

Investigating RNA dynamics from single molecule transcriptomes.

Sahiti Somalraju¹, Doaa Hassan Salem², Sarath Chandra Janga³

¹Department of Biomedical Engineering and Informatics, Luddy School of Informatics, Computing and Engineering, Indiana University Indianapolis (IUI), Indianapolis, IN, USA.

Trends in Genetics : TIG

|June 5, 2025

Summary

Long-read sequencing technologies like PacBio and ONT reveal RNA dynamics, including splicing and modifications. These methods offer new ways to study gene regulation and cellular processes at high resolution.

Keywords:

RNA bioinformatics RNA isoform RNA modifications poly(A) tail single molecule sequencing transcriptomics

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Metabolic Labeling of Newly Transcribed RNA for High Resolution Gene Expression Profiling of RNA Synthesis, Processing and Decay in Cell Culture

Metabolic Labeling of Newly Transcribed RNA for High Resolution Gene Expression Profiling of RNA Synthesis, Processing and Decay in Cell Culture

Published on: August 8, 2013

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Understanding RNA dynamics is key to cellular function and disease.
Alternative splicing, RNA stability, and modifications are critical RNA processes.
Therapeutic target identification relies on comprehending RNA regulation.

Purpose of the Study:

To review protocols and methods for analyzing RNA dynamics using long-read sequencing.
To highlight advancements in isoform detection, poly(A) tail quantification, and RNA modification mapping.
To discuss the potential of these technologies in transforming RNA research.

Main Methods:

Focus on long-read sequencing technologies, specifically Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT).
Examination of protocols for analyzing single-molecule RNA dynamics.
Integration of high-throughput, transcriptome-wide data with software systems.

Main Results:

Long-read sequencing provides single-molecule and single-nucleotide resolution of RNA dynamics.
Established methods for isoform detection, poly(A) tail length quantification, and RNA modification mapping.
Development of integrated software systems for data analysis.

Conclusions:

Long-read sequencing technologies are revolutionizing the study of RNA dynamics.
These advancements offer deeper insights into gene regulation and cellular processes.
Future workflows will leverage high-throughput data for comprehensive RNA analysis.