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RNA-seq

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Related Experiment Video

Updated: Aug 30, 2025

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms

Published on: February 2, 2024

Internally controlled RNA sequencing comparisons using nucleoside recoding chemistry.

Meaghan C S Courvan^1,2, Rachel O Niederer¹, Isaac W Vock^1,2

¹Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06536, USA.

Nucleic Acids Research

|August 26, 2022

Summary

This summary is machine-generated.

Transcript Regulation Identified by Labeling with Nucleoside Analogues in Cell Culture (TILAC) enables accurate RNA comparisons. This method distinguishes biological variation from sample preparation, improving biological insights.

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2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

Published on: July 10, 2020

Area of Science:

Molecular Biology
Genomics
Biochemistry

Background:

Quantitative RNA analysis is crucial for biological understanding.
Distinguishing biological variation from technical variability in sample preparation is challenging.
Complex biochemical procedures, like polysome isolation for translation studies, exacerbate these challenges.

Purpose of the Study:

To present Transcript Regulation Identified by Labeling with Nucleoside Analogues in Cell Culture (TILAC), an internally controlled method for quantitative RNA comparisons.
To enable reliable RNA quantification by pooling samples before complex manipulations.
To improve biological insights by accurately comparing RNA content across different conditions.

Main Methods:

TILAC utilizes two metabolic labels: 4-thiouridine (s4U) and 6-thioguanosine (s6G) for differential RNA labeling.
Experimental and control samples are pooled before downstream processing.
Nucleoside recoding chemistry generates unique sequencing signatures for each label, analyzed via statistical modeling.

Main Results:

TILAC performance was validated in transcriptome-wide experiments, including RNA polymerase II inhibition and heat shock.
The method was applied to quantify mRNA-ribosome association changes during sodium arsenite stress.
A subset of translationally upregulated transcripts, including MCM2 and DDX5, was identified.

Conclusions:

TILAC provides a robust, internally controlled approach for quantitative RNA comparisons.
The method effectively distinguishes biological variation from technical noise.
TILAC is broadly applicable for uncovering sample differences and enhancing biological discoveries.