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RNA Splicing

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...

Alternative RNA Splicing

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...

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...

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Related Experiment Video

Updated: May 13, 2025

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Published on: September 28, 2017

Photoaffinity enabled transcriptome-wide identification of splice modulating small molecule-RNA binding events in

Raven Shah¹, Wanlin Yan¹, Joyce Rigal¹

¹Novartis Biomedical Research, Discovery Sciences Cambridge MA USA andrea.byrnes@novartis.com jason.thomas@novartis.com.

RSC Chemical Biology

|April 14, 2025

Summary

This summary is machine-generated.

Researchers identified the telomerase RNA component (TERC) as a direct target of splice-modulating small molecules using photoaffinity labeling. This discovery advances understanding of small molecule interactions with RNA targets.

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Last Updated: May 13, 2025

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

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Published on: September 28, 2017

A Reporter Based Cellular Assay for Monitoring Splicing Efficiency

A Reporter Based Cellular Assay for Monitoring Splicing Efficiency

Published on: September 15, 2021

A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

Published on: December 2, 2009

Area of Science:

Molecular Biology
RNA Therapeutics
Chemical Biology

Background:

Splice-modulating small molecules are designed to alter U1 snRNP engagement with pre-mRNAs.
Transcriptomic profiling can detect compound-affected RNAs but struggles to distinguish direct from indirect effects.

Purpose of the Study:

To identify direct RNA targets of splice-modulating small molecules.
To investigate the binding site of these molecules on identified RNA targets.

Main Methods:

Photoaffinity labeling (PAL)-based Chem-CLIP was employed to capture direct RNA-compound interactions.
Cellular ΔSHAPE-MaP was used for orthogonal validation and precise binding site determination.
Analysis of competed RNAs within the Chem-CLIP data was performed to refine hit identification.

Main Results:

The telomerase RNA component (TERC) was identified as a novel direct target of splice-modulating small molecules.
The conserved CR4/5 domain of TERC was validated as the likely small molecule binding site.
Considering competed RNAs improved the identification of direct RNA targets, even those with low enrichment.

Conclusions:

TERC is a previously unrecognized direct target of clinically relevant splice-modulating small molecules.
The CR4/5 domain of TERC is a key interaction site for these compounds.
PAL-based Chem-CLIP, with analysis of competed RNAs, is a powerful method for identifying direct RNA-small molecule interactions.