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Ribosome Profiling

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Updated: Nov 1, 2025

Novel RNA-Binding Proteins Isolation by the RaPID Methodology

Novel RNA-Binding Proteins Isolation by the RaPID Methodology

Published on: September 30, 2016

Methods to Study Protein-Binding to Pseudogene Transcripts.

Eusebio Chiefari¹, Biagio Arcidiacono¹, Maria Mirabelli¹

¹Department of Health Sciences, University of Catanzaro "Magna Græcia", Catanzaro, Italy.

Methods in Molecular Biology (Clifton, N.J.)

|June 24, 2021

Summary

Processed pseudogenes can affect parental gene expression by competing for RNA-binding proteins (RBPs). Understanding these interactions, like HMGA1-p/HMGA1 with αCP1, aids in disease biomarker discovery.

Keywords:

HMGA1-p Immunoprecipitation RNA-EMSA RNA-binding protein αCP1

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Last Updated: Nov 1, 2025

Novel RNA-Binding Proteins Isolation by the RaPID Methodology

Novel RNA-Binding Proteins Isolation by the RaPID Methodology

Published on: September 30, 2016

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

Area of Science:

Molecular Biology
Genomics
Biochemistry

Background:

Processed pseudogenes share high sequence similarity with parental coding genes.
This similarity leads to competition for posttranscriptional regulators, including RNA-binding proteins (RBPs).
Dysregulation of this competition can alter protein synthesis, potentially causing pathological consequences.

Purpose of the Study:

To investigate the interactions between pseudogene-parental gene RNA pairs and RBPs.
To provide protocols for studying these interactions, focusing on the HMGA1-p/HMGA1 pair and the protein αCP1.
To introduce bioinformatic tools for predicting RBP binding sites on pseudogene transcripts.

Main Methods:

Plasmid-based molecular cloning.
RNA-electrophoretic mobility shift assay (EMSA) for analyzing protein-RNA interactions.
Overview of RNA immunoprecipitation (RIP) procedures.
Development of novel bioinformatic tools for RBP binding site prediction.

Main Results:

Detailed protocols for molecular cloning and EMSA are provided.
The interaction between the HMGA1-p/HMGA1 RNA pair and the protein αCP1 was investigated.
Novel bioinformatic tools for predicting RBP binding sites on pseudogenes were presented.

Conclusions:

Understanding pseudogene-RBP interactions is crucial for elucidating disease mechanisms.
These interactions may offer insights into complex diseases like cancer and diabetes.
Identified interactions and tools can aid in discovering novel predictive and prognostic biomarkers.