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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...

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Updated: Aug 16, 2025

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

AIDmut-Seq: a Three-Step Method for Detecting Protein-DNA Binding Specificity.

Feixuan Li¹, Xiao-Yu Liu², Lei Ni³

¹Hefei National Research Center for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, People's Republic of China.

Microbiology Spectrum

|December 19, 2022

Summary

This summary is machine-generated.

AIDmut-Seq is a new, simple method to identify where transcription factors bind on the genome. This tool helps researchers study gene regulatory networks by detecting protein-DNA interactions more easily.

Keywords:

Pseudomonas aeruginosa activation induced cytidine deaminase protein-DNA interactions

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Last Updated: Aug 16, 2025

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

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

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Published on: February 17, 2023

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Published on: June 3, 2017

Area of Science:

Molecular Biology
Genomics
Systems Biology

Background:

Gene regulatory networks (GRNs) are governed by transcriptional factors (TFs) and their regulons.
Studying genome-wide protein-DNA interactions (PDI) is crucial for understanding GRNs but often involves complex experimental procedures.
Existing methods for PDI analysis limit broad adoption by the scientific community.

Purpose of the Study:

To develop and validate a simplified, in vivo method for detecting TF targets across the genome.
To establish a user-friendly technique for identifying genome-wide protein-DNA interactions.
To assess the efficiency and limitations of the new method for various transcriptional regulators.

Main Methods:

Developed AIDmut-Seq, a method combining TF-directed activation-induced cytidine deaminase (AID) mutagenesis with whole-genome sequencing.
The process involves expressing an AID-TF fusion protein, performing whole-genome sequencing, and profiling single nucleotide polymorphisms (SNPs).
Validated AIDmut-Seq using multiple transcription factors, including LasR, FleQ, ErdR, GacA, ExsA, RsaL, and AmrZ in Pseudomonas aeruginosa.

Main Results:

AIDmut-Seq successfully detected TF-guided C-to-T (or G-to-A) conversions near TF binding sites, identifying known and novel binding sites for LasR.
The method demonstrated high efficiency for most transcriptional activators tested.
AIDmut-Seq showed lower efficiency for small transcriptional repressors, potentially due to TF dysfunction or low target promoter transcription rates.

Conclusions:

AIDmut-Seq is a valuable, complementary tool for studying genome-wide protein-DNA interactions, particularly in the early stages of research.
The method's simplicity makes it accessible to junior and interdisciplinary researchers.
While acknowledging potential false-positive and false-negative results, AIDmut-Seq offers a practical approach to mapping TF-DNA interactions in vivo.