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Related Experiment Video

Updated: Jan 12, 2026

RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA

RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA

Published on: April 10, 2018

LncRNA:DNA Binding Prediction Using LongTarget and Its Revised Version.

Jie Lin^1,2, Yujian Wen¹, Hai Zhang³

¹Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.

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

|November 1, 2025

Summary

This summary is machine-generated.

Predicting long noncoding RNA (lncRNA) DNA-binding sites is crucial for understanding gene regulation. This study details LongTarget and Fasim-LongTarget tools for accurate computational prediction of lncRNA:DNA interactions.

Keywords:

Epigenetic regulation Fasim-LongTarget LongTarget Triplex lncRNA lncRNA:DNA binding

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Last Updated: Jan 12, 2026

RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA

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Published on: April 10, 2018

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Published on: July 9, 2021

Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay

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Published on: May 25, 2015

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Long noncoding RNAs (lncRNAs) regulate gene expression by binding to DNA.
Experimental identification of lncRNA:DNA-binding sites (DBSs) is challenging genome-wide.
Computational prediction of lncRNA:DNA interactions is essential.

Purpose of the Study:

To describe step-by-step usage of LongTarget and Fasim-LongTarget for predicting DNA-binding domains (DBDs) and DBSs.
To introduce the LongMan database for exploring mammalian lncRNAs and their DNA binding.
To demonstrate evaluation of predicted DBDs and DBSs using public data.

Main Methods:

Utilized LongTarget and Fasim-LongTarget software for computational prediction.
Employed the LongMan database for comparative genomics of lncRNAs.
Applied UCSC Genome Browser for validation of predicted binding sites.

Main Results:

Provided detailed protocols for using LongTarget and Fasim-LongTarget.
Enabled exploration of species-specific lncRNAs and their DNA interactions via LongMan.
Demonstrated effective evaluation strategies for predicted DBDs and DBSs.

Conclusions:

LongTarget and Fasim-LongTarget offer efficient computational tools for predicting lncRNA:DNA binding.
The LongMan database facilitates cross-species analysis of lncRNA function.
Accurate prediction and evaluation methods are key to understanding lncRNA-mediated gene regulation.