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lncRNA - Long Non-coding RNAs

lncRNA - Long Non-coding RNAs

In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA...

Nucleic Acid Structure

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′ to 3′ phosphodiester linkage.
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Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in regulating gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
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Updated: Aug 9, 2025

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA

Published on: July 9, 2021

Computational Methods to Study DNA:DNA:RNA Triplex Formation by lncRNAs.

Timothy Warwick^1,2, Ralf P Brandes^1,2, Matthias S Leisegang^1,2

¹Institute for Cardiovascular Physiology, Goethe University, 60590 Frankfurt, Germany.

|February 24, 2023

Summary

This summary is machine-generated.

Computational tools predict DNA:DNA:RNA triplexes formed by long non-coding RNAs (lncRNAs). These interactions are crucial for understanding lncRNA function and gene expression regulation.

Keywords:

DNA:DNA:RNA triplex formation DNA–RNA triplex interaction of DNA and RNA long non-coding RNA triplex

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Last Updated: Aug 9, 2025

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA

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Published on: March 25, 2012

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Long non-coding RNAs (lncRNAs) regulate cellular functions through diverse mechanisms.
Nuclear interactions between lncRNAs and DNA, forming non-canonical nucleic acid structures like DNA:DNA:RNA triplexes, are significant.
Identifying specific lncRNA-DNA interactions within these triplexes is challenging but vital for understanding lncRNA roles.

Purpose of the Study:

To review recent advancements in computational methods for predicting DNA:DNA:RNA triplex formation.
To highlight key DNA:DNA:RNA triplexes and their biological relevance.
To discuss the application of prediction tools using experimentally validated lncRNAs.

Main Methods:

Review of existing literature on lncRNA-DNA interactions and triplex formation.
Discussion of various computational prediction tools: Triplexator, LongTarget, TRIPLEXES, Triplex Domain Finder, TriplexFFP, TriplexAligner, and Fasim-LongTarget.
Exemplification of tool usage with experimentally validated lncRNAs.

Main Results:

Several computational tools are available for predicting DNA:DNA:RNA triplexes.
These tools, when applied to lncRNAs, reveal a high likelihood of triplex formation.
Experimentally validated lncRNAs demonstrate the utility of these prediction methods.

Conclusions:

DNA:DNA:RNA triplexes are likely abundant in the genome.
These triplexes play a significant role in regulating gene expression.
Advancements in computational prediction are crucial for elucidating lncRNA functions.