» Articles » PMID: 23927838

3S: Shotgun Secondary Structure Determination of Long Non-coding RNAs

Overview
Journal Methods
Specialty Biochemistry
Date 2013 Aug 10
PMID 23927838
Citations 32
Authors
Affiliations
Soon will be listed here.
Abstract

Long non-coding RNAs (lncRNAs) have emerged as an important class of RNAs playing key roles in development, disease and epigenetics. Knowledge of lncRNA structure may be critical in understanding function for many lncRNA systems. Due to the enormous number of possible folds for these sequences, secondary structure determination presents a significant challenge, both experimentally and computationally. Here, we present a new strategy capable of determining the RNA secondary structure in the wet lab without significant reliance on computational predictions. First, we chemically probe the entire lncRNA. Next, using a shotgun approach, we divide the RNA into overlapping fragments and probe these fragments. We then compare probing profiles of fragments with the profiles of the full RNA and identify similarities. Sequence regions with profiles that are similar in the fragment and full-length transcript possess only base pairing partners within the fragment. Thus, by experimentally folding smaller and smaller fragments of the full RNA and probing these chemically, we are able to isolate modular sub-domains, dramatically reducing the number of possible folds. The method also eliminates the possibility of pseudoknots within a modular sub-domain. The 3S technique is ideally suited for lncRNAs because it is designed for long RNA sequences. The 3S-determined secondary structure of a specific lncRNA in one species (e.g., human) enables searches for instances of the same lncRNA in other species.

Citing Articles

LncRNA SChLAP1 promotes cancer cell proliferation and invasion via its distinct structural domains and conserved regions.

Oh M, Kadam R, Charania Z, Somarowthu S bioRxiv. 2025; .

PMID: 39975023 PMC: 11838354. DOI: 10.1101/2025.01.28.635288.


Functional Relationships between Long Non-Coding RNAs and Estrogen Receptor Alpha: A New Frontier in Hormone-Responsive Breast Cancer Management.

Melone V, Salvati A, Brusco N, Alexandrova E, DAgostino Y, Palumbo D Int J Mol Sci. 2023; 24(2).

PMID: 36674656 PMC: 9863308. DOI: 10.3390/ijms24021145.


Modulation of pre-mRNA structure by hnRNP proteins regulates alternative splicing of .

Jones A, Grass C, Meininger I, Geerlof A, Klostermann M, Zarnack K Sci Adv. 2022; 8(31):eabp9153.

PMID: 35921415 PMC: 9348792. DOI: 10.1126/sciadv.abp9153.


Mapping Intellectual Structure for the Long Non-Coding RNA in Hepatocellular Carcinoma Development Research.

Lin Z, Ji X, Tian N, Gan Y, Ke L Front Genet. 2022; 12:771810.

PMID: 35047004 PMC: 8762053. DOI: 10.3389/fgene.2021.771810.


Getting to the bottom of lncRNA mechanism: structure-function relationships.

Sanbonmatsu K Mamm Genome. 2021; 33(2):343-353.

PMID: 34642784 PMC: 8509902. DOI: 10.1007/s00335-021-09924-x.