Self containment, a property of modular RNA structures, distinguishes microRNAs.

PLoS Computational Biology
Miler T Lee, Junhyong Kim

Abstract

RNA molecules will tend to adopt a folded conformation through the pairing of bases on a single strand; the resulting so-called secondary structure is critical to the function of many types of RNA. The secondary structure of a particular substring of functional RNA may depend on its surrounding sequence. Yet, some RNAs such as microRNAs retain their specific structures during biogenesis, which involves extraction of the substructure from a larger structural context, while other functional RNAs may be composed of a fusion of independent substructures. Such observations raise the question of whether particular functional RNA substructures may be selected for invariance of secondary structure to their surrounding nucleotide context. We define the property of self containment to be the tendency for an RNA sequence to robustly adopt the same optimal secondary structure regardless of whether it exists in isolation or is a substring of a longer sequence of arbitrary nucleotide content. We measured degree of self containment using a scoring method we call the self-containment index and found that miRNA stem loops exhibit high self containment, consistent with the requirement for structural invariance imposed by the miRNA biogenesis pat...Continue Reading

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Citations

Mar 14, 2012·Proceedings of the National Academy of Sciences of the United States of America·François CartaultAlexandra Henrion-Caude
Sep 27, 2012·Nucleic Acids Research·Supatcha LertampaipornMarasri Ruengjitchatchawalya
Feb 15, 2013·Genome Biology and Evolution·Yuanhui MaoShiheng Tao
Apr 29, 2014·Nucleic Acids Research·Supatcha LertampaipornMarasri Ruengjitchatchawalya
Nov 12, 2019·Briefings in Bioinformatics·Francis E AgamahEmile R Chimusa
Sep 16, 2017·Nucleic Acids Research·Tobias FehlmannAndreas Keller

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Software Mentioned

RNAsubopt
RNAinverse
RNAfold
Dicer
hit
Linux
Python
Vienna RNA Secondary Structure Package
Vienna
Vienna RNA Package

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