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

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 sequ...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Miler T Lee, Junhyong Kim
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2008
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/28e47b0a82cd4488b542083c6a97396c
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:28e47b0a82cd4488b542083c6a97396c
record_format	dspace
spelling	oai:doaj.org-article:28e47b0a82cd4488b542083c6a97396c2021-11-25T05:42:01ZSelf containment, a property of modular RNA structures, distinguishes microRNAs.1553-734X1553-735810.1371/journal.pcbi.1000150https://doaj.org/article/28e47b0a82cd4488b542083c6a97396c2008-08-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18725951/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358RNA 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 pathway, while most other structured RNAs do not. Further analysis revealed a trend toward higher self containment among clustered and conserved miRNAs, suggesting that high self containment may be a characteristic of novel miRNAs acquiring new genomic contexts. We found that miRNAs display significantly enhanced self containment compared to other functional RNAs, but we also found a trend toward natural selection for self containment in most functional RNA classes. We suggest that self containment arises out of selection for robustness against perturbations, invariance during biogenesis, and modular composition of structural function. Analysis of self containment will be important for both annotation and design of functional RNAs. A Python implementation and Web interface to calculate the self-containment index are available at http://kim.bio.upenn.edu/software/.Miler T LeeJunhyong KimPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 4, Iss 8, p e1000150 (2008)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Miler T Lee Junhyong Kim Self containment, a property of modular RNA structures, distinguishes microRNAs.
description	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 pathway, while most other structured RNAs do not. Further analysis revealed a trend toward higher self containment among clustered and conserved miRNAs, suggesting that high self containment may be a characteristic of novel miRNAs acquiring new genomic contexts. We found that miRNAs display significantly enhanced self containment compared to other functional RNAs, but we also found a trend toward natural selection for self containment in most functional RNA classes. We suggest that self containment arises out of selection for robustness against perturbations, invariance during biogenesis, and modular composition of structural function. Analysis of self containment will be important for both annotation and design of functional RNAs. A Python implementation and Web interface to calculate the self-containment index are available at http://kim.bio.upenn.edu/software/.
format	article
author	Miler T Lee Junhyong Kim
author_facet	Miler T Lee Junhyong Kim
author_sort	Miler T Lee
title	Self containment, a property of modular RNA structures, distinguishes microRNAs.
title_short	Self containment, a property of modular RNA structures, distinguishes microRNAs.
title_full	Self containment, a property of modular RNA structures, distinguishes microRNAs.
title_fullStr	Self containment, a property of modular RNA structures, distinguishes microRNAs.
title_full_unstemmed	Self containment, a property of modular RNA structures, distinguishes microRNAs.
title_sort	self containment, a property of modular rna structures, distinguishes micrornas.
publisher	Public Library of Science (PLoS)
publishDate	2008
url	https://doaj.org/article/28e47b0a82cd4488b542083c6a97396c
work_keys_str_mv	AT milertlee selfcontainmentapropertyofmodularrnastructuresdistinguishesmicrornas AT junhyongkim selfcontainmentapropertyofmodularrnastructuresdistinguishesmicrornas
_version_	1718414507855839232

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

Ejemplares similares