Mining small RNA structure elements in untranslated regions of human and mouse mRNAs using structure-based alignment

Mugdha Khaladkar,Jianghui Liu,Bin Tian,Jason Tl Wang,Dongrong Wen

doi:10.1186/1471-2164-9-189

Mugdha Khaladkar, Jianghui Liu + Show 3 more

Open Access

https://doi.org/10.1186/1471-2164-9-189

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Abstract

BackgroundUnTranslated Regions (UTRs) of mRNAs contain regulatory elements for various aspects of mRNA metabolism, such as mRNA localization, translation, and mRNA stability. Several RNA stem-loop structures in UTRs have been experimentally identified, including the histone 3' UTR stem-loop structure (HSL3) and iron response element (IRE). These stem-loop structures are conserved among mammalian orthologs, and exist in a group of genes encoding proteins involved in the same biological pathways. It is not known to what extent RNA structures like these exist in all mammalian UTRs.ResultsIn this paper we took a systematic approach, named GLEAN-UTR, to identify small stem-loop RNA structure elements in UTRs that are conserved between human and mouse orthologs and exist in multiple genes with common Gene Ontology terms. This approach resulted in 90 distinct RNA structure groups containing 748 structures, with HSL3 and IRE among the top hits based on conservation of structure.ConclusionOur result indicates that there may exist many conserved stem-loop structures in mammalian UTRs that are involved in coordinate post-transcriptional regulation of biological pathways.

Highlights

UnTranslated Regions (UTRs) of mRNAs contain regulatory elements for various aspects of mRNA metabolism, such as mRNA localization, translation, and mRNA stability
iron response element (IRE) and HSL3 elements are highly similar to one another within each type; some divergence has been reported for Selenocysteine Insertion Sequence (SECIS) [11]; and there is no extensive similarity in primary sequence or secondary structure among Internal Ribosome Entry Site (IRES) elements [9]
Using cluster analysis and Gene Ontology (GO) information, we identified RNA structures that exist in multiple genes that share common biological pathways

Summary

Introduction

UnTranslated Regions (UTRs) of mRNAs contain regulatory elements for various aspects of mRNA metabolism, such as mRNA localization, translation, and mRNA stability. It is not known to what extent RNA structures like these exist in all mammalian UTRs. RNA cis elements residing in the UnTranslated Regions (UTRs) of mRNAs have been shown to play various roles in post-transcriptional gene regulation, including mRNA localization, translation, and mRNA stability [1,2,3,4]. IRE and HSL3 elements are highly similar to one another within each type; some divergence has been reported for SECIS [11]; and there is no extensive similarity in primary sequence or secondary structure among IRES elements [9] These characteristics reflect the ways that the RNA structures function. Various gene-specific structure elements in 5' or 3'UTRs have been shown to play roles in various aspects of RNA metabolism [1]

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