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Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs

It has been recently suggested that transposable elements (TEs) are re-used as functional elements of long non-coding RNAs (lncRNAs). This is supported by some examples such as the human endogenous retrovirus subfamily H (HERVH) elements contained within lncRNAs and expressed specifically in human e...

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Autores principales: Chishima, Takafumi, Iwakiri, Junichi, Hamada, Michiaki
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793176/
https://www.ncbi.nlm.nih.gov/pubmed/29315213
http://dx.doi.org/10.3390/genes9010023
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author Chishima, Takafumi
Iwakiri, Junichi
Hamada, Michiaki
author_facet Chishima, Takafumi
Iwakiri, Junichi
Hamada, Michiaki
author_sort Chishima, Takafumi
collection PubMed
description It has been recently suggested that transposable elements (TEs) are re-used as functional elements of long non-coding RNAs (lncRNAs). This is supported by some examples such as the human endogenous retrovirus subfamily H (HERVH) elements contained within lncRNAs and expressed specifically in human embryonic stem cells (hESCs), as required to maintain hESC identity. There are at least two unanswered questions about all lncRNAs. How many TEs are re-used within lncRNAs? Are there any other TEs that affect tissue specificity of lncRNA expression? To answer these questions, we comprehensively identify TEs that are significantly related to tissue-specific expression levels of lncRNAs. We downloaded lncRNA expression data corresponding to normal human tissue from the Expression Atlas and transformed the data into tissue specificity estimates. Then, Fisher’s exact tests were performed to verify whether the presence or absence of TE-derived sequences influences the tissue specificity of lncRNA expression. Many TE–tissue pairs associated with tissue-specific expression of lncRNAs were detected, indicating that multiple TE families can be re-used as functional domains or regulatory sequences of lncRNAs. In particular, we found that the antisense promoter region of L1PA2, a LINE-1 subfamily, appears to act as a promoter for lncRNAs with placenta-specific expression.
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spelling pubmed-57931762018-02-07 Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs Chishima, Takafumi Iwakiri, Junichi Hamada, Michiaki Genes (Basel) Article It has been recently suggested that transposable elements (TEs) are re-used as functional elements of long non-coding RNAs (lncRNAs). This is supported by some examples such as the human endogenous retrovirus subfamily H (HERVH) elements contained within lncRNAs and expressed specifically in human embryonic stem cells (hESCs), as required to maintain hESC identity. There are at least two unanswered questions about all lncRNAs. How many TEs are re-used within lncRNAs? Are there any other TEs that affect tissue specificity of lncRNA expression? To answer these questions, we comprehensively identify TEs that are significantly related to tissue-specific expression levels of lncRNAs. We downloaded lncRNA expression data corresponding to normal human tissue from the Expression Atlas and transformed the data into tissue specificity estimates. Then, Fisher’s exact tests were performed to verify whether the presence or absence of TE-derived sequences influences the tissue specificity of lncRNA expression. Many TE–tissue pairs associated with tissue-specific expression of lncRNAs were detected, indicating that multiple TE families can be re-used as functional domains or regulatory sequences of lncRNAs. In particular, we found that the antisense promoter region of L1PA2, a LINE-1 subfamily, appears to act as a promoter for lncRNAs with placenta-specific expression. MDPI 2018-01-09 /pmc/articles/PMC5793176/ /pubmed/29315213 http://dx.doi.org/10.3390/genes9010023 Text en © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Chishima, Takafumi
Iwakiri, Junichi
Hamada, Michiaki
Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs
title Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs
title_full Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs
title_fullStr Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs
title_full_unstemmed Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs
title_short Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs
title_sort identification of transposable elements contributing to tissue-specific expression of long non-coding rnas
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793176/
https://www.ncbi.nlm.nih.gov/pubmed/29315213
http://dx.doi.org/10.3390/genes9010023
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