Nuclear and mitochondrial tRNA-lookalikes in the human genome

We are interested in identifying and characterizing loci of the human genome that harbor sequences resembling known mitochondrial and nuclear tRNAs. To this end, we used the known nuclear and mitochondrial tRNA genes (the tRNA-Reference set) to search for tRNA-lookalikes and found many such loci at...

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Main Authors: Aristeidis G Telonis, Phillipe eLoher, Yohei eKirino, Isidore eRigoutsos
Format: Article
Language:English
Published: Frontiers Media S.A. 2014-10-01
Series:Frontiers in Genetics
Subjects:
Online Access:http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00344/full
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spelling doaj-96c1a05f737f400482f303138f38c0a02020-11-24T22:32:39ZengFrontiers Media S.A.Frontiers in Genetics1664-80212014-10-01510.3389/fgene.2014.00344111053Nuclear and mitochondrial tRNA-lookalikes in the human genomeAristeidis G Telonis0Phillipe eLoher1Yohei eKirino2Isidore eRigoutsos3Thomas Jefferson UniversityThomas Jefferson UniversityThomas Jefferson UniversityThomas Jefferson UniversityWe are interested in identifying and characterizing loci of the human genome that harbor sequences resembling known mitochondrial and nuclear tRNAs. To this end, we used the known nuclear and mitochondrial tRNA genes (the tRNA-Reference set) to search for tRNA-lookalikes and found many such loci at different levels of sequence conservation. We find that the large majority of these tRNA-lookalikes resemble mitochondrial tRNAs and exhibit a skewed over-representation in favor of some mitochondrial anticodons. Our analysis shows that the tRNA-lookalikes have infiltrated specific chromosomes and are preferentially located in close proximity to known nuclear tRNAs (z-score=-2.54, P-val ≤ 0.00394). Examination of the transcriptional potential of these tRNA-lookalike loci using public transcript annotations revealed that more than 20% of the lookalikes are transcribed as part of either known protein-coding pre-mRNAs, known lncRNAs, or known non-protein-coding RNAs, while public RNA-seq data perfectly agreed with the endpoints of tRNA-lookalikes. Interestingly, we found that tRNA-lookalikes are significantly depleted in known genetic variations associated with human health and disease whereas the known tRNAs are enriched in such variations. Lastly, a manual comparative analysis of the cloverleaf structure of the transcribed tRNA-lookalikes revealed no disruptive mutations suggesting the possibility that these loci give rise to functioning tRNA molecules.http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00344/fulltRNAhuman genomemitochondrial tRNAtRNA fragmentnuclear tRNA
collection DOAJ
language English
format Article
sources DOAJ
author Aristeidis G Telonis
Phillipe eLoher
Yohei eKirino
Isidore eRigoutsos
spellingShingle Aristeidis G Telonis
Phillipe eLoher
Yohei eKirino
Isidore eRigoutsos
Nuclear and mitochondrial tRNA-lookalikes in the human genome
Frontiers in Genetics
tRNA
human genome
mitochondrial tRNA
tRNA fragment
nuclear tRNA
author_facet Aristeidis G Telonis
Phillipe eLoher
Yohei eKirino
Isidore eRigoutsos
author_sort Aristeidis G Telonis
title Nuclear and mitochondrial tRNA-lookalikes in the human genome
title_short Nuclear and mitochondrial tRNA-lookalikes in the human genome
title_full Nuclear and mitochondrial tRNA-lookalikes in the human genome
title_fullStr Nuclear and mitochondrial tRNA-lookalikes in the human genome
title_full_unstemmed Nuclear and mitochondrial tRNA-lookalikes in the human genome
title_sort nuclear and mitochondrial trna-lookalikes in the human genome
publisher Frontiers Media S.A.
series Frontiers in Genetics
issn 1664-8021
publishDate 2014-10-01
description We are interested in identifying and characterizing loci of the human genome that harbor sequences resembling known mitochondrial and nuclear tRNAs. To this end, we used the known nuclear and mitochondrial tRNA genes (the tRNA-Reference set) to search for tRNA-lookalikes and found many such loci at different levels of sequence conservation. We find that the large majority of these tRNA-lookalikes resemble mitochondrial tRNAs and exhibit a skewed over-representation in favor of some mitochondrial anticodons. Our analysis shows that the tRNA-lookalikes have infiltrated specific chromosomes and are preferentially located in close proximity to known nuclear tRNAs (z-score=-2.54, P-val ≤ 0.00394). Examination of the transcriptional potential of these tRNA-lookalike loci using public transcript annotations revealed that more than 20% of the lookalikes are transcribed as part of either known protein-coding pre-mRNAs, known lncRNAs, or known non-protein-coding RNAs, while public RNA-seq data perfectly agreed with the endpoints of tRNA-lookalikes. Interestingly, we found that tRNA-lookalikes are significantly depleted in known genetic variations associated with human health and disease whereas the known tRNAs are enriched in such variations. Lastly, a manual comparative analysis of the cloverleaf structure of the transcribed tRNA-lookalikes revealed no disruptive mutations suggesting the possibility that these loci give rise to functioning tRNA molecules.
topic tRNA
human genome
mitochondrial tRNA
tRNA fragment
nuclear tRNA
url http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00344/full
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