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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2014-10-01
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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 |
work_keys_str_mv |
AT aristeidisgtelonis nuclearandmitochondrialtrnalookalikesinthehumangenome AT phillipeeloher nuclearandmitochondrialtrnalookalikesinthehumangenome AT yoheiekirino nuclearandmitochondrialtrnalookalikesinthehumangenome AT isidoreerigoutsos nuclearandmitochondrialtrnalookalikesinthehumangenome |
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