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Purine-rich low complexity regions are potential RNA binding hubs in the human genome

Many long noncoding RNAs are bound to the chromatin and some of these interactions are mediated by triple helices. It is usually assumed that a transcript can form triplexes with a distinct set of genomic loci also known as triplex target sites (TTSs). Here we performed computational analyses of the...

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Autores principales: Antonov, Ivan, Medvedeva, Yulia A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6518440/
https://www.ncbi.nlm.nih.gov/pubmed/31131080
http://dx.doi.org/10.12688/f1000research.13522.2
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author Antonov, Ivan
Medvedeva, Yulia A.
author_facet Antonov, Ivan
Medvedeva, Yulia A.
author_sort Antonov, Ivan
collection PubMed
description Many long noncoding RNAs are bound to the chromatin and some of these interactions are mediated by triple helices. It is usually assumed that a transcript can form triplexes with a distinct set of genomic loci also known as triplex target sites (TTSs). Here we performed computational analyses of the TTSs that have been experimentally identified for particular RNAs. To assess the ability of these TTSs to bind other transcripts we developed a method to estimate the statistical significance of the predicted number of triplexes for a given RNA-DNA pair. We demonstrated that each DNA set included a subset of sequences that have a potential to form a statistically significant (adjusted p-value < 0.01) number of triplexes with the majority (>90%) of the analyzed transcripts. Due to the predicted ability of these DNA sequences to interact with a wide range of different RNAs, we called them "universal TTSs". While the universal TTSs were quite rare in the human genome (around 0.5%), they were  more frequent (>15%) among the MEG3 binding sites (ChOP-seq peaks) and especially among the shared Capture-seq peaks (40%). The universal TTSs were enriched with the purine-rich low complexity regions. Nowadays, the role of the chromatin bound RNAs in the formation of 3D chromatin structure is actively discussed. We speculated that such universal TTSs may contribute to establishing long-distance chromosomal contacts and may facilitate distal enhancer-promoter interactions. All the scripts and the data files related to this study are available at: https://github.com/vanya-antonov/universal_tts
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spelling pubmed-65184402019-05-24 Purine-rich low complexity regions are potential RNA binding hubs in the human genome Antonov, Ivan Medvedeva, Yulia A. F1000Res Research Note Many long noncoding RNAs are bound to the chromatin and some of these interactions are mediated by triple helices. It is usually assumed that a transcript can form triplexes with a distinct set of genomic loci also known as triplex target sites (TTSs). Here we performed computational analyses of the TTSs that have been experimentally identified for particular RNAs. To assess the ability of these TTSs to bind other transcripts we developed a method to estimate the statistical significance of the predicted number of triplexes for a given RNA-DNA pair. We demonstrated that each DNA set included a subset of sequences that have a potential to form a statistically significant (adjusted p-value < 0.01) number of triplexes with the majority (>90%) of the analyzed transcripts. Due to the predicted ability of these DNA sequences to interact with a wide range of different RNAs, we called them "universal TTSs". While the universal TTSs were quite rare in the human genome (around 0.5%), they were  more frequent (>15%) among the MEG3 binding sites (ChOP-seq peaks) and especially among the shared Capture-seq peaks (40%). The universal TTSs were enriched with the purine-rich low complexity regions. Nowadays, the role of the chromatin bound RNAs in the formation of 3D chromatin structure is actively discussed. We speculated that such universal TTSs may contribute to establishing long-distance chromosomal contacts and may facilitate distal enhancer-promoter interactions. All the scripts and the data files related to this study are available at: https://github.com/vanya-antonov/universal_tts F1000 Research Limited 2019-05-09 /pmc/articles/PMC6518440/ /pubmed/31131080 http://dx.doi.org/10.12688/f1000research.13522.2 Text en Copyright: © 2019 Antonov I and Medvedeva YA http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Note
Antonov, Ivan
Medvedeva, Yulia A.
Purine-rich low complexity regions are potential RNA binding hubs in the human genome
title Purine-rich low complexity regions are potential RNA binding hubs in the human genome
title_full Purine-rich low complexity regions are potential RNA binding hubs in the human genome
title_fullStr Purine-rich low complexity regions are potential RNA binding hubs in the human genome
title_full_unstemmed Purine-rich low complexity regions are potential RNA binding hubs in the human genome
title_short Purine-rich low complexity regions are potential RNA binding hubs in the human genome
title_sort purine-rich low complexity regions are potential rna binding hubs in the human genome
topic Research Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6518440/
https://www.ncbi.nlm.nih.gov/pubmed/31131080
http://dx.doi.org/10.12688/f1000research.13522.2
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