lncRNA-RNA Interactions across the Human Transcriptome.
Long non-coding RNAs (lncRNAs) represent a numerous class of non-protein coding transcripts longer than 200 nucleotides. There is possibility that a fraction of lncRNAs are not functional and represent mere transcriptional noise but a growing body of evidence shows they are engaged in a plethora of...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2016-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4773119?pdf=render |
| _version_ | 1819096222499078144 |
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| author | Michał Wojciech Szcześniak Izabela Makałowska |
| author_facet | Michał Wojciech Szcześniak Izabela Makałowska |
| author_sort | Michał Wojciech Szcześniak |
| collection | DOAJ |
| description | Long non-coding RNAs (lncRNAs) represent a numerous class of non-protein coding transcripts longer than 200 nucleotides. There is possibility that a fraction of lncRNAs are not functional and represent mere transcriptional noise but a growing body of evidence shows they are engaged in a plethora of molecular functions and contribute considerably to the observed diversification of eukaryotic transcriptomes and proteomes. Still, however, only ca. 1% of lncRNAs have well established functions and much remains to be done towards decipherment of their biological roles. One of the least studied aspects of lncRNAs biology is their engagement in gene expression regulation through RNA-RNA interactions. By hybridizing with mate RNA molecules, lncRNAs could potentially participate in modulation of pre-mRNA splicing, RNA editing, mRNA stability control, translation activation, or abrogation of miRNA-induced repression. Here, we implemented a similarity-search based method for transcriptome-wide identification of RNA-RNA interactions, which enabled us to find 18,871,097 lncRNA-RNA base-pairings in human. Further analyses showed that the interactions could be involved in processing, stability control and functions of 57,303 transcripts. An extensive use of RNA-Seq data provided support for approximately one third of the interactions, at least in terms of the two RNA components being co-expressed. The results suggest that lncRNA-RNA interactions are broadly used to regulate and diversify the human transcriptome. |
| first_indexed | 2024-12-21T23:55:46Z |
| format | Article |
| id | doaj.art-817cfc588cd84880b116f9f6d4cd822e |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-21T23:55:46Z |
| publishDate | 2016-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-817cfc588cd84880b116f9f6d4cd822e2022-12-21T18:45:49ZengPublic Library of Science (PLoS)PLoS ONE1932-62032016-01-01113e015035310.1371/journal.pone.0150353lncRNA-RNA Interactions across the Human Transcriptome.Michał Wojciech SzcześniakIzabela MakałowskaLong non-coding RNAs (lncRNAs) represent a numerous class of non-protein coding transcripts longer than 200 nucleotides. There is possibility that a fraction of lncRNAs are not functional and represent mere transcriptional noise but a growing body of evidence shows they are engaged in a plethora of molecular functions and contribute considerably to the observed diversification of eukaryotic transcriptomes and proteomes. Still, however, only ca. 1% of lncRNAs have well established functions and much remains to be done towards decipherment of their biological roles. One of the least studied aspects of lncRNAs biology is their engagement in gene expression regulation through RNA-RNA interactions. By hybridizing with mate RNA molecules, lncRNAs could potentially participate in modulation of pre-mRNA splicing, RNA editing, mRNA stability control, translation activation, or abrogation of miRNA-induced repression. Here, we implemented a similarity-search based method for transcriptome-wide identification of RNA-RNA interactions, which enabled us to find 18,871,097 lncRNA-RNA base-pairings in human. Further analyses showed that the interactions could be involved in processing, stability control and functions of 57,303 transcripts. An extensive use of RNA-Seq data provided support for approximately one third of the interactions, at least in terms of the two RNA components being co-expressed. The results suggest that lncRNA-RNA interactions are broadly used to regulate and diversify the human transcriptome.http://europepmc.org/articles/PMC4773119?pdf=render |
| spellingShingle | Michał Wojciech Szcześniak Izabela Makałowska lncRNA-RNA Interactions across the Human Transcriptome. PLoS ONE |
| title | lncRNA-RNA Interactions across the Human Transcriptome. |
| title_full | lncRNA-RNA Interactions across the Human Transcriptome. |
| title_fullStr | lncRNA-RNA Interactions across the Human Transcriptome. |
| title_full_unstemmed | lncRNA-RNA Interactions across the Human Transcriptome. |
| title_short | lncRNA-RNA Interactions across the Human Transcriptome. |
| title_sort | lncrna rna interactions across the human transcriptome |
| url | http://europepmc.org/articles/PMC4773119?pdf=render |
| work_keys_str_mv | AT michałwojciechszczesniak lncrnarnainteractionsacrossthehumantranscriptome AT izabelamakałowska lncrnarnainteractionsacrossthehumantranscriptome |