Identification of non-coding RNAs associated with telomeres using a combination of enChIP and RNA sequencing.
Accumulating evidence suggests that RNAs interacting with genomic regions play important roles in the regulation of genome functions, including X chromosome inactivation and gene expression. However, to our knowledge, no non-biased methods of identifying RNAs that interact with a specific genomic re...
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doaj-f551e97ead824ed4b2656f915299985d2020-11-24T21:08:12ZengPublic Library of Science (PLoS)PLoS ONE1932-62032015-01-01104e012338710.1371/journal.pone.0123387Identification of non-coding RNAs associated with telomeres using a combination of enChIP and RNA sequencing.Toshitsugu FujitaMiyuki YunoDaisuke OkuzakiRieko OhkiHodaka FujiiAccumulating evidence suggests that RNAs interacting with genomic regions play important roles in the regulation of genome functions, including X chromosome inactivation and gene expression. However, to our knowledge, no non-biased methods of identifying RNAs that interact with a specific genomic region have been reported. Here, we used enChIP-RNA-Seq, a combination of engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) and RNA sequencing (RNA-Seq), to perform a non-biased search for RNAs interacting with telomeres. In enChIP-RNA-Seq, the target genomic regions are captured using an engineered DNA-binding molecule such as a transcription activator-like protein. Subsequently, RNAs that interact with the target genomic regions are purified and sequenced. The RNAs detected by enChIP-RNA-Seq contained known telomere-binding RNAs, including the telomerase RNA component (Terc), the RNA component of mitochondrial RNA processing endoribonuclease (Rmrp), and Cajal body-specific RNAs. In addition, a number of novel telomere-binding non-coding RNAs were also identified. Binding of two candidate non-coding RNAs to telomeres was confirmed by immunofluorescence microscopy and RNA fluorescence in situ hybridization (RNA-FISH) analyses. The novel telomere-binding non-coding RNAs identified here may play important roles in telomere functions. To our knowledge, this study is the first non-biased identification of RNAs associated with specific genomic regions. The results presented here suggest that enChIP-RNA-Seq analyses are useful for the identification of RNAs interacting with specific genomic regions, and may help to contribute to current understanding of the regulation of genome functions.http://europepmc.org/articles/PMC4395285?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Toshitsugu Fujita Miyuki Yuno Daisuke Okuzaki Rieko Ohki Hodaka Fujii |
spellingShingle |
Toshitsugu Fujita Miyuki Yuno Daisuke Okuzaki Rieko Ohki Hodaka Fujii Identification of non-coding RNAs associated with telomeres using a combination of enChIP and RNA sequencing. PLoS ONE |
author_facet |
Toshitsugu Fujita Miyuki Yuno Daisuke Okuzaki Rieko Ohki Hodaka Fujii |
author_sort |
Toshitsugu Fujita |
title |
Identification of non-coding RNAs associated with telomeres using a combination of enChIP and RNA sequencing. |
title_short |
Identification of non-coding RNAs associated with telomeres using a combination of enChIP and RNA sequencing. |
title_full |
Identification of non-coding RNAs associated with telomeres using a combination of enChIP and RNA sequencing. |
title_fullStr |
Identification of non-coding RNAs associated with telomeres using a combination of enChIP and RNA sequencing. |
title_full_unstemmed |
Identification of non-coding RNAs associated with telomeres using a combination of enChIP and RNA sequencing. |
title_sort |
identification of non-coding rnas associated with telomeres using a combination of enchip and rna sequencing. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2015-01-01 |
description |
Accumulating evidence suggests that RNAs interacting with genomic regions play important roles in the regulation of genome functions, including X chromosome inactivation and gene expression. However, to our knowledge, no non-biased methods of identifying RNAs that interact with a specific genomic region have been reported. Here, we used enChIP-RNA-Seq, a combination of engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) and RNA sequencing (RNA-Seq), to perform a non-biased search for RNAs interacting with telomeres. In enChIP-RNA-Seq, the target genomic regions are captured using an engineered DNA-binding molecule such as a transcription activator-like protein. Subsequently, RNAs that interact with the target genomic regions are purified and sequenced. The RNAs detected by enChIP-RNA-Seq contained known telomere-binding RNAs, including the telomerase RNA component (Terc), the RNA component of mitochondrial RNA processing endoribonuclease (Rmrp), and Cajal body-specific RNAs. In addition, a number of novel telomere-binding non-coding RNAs were also identified. Binding of two candidate non-coding RNAs to telomeres was confirmed by immunofluorescence microscopy and RNA fluorescence in situ hybridization (RNA-FISH) analyses. The novel telomere-binding non-coding RNAs identified here may play important roles in telomere functions. To our knowledge, this study is the first non-biased identification of RNAs associated with specific genomic regions. The results presented here suggest that enChIP-RNA-Seq analyses are useful for the identification of RNAs interacting with specific genomic regions, and may help to contribute to current understanding of the regulation of genome functions. |
url |
http://europepmc.org/articles/PMC4395285?pdf=render |
work_keys_str_mv |
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