ArticlePloS one2015
Identification of non-coding RNAs associated with telomeres using a combination of enChIP and RNA sequencing.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
16 citing papers in PubMed, 36 citations in OpenAlex.
- Phase II trial of imatinib mesylate in patients with PDGFRA/B-negative hypereosinophilic syndrome.British journal of haematology · 2024Trial
- Transcriptome analysis reveals age-specific growth characteristics in the rumen of Hanwoo (Korean native cattle) steers.BMC genomics · 2025Article
- Many Functions of Telomerase Components: Certainties, Doubts, and Inconsistencies.International journal of molecular sciences · 2022Review
- An enChIP system for the analysis of genome functions in budding yeast.Biology methods & protocols · 2022Article
- MSCV-based retroviral plasmids expressing 3xFLAG-Sp-dCas9 for enChIP analysis.Biology methods & protocols · 2021Article
- Analysis of U8 snoRNA Variants in Zebrafish Reveals How Bi-allelic Variants Cause Leukoencephalopathy with Calcifications and Cysts.American journal of human genetics · 2020Article
- Telomere Dynamics Throughout Spermatogenesis.Genes · 2019Article
- Purification of specific DNA species using the CRISPR system.Biology methods & protocols · 2019Review
- An enChIP system for the analysis of bacterial genome functions.BMC research notes · 2018Article
- enChIP systems using different CRISPR orthologues and epitope tags.BMC research notes · 2018Article
- Locus-specific ChIP combined with NGS analysis reveals genomic regulatory regions that physically interact with the Pax5 promoter in a chicken B cell line.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Allele-specific locus binding and genome editing by CRISPR at the p16INK4a locus.Scientific reports · 2016Article
- Isolation of Specific Genomic Regions and Identification of Associated Molecules by enChIP.Journal of visualized experiments : JoVE · 2016Article
- Biochemical Analysis of Genome Functions Using Locus-Specific Chromatin Immunoprecipitation Technologies.Gene regulation and systems biology · 2016Review
- Applications of Engineered DNA-Binding Molecules Such as TAL Proteins and the CRISPR/Cas System in Biology Research.International journal of molecular sciences · 2015Review
- Isolation of Specific Genomic Regions and Identification of Their Associated Molecules by Engineered DNA-Binding Molecule-Mediated Chromatin Immunoprecipitation (enChIP) Using the CRISPR System and TAL Proteins.International journal of molecular sciences · 2015Review
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.