Genome-Wide Technologies to Study RNA–Chromatin Interactions
An increasing number of studies have revealed that long non-coding RNAs (lncRNAs) play important roles in gene regulation and nuclear organization. Although the mechanisms are still largely unknown, many lncRNAs have been shown to interact with chromatin. Thus, one approach to understanding the func...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-05-01
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| Series: | Non-Coding RNA |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2311-553X/6/2/20 |
| _version_ | 1827716049923997696 |
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| author | Masaki Kato Piero Carninci |
| author_facet | Masaki Kato Piero Carninci |
| author_sort | Masaki Kato |
| collection | DOAJ |
| description | An increasing number of studies have revealed that long non-coding RNAs (lncRNAs) play important roles in gene regulation and nuclear organization. Although the mechanisms are still largely unknown, many lncRNAs have been shown to interact with chromatin. Thus, one approach to understanding the function of these lncRNAs is to identify their sites of genomic interaction. Hybridization capture methods using oligonucleotide probes have been used for years to study chromatin-associated RNA. Recently, several groups have developed novel methods based on proximity ligation to investigate RNA–chromatin interactions at a genome-wide scale. This review discusses these technologies and highlights their advantages and disadvantages for the consideration of potential users. |
| first_indexed | 2024-03-10T19:33:23Z |
| format | Article |
| id | doaj.art-12977ef19bbb486da2688d424df1f032 |
| institution | Directory Open Access Journal |
| issn | 2311-553X |
| language | English |
| last_indexed | 2024-03-10T19:33:23Z |
| publishDate | 2020-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Non-Coding RNA |
| spelling | doaj.art-12977ef19bbb486da2688d424df1f0322023-11-20T01:55:12ZengMDPI AGNon-Coding RNA2311-553X2020-05-01622010.3390/ncrna6020020Genome-Wide Technologies to Study RNA–Chromatin InteractionsMasaki Kato0Piero Carninci1Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, JapanLaboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, JapanAn increasing number of studies have revealed that long non-coding RNAs (lncRNAs) play important roles in gene regulation and nuclear organization. Although the mechanisms are still largely unknown, many lncRNAs have been shown to interact with chromatin. Thus, one approach to understanding the function of these lncRNAs is to identify their sites of genomic interaction. Hybridization capture methods using oligonucleotide probes have been used for years to study chromatin-associated RNA. Recently, several groups have developed novel methods based on proximity ligation to investigate RNA–chromatin interactions at a genome-wide scale. This review discusses these technologies and highlights their advantages and disadvantages for the consideration of potential users.https://www.mdpi.com/2311-553X/6/2/20long non-coding RNAchromatin-associated RNARNA-chromatin interactiongene regulation |
| spellingShingle | Masaki Kato Piero Carninci Genome-Wide Technologies to Study RNA–Chromatin Interactions Non-Coding RNA long non-coding RNA chromatin-associated RNA RNA-chromatin interaction gene regulation |
| title | Genome-Wide Technologies to Study RNA–Chromatin Interactions |
| title_full | Genome-Wide Technologies to Study RNA–Chromatin Interactions |
| title_fullStr | Genome-Wide Technologies to Study RNA–Chromatin Interactions |
| title_full_unstemmed | Genome-Wide Technologies to Study RNA–Chromatin Interactions |
| title_short | Genome-Wide Technologies to Study RNA–Chromatin Interactions |
| title_sort | genome wide technologies to study rna chromatin interactions |
| topic | long non-coding RNA chromatin-associated RNA RNA-chromatin interaction gene regulation |
| url | https://www.mdpi.com/2311-553X/6/2/20 |
| work_keys_str_mv | AT masakikato genomewidetechnologiestostudyrnachromatininteractions AT pierocarninci genomewidetechnologiestostudyrnachromatininteractions |