Rapidly Growing Protein-Centric Technologies to Extensively Identify Protein–RNA Interactions: Application to the Analysis of Co-Transcriptional RNA Processing
During mRNA transcription, diverse RNA-binding proteins (RBPs) are recruited to RNA polymerase II (RNAP II) transcription machinery. These RBPs bind to distinct sites of nascent RNA to co-transcriptionally operate mRNA processing. Recent studies have revealed a close relationship between transcripti...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-05-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/10/5312 |
| _version_ | 1797533596907470848 |
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| author | Akio Masuda Toshihiko Kawachi Kinji Ohno |
| author_facet | Akio Masuda Toshihiko Kawachi Kinji Ohno |
| author_sort | Akio Masuda |
| collection | DOAJ |
| description | During mRNA transcription, diverse RNA-binding proteins (RBPs) are recruited to RNA polymerase II (RNAP II) transcription machinery. These RBPs bind to distinct sites of nascent RNA to co-transcriptionally operate mRNA processing. Recent studies have revealed a close relationship between transcription and co-transcriptional RNA processing, where one affects the other’s activity, indicating an essential role of protein–RNA interactions for the fine-tuning of mRNA production. Owing to their limited amount in cells, the detection of protein–RNA interactions specifically assembled on the transcribing RNAP II machinery still remains challenging. Currently, cross-linking and immunoprecipitation (CLIP) has become a standard method to detect in vivo protein–RNA interactions, although it requires a large amount of input materials. Several improved methods, such as infrared-CLIP (irCLIP), enhanced CLIP (eCLIP), and target RNA immunoprecipitation (tRIP), have shown remarkable enhancements in the detection efficiency. Furthermore, the utilization of an RNA editing mechanism or proximity labeling strategy has achieved the detection of faint protein–RNA interactions in cells without depending on crosslinking. This review aims to explore various methods being developed to detect endogenous protein–RNA interaction sites and discusses how they may be applied to the analysis of co-transcriptional RNA processing. |
| first_indexed | 2024-03-10T11:16:51Z |
| format | Article |
| id | doaj.art-2aff74760c49492393bbae0b372b00e7 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T11:16:51Z |
| publishDate | 2021-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-2aff74760c49492393bbae0b372b00e72023-11-21T20:18:34ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-05-012210531210.3390/ijms22105312Rapidly Growing Protein-Centric Technologies to Extensively Identify Protein–RNA Interactions: Application to the Analysis of Co-Transcriptional RNA ProcessingAkio Masuda0Toshihiko Kawachi1Kinji Ohno2Center for Neurological Diseases and Cancer, Division of Neurogenetics, Nagoya University Graduate School of Medicine, Nagoya 466-8550, JapanCenter for Neurological Diseases and Cancer, Division of Neurogenetics, Nagoya University Graduate School of Medicine, Nagoya 466-8550, JapanCenter for Neurological Diseases and Cancer, Division of Neurogenetics, Nagoya University Graduate School of Medicine, Nagoya 466-8550, JapanDuring mRNA transcription, diverse RNA-binding proteins (RBPs) are recruited to RNA polymerase II (RNAP II) transcription machinery. These RBPs bind to distinct sites of nascent RNA to co-transcriptionally operate mRNA processing. Recent studies have revealed a close relationship between transcription and co-transcriptional RNA processing, where one affects the other’s activity, indicating an essential role of protein–RNA interactions for the fine-tuning of mRNA production. Owing to their limited amount in cells, the detection of protein–RNA interactions specifically assembled on the transcribing RNAP II machinery still remains challenging. Currently, cross-linking and immunoprecipitation (CLIP) has become a standard method to detect in vivo protein–RNA interactions, although it requires a large amount of input materials. Several improved methods, such as infrared-CLIP (irCLIP), enhanced CLIP (eCLIP), and target RNA immunoprecipitation (tRIP), have shown remarkable enhancements in the detection efficiency. Furthermore, the utilization of an RNA editing mechanism or proximity labeling strategy has achieved the detection of faint protein–RNA interactions in cells without depending on crosslinking. This review aims to explore various methods being developed to detect endogenous protein–RNA interaction sites and discusses how they may be applied to the analysis of co-transcriptional RNA processing.https://www.mdpi.com/1422-0067/22/10/5312CLIPtRIPRNA polymerase IIRNA-binding proteinco-transcriptional RNA processing |
| spellingShingle | Akio Masuda Toshihiko Kawachi Kinji Ohno Rapidly Growing Protein-Centric Technologies to Extensively Identify Protein–RNA Interactions: Application to the Analysis of Co-Transcriptional RNA Processing International Journal of Molecular Sciences CLIP tRIP RNA polymerase II RNA-binding protein co-transcriptional RNA processing |
| title | Rapidly Growing Protein-Centric Technologies to Extensively Identify Protein–RNA Interactions: Application to the Analysis of Co-Transcriptional RNA Processing |
| title_full | Rapidly Growing Protein-Centric Technologies to Extensively Identify Protein–RNA Interactions: Application to the Analysis of Co-Transcriptional RNA Processing |
| title_fullStr | Rapidly Growing Protein-Centric Technologies to Extensively Identify Protein–RNA Interactions: Application to the Analysis of Co-Transcriptional RNA Processing |
| title_full_unstemmed | Rapidly Growing Protein-Centric Technologies to Extensively Identify Protein–RNA Interactions: Application to the Analysis of Co-Transcriptional RNA Processing |
| title_short | Rapidly Growing Protein-Centric Technologies to Extensively Identify Protein–RNA Interactions: Application to the Analysis of Co-Transcriptional RNA Processing |
| title_sort | rapidly growing protein centric technologies to extensively identify protein rna interactions application to the analysis of co transcriptional rna processing |
| topic | CLIP tRIP RNA polymerase II RNA-binding protein co-transcriptional RNA processing |
| url | https://www.mdpi.com/1422-0067/22/10/5312 |
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