RNA-Centric Approaches to Profile the RNA–Protein Interaction Landscape on Selected RNAs
RNA–protein interactions frame post-transcriptional regulatory networks and modulate transcription and epigenetics. While the technological advances in RNA sequencing have significantly expanded the repertoire of RNAs, recently developed biochemical approaches combined with sensitive mass-spectromet...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-02-01
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| Series: | Non-Coding RNA |
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| Online Access: | https://www.mdpi.com/2311-553X/7/1/11 |
| _version_ | 1797396543755517952 |
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| author | André P. Gerber |
| author_facet | André P. Gerber |
| author_sort | André P. Gerber |
| collection | DOAJ |
| description | RNA–protein interactions frame post-transcriptional regulatory networks and modulate transcription and epigenetics. While the technological advances in RNA sequencing have significantly expanded the repertoire of RNAs, recently developed biochemical approaches combined with sensitive mass-spectrometry have revealed hundreds of previously unrecognized and potentially novel RNA-binding proteins. Nevertheless, a major challenge remains to understand how the thousands of RNA molecules and their interacting proteins assemble and control the fate of each individual RNA in a cell. Here, I review recent methodological advances to approach this problem through systematic identification of proteins that interact with particular RNAs in living cells. Thereby, a specific focus is given to in vivo approaches that involve crosslinking of RNA–protein interactions through ultraviolet irradiation or treatment of cells with chemicals, followed by capture of the RNA under study with antisense-oligonucleotides and identification of bound proteins with mass-spectrometry. Several recent studies defining interactomes of long non-coding RNAs, viral RNAs, as well as mRNAs are highlighted, and short reference is given to recent in-cell protein labeling techniques. These recent experimental improvements could open the door for broader applications and to study the remodeling of RNA–protein complexes upon different environmental cues and in disease. |
| first_indexed | 2024-03-09T00:52:54Z |
| format | Article |
| id | doaj.art-bf60cef9759e443e9ffdb134f29c6fba |
| institution | Directory Open Access Journal |
| issn | 2311-553X |
| language | English |
| last_indexed | 2024-03-09T00:52:54Z |
| publishDate | 2021-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Non-Coding RNA |
| spelling | doaj.art-bf60cef9759e443e9ffdb134f29c6fba2023-12-11T17:08:02ZengMDPI AGNon-Coding RNA2311-553X2021-02-01711110.3390/ncrna7010011RNA-Centric Approaches to Profile the RNA–Protein Interaction Landscape on Selected RNAsAndré P. Gerber0Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UKRNA–protein interactions frame post-transcriptional regulatory networks and modulate transcription and epigenetics. While the technological advances in RNA sequencing have significantly expanded the repertoire of RNAs, recently developed biochemical approaches combined with sensitive mass-spectrometry have revealed hundreds of previously unrecognized and potentially novel RNA-binding proteins. Nevertheless, a major challenge remains to understand how the thousands of RNA molecules and their interacting proteins assemble and control the fate of each individual RNA in a cell. Here, I review recent methodological advances to approach this problem through systematic identification of proteins that interact with particular RNAs in living cells. Thereby, a specific focus is given to in vivo approaches that involve crosslinking of RNA–protein interactions through ultraviolet irradiation or treatment of cells with chemicals, followed by capture of the RNA under study with antisense-oligonucleotides and identification of bound proteins with mass-spectrometry. Several recent studies defining interactomes of long non-coding RNAs, viral RNAs, as well as mRNAs are highlighted, and short reference is given to recent in-cell protein labeling techniques. These recent experimental improvements could open the door for broader applications and to study the remodeling of RNA–protein complexes upon different environmental cues and in disease.https://www.mdpi.com/2311-553X/7/1/11RNA–protein interactionnon-coding RNARNA aptamerantisense oligonucleotidesaffinity isolationCRISPR/Cas9 |
| spellingShingle | André P. Gerber RNA-Centric Approaches to Profile the RNA–Protein Interaction Landscape on Selected RNAs Non-Coding RNA RNA–protein interaction non-coding RNA RNA aptamer antisense oligonucleotides affinity isolation CRISPR/Cas9 |
| title | RNA-Centric Approaches to Profile the RNA–Protein Interaction Landscape on Selected RNAs |
| title_full | RNA-Centric Approaches to Profile the RNA–Protein Interaction Landscape on Selected RNAs |
| title_fullStr | RNA-Centric Approaches to Profile the RNA–Protein Interaction Landscape on Selected RNAs |
| title_full_unstemmed | RNA-Centric Approaches to Profile the RNA–Protein Interaction Landscape on Selected RNAs |
| title_short | RNA-Centric Approaches to Profile the RNA–Protein Interaction Landscape on Selected RNAs |
| title_sort | rna centric approaches to profile the rna protein interaction landscape on selected rnas |
| topic | RNA–protein interaction non-coding RNA RNA aptamer antisense oligonucleotides affinity isolation CRISPR/Cas9 |
| url | https://www.mdpi.com/2311-553X/7/1/11 |
| work_keys_str_mv | AT andrepgerber rnacentricapproachestoprofilethernaproteininteractionlandscapeonselectedrnas |