Analysis of RNA-protein networks with RNP-MaP defines functional hubs on RNA
RNA-protein interaction networks govern many biological processes but are difficult to examine comprehensively. We devised ribonucleoprotein networks analyzed by mutational profiling (RNP-MaP), a live-cell chemical probing strategy that maps cooperative interactions among multiple proteins bound to single RNA molecules at nucleotide resolution. RNP-MaP uses a hetero-bifunctional crosslinker to freeze interacting proteins in place on RNA and then maps multiple bound proteins on single RNA strands by read-through reverse transcription and DNA sequencing. RNP-MaP revealed that RNase P and RMRP, two sequence-divergent but structurally related non-coding RNAs, share RNP networks and that network hubs define functional sites in these RNAs. RNP-MaP also identified protein interaction networks conserved between mouse and human XIST long non-coding RNAs and defined protein communities whose binding sites colocalize and form networks in functional regions of XIST. RNP-MaP enables discovery and efficient validation of functional protein interaction networks on long RNAs in living cells.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2021 |
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| Erschienen: |
2021 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:39 |
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| Enthalten in: |
Nature biotechnology - 39(2021), 3 vom: 16. März, Seite 347-356 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Weidmann, Chase A [VerfasserIn] |
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| Links: |
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| Anmerkungen: |
Date Completed 14.04.2021 Date Revised 31.03.2024 published: Print-Electronic Citation Status MEDLINE |
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| doi: |
10.1038/s41587-020-0709-7 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| 520 | |a RNA-protein interaction networks govern many biological processes but are difficult to examine comprehensively. We devised ribonucleoprotein networks analyzed by mutational profiling (RNP-MaP), a live-cell chemical probing strategy that maps cooperative interactions among multiple proteins bound to single RNA molecules at nucleotide resolution. RNP-MaP uses a hetero-bifunctional crosslinker to freeze interacting proteins in place on RNA and then maps multiple bound proteins on single RNA strands by read-through reverse transcription and DNA sequencing. RNP-MaP revealed that RNase P and RMRP, two sequence-divergent but structurally related non-coding RNAs, share RNP networks and that network hubs define functional sites in these RNAs. RNP-MaP also identified protein interaction networks conserved between mouse and human XIST long non-coding RNAs and defined protein communities whose binding sites colocalize and form networks in functional regions of XIST. RNP-MaP enables discovery and efficient validation of functional protein interaction networks on long RNAs in living cells | ||
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| 650 | 4 | |a Research Support, U.S. Gov't, Non-P.H.S. | |
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| 700 | 1 | |a Mustoe, Anthony M |e verfasserin |4 aut | |
| 700 | 1 | |a Jariwala, Parth B |e verfasserin |4 aut | |
| 700 | 1 | |a Calabrese, J Mauro |e verfasserin |4 aut | |
| 700 | 1 | |a Weeks, Kevin M |e verfasserin |4 aut | |
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