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  CAPRI enables comparison of evolutionary conserved RNA interacting regions

Panhale, A., Richter, F. M., Ramírez, F., Shvedunova, M., Manke, T., Mittler, G., et al. (2019). CAPRI enables comparison of evolutionary conserved RNA interacting regions. Nature Communications, 10: 2682 (2019). doi:10.1038/s41467-019-10585-3.

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Panhale et al..pdf (Publisher version), 13MB
 
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Panhale, Amol1, Author
Richter , Florian M.2, Author
Ramírez, Fidel2, Author              
Shvedunova, Maria1, Author
Manke, Thomas2, Author              
Mittler, Gerhard2, Author              
Akhtar, Asifa1, Author              
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1Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society, ou_2243643              
2Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society, ou_2243641              

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 Abstract: RNA-protein complexes play essential regulatory roles at nearly all levels of gene expression. Using in vivo crosslinking and RNA capture, we report a comprehensive RNA-protein interactome in a metazoan at four levels of resolution: single amino acids, domains, proteins and multisubunit complexes. We devise CAPRI, a method to map RNA-binding domains (RBDs) by simultaneous identification of RNA interacting crosslinked peptides and peptides adjacent to such crosslinked sites. CAPRI identifies more than 3000 RNA proximal peptides in Drosophila and human proteins with more than 45% of them forming new interaction interfaces. The comparison of orthologous proteins enables the identification of evolutionary conserved RBDs in globular domains and intrinsically disordered regions (IDRs). By comparing the sequences of IDRs through evolution, we classify them based on the type of motif, accumulation of tandem repeats, conservation of amino acid composition and high sequence divergence.

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Language(s): eng - English
 Dates: 2019-06-18
 Publication Status: Published online
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 Rev. Type: Peer
 Identifiers: DOI: 10.1038/s41467-019-10585-3
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Title: Nature Communications
  Abbreviation : Nat. Commun.
Source Genre: Journal
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Publ. Info: London : Nature Publishing Group
Pages: - Volume / Issue: 10 Sequence Number: 2682 (2019) Start / End Page: - Identifier: ISSN: 2041-1723
CoNE: https://pure.mpg.de/cone/journals/resource/2041-1723