CAPRI enables comparison of evolutionarily conserved RNA interacting regions

Amol Panhale, Florian M. Richter, Fidel Ramírez, Maria Shvedunova, Thomas Manke, Gerhard Mittler () and Asifa Akhtar ()
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Amol Panhale: Max Planck Institute of Immunobiology and Epigenetics
Florian M. Richter: Max Planck Institute of Immunobiology and Epigenetics
Fidel Ramírez: Max Planck Institute of Immunobiology and Epigenetics
Maria Shvedunova: Max Planck Institute of Immunobiology and Epigenetics
Thomas Manke: Max Planck Institute of Immunobiology and Epigenetics
Gerhard Mittler: Max Planck Institute of Immunobiology and Epigenetics
Asifa Akhtar: Max Planck Institute of Immunobiology and Epigenetics

Nature Communications, 2019, vol. 10, issue 1, 1-22

Abstract: 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.

Date: 2019
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DOI: 10.1038/s41467-019-10585-3

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