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Cited by 17RNA Research and SplicingGenomics and Chromatin DynamicsRNA and protein synthesis mechanisms

Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA

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Keil, Philipp, Wulf, Alexander, Kachariya, Nitin, Reuscher, Samira, Hühn, Kristin, Silbern, Ivan, Altmüller, Janine, Keller, Mario, Stehle, Ralf, Zarnack, Kathi, Sattler, Michael, Urlaub, Henning, Sträßer, Katja·2023·Nucleic Acids Research
DOI 10.1093/nar/gkac1206PMC PMC9881175

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Abstract

RNA-binding proteins (RBPs) control every RNA metabolic process by multiple protein–RNA and protein–protein interactions. Their roles have largely been analyzed by crude mutations, which abrogate multiple functions at once and likely impact the structural integrity of the large ribonucleoprotein particles (RNPs) these proteins function in. Using UV-induced RNA–protein crosslinking of entire cells, protein complex purification and mass spectrometric analysis, we identified >100 in vivo RNA crosslinks in 16 nuclear mRNP components in Saccharomyces cerevisiae. For functional analysis, we chose Npl3, which displayed crosslinks in its two RNA recognition motifs (RRMs) and in the connecting flexible linker region. Both RRM domains and the linker uniquely contribute to RNA recognition as revealed by NMR and structural analyses. Interestingly, mutations in these regions cause different phenotypes, indicating distinct functions of the different RNA-binding domains. Notably, an npl3-Linker mutation strongly impairs recruitment of several mRNP components to chromatin and incorporation of other mRNP components into nuclear mRNPs, establishing a so far unknown function of Npl3 in nuclear mRNP assembly. Taken together, our integrative analysis uncovers a specific function of the RNA-binding activity of the nuclear mRNP component Npl3. This approach can be readily applied to RBPs in any RNA metabolic process.

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Authors
Keil, P., Wulf, A., Kachariya, N., Reuscher, S., Hühn, K., Silbern, I., Altmüller, J., Keller, M., Stehle, R., Zarnack, K., Sattler, M., Urlaub, H., & Sträßer, K.
Affiliations
  • Justus-Liebig-Universität Gießen (DE)
  • Universitätsmedizin Göttingen (DE)
  • Helmholtz Munich (DE)
  • Goethe University Frankfurt (DE)
  • University of Cologne (DE)
Corresponding author
  • Sattler, Michael
  • Urlaub, Henning
  • Sträßer, Katja
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2022-12-30
Volume
51
Issue
2
Pages
831-851
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkac1206
PMC
PMC9881175
OpenAlex
W4313311738
Cited by
17
References
2
Citations by year
2026: 5 · 2025: 4 · 2024: 3 · 2023: 5
FWCI
0.98
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (acceptedVersion, other-oa)
  • mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion, other-oa)
  • Site cant be reached (submittedVersion, cc-by-nc)
  • GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (submittedVersion)
  • Publication Server of Goethe University Frankfurt am Main (Goethe University Frankfurt) (submittedVersion, cc-by-nc)
  • PuSH - Publication Server of Helmholtz Zentrum München (submittedVersion, cc-by-nc)
Funders
  • DFG (SPP1935, GRK1721, SFB1035, SFB1286, GRK2355)
  • EU (mRNP-PackArt)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
Npl3, RNA-binding proteins, RNA recognition motif, RNA-protein crosslinking, Saccharomyces cerevisiae, chromatin recruitment, linker region, RNA-binding domain, transcription sites
MeSH terms
Nuclear Proteins, Ribonucleoproteins, RNA, Messenger, Saccharomyces cerevisiae, RNA-Binding Proteins, Saccharomyces cerevisiae Proteins

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