Systematic identification of NF90 target RNAs by iCLIP analysis

RNA-binding proteins (RBPs) interact with and determine the fate of many cellular RNAs directing numerous essential roles in cellular physiology. Nuclear Factor 90 (NF90) is an RBP encoded by the interleukin enhancer-binding factor 3 ( ILF3 ) gene that has been found to influence RNA metabolism at s...

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Bibliographic Details
Published in:Scientific reports Vol. 12; no. 1; pp. 364 - 17
Main Authors: Lodde, Valeria, Floris, Matteo, Munk, Rachel, Martindale, Jennifer L., Piredda, Davide, Napodano, Catello Mario Panu, Cucca, Francesco, Uzzau, Sergio, Abdelmohsen, Kotb, Gorospe, Myriam, Noh, Ji Heon, Idda, M. Laura
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 10.01.2022
Nature Publishing Group
Nature Portfolio
Subjects:
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631/337
631/80
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Cells, Cultured
COVID-19 - metabolism
COVID-19 - virology
Embryo fibroblasts
HEK293 Cells
Humanities and Social Sciences
Humans
Immune response
Immunoprecipitation
Immunoprecipitation - methods
Interferon
Interferon regulatory factor 3
Interferon Regulatory Factor-3 - genetics
Interferon Regulatory Factor-3 - metabolism
Interferon-Stimulated Gene Factor 3, gamma Subunit - genetics
Interferon-Stimulated Gene Factor 3, gamma Subunit - metabolism
Metabolism
mRNA turnover
multidisciplinary
Nuclear Factor 90 Proteins - genetics
Nuclear Factor 90 Proteins - metabolism
Protein Binding
Proteins
RNA - genetics
RNA - metabolism
RNA Interference
RNA Stability
RNA, Messenger - genetics
RNA, Messenger - metabolism
RNA-binding protein
RNA-Binding Proteins - genetics
RNA-Binding Proteins - metabolism
RNA-Seq - methods
SARS-CoV-2 - genetics
SARS-CoV-2 - metabolism
SARS-CoV-2 - physiology
Science
Science (multidisciplinary)
Severe acute respiratory syndrome coronavirus 2
ISSN:2045-2322, 2045-2322
Online Access:Get full text
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Summary:RNA-binding proteins (RBPs) interact with and determine the fate of many cellular RNAs directing numerous essential roles in cellular physiology. Nuclear Factor 90 (NF90) is an RBP encoded by the interleukin enhancer-binding factor 3 ( ILF3 ) gene that has been found to influence RNA metabolism at several levels, including pre-RNA splicing, mRNA turnover, and translation. To systematically identify the RNAs that interact with NF90, we carried out iCLIP (individual-nucleotide resolution UV crosslinking and immunoprecipitation) analysis in the human embryonic fibroblast cell line HEK-293. Interestingly, many of the identified RNAs encoded proteins involved in the response to viral infection and RNA metabolism. We validated a subset of targets and investigated the impact of NF90 on their expression levels. Two of the top targets, IRF3 and IRF9 mRNAs, encode the proteins IRF3 and IRF9, crucial regulators of the interferon pathway involved in the SARS-CoV-2 immune response. Our results support a role for NF90 in modulating key genes implicated in the immune response and offer insight into the immunological response to the SARS-CoV-2 infection.
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ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-021-04101-1