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| Status |
Public on Sep 01, 2024 |
| Title |
Modulation of host gene expression by the zinc finger antiviral protein [CLIP-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
The zinc finger antiviral protein (ZAP) depletes non-self RNAs through recognition of their elevated CpG dinucleotide content. CpG dinucleotides are sparse in most endogenous mammalian mRNAs, but a subset might potentially be modulated by ZAP. While CpG frequency alone is insufficient to predict ZAP-regulation, we developed an algorithm using experimentally determined compositional features to predict which endogenous mRNAs may be ZAP-regulated. Using ZAP-knockout mice, we demonstrate that levels of many host mRNAs that are algorithmically predicted ZAP targets are indeed increased when ZAP is absent. ZAP is interferon-inducibel and we also identify genes that are downregulated by ZAP during an innate immune response. Many ZAP-regulated gene products are extracellular matrix or of nucleosome components, whose ZAP mediated control is conserved in human cells. Overall, we provide a new tool for the prediction of ZAP target genes and reveal host mRNAs that are ZAP-regulated.
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| Overall design |
The goal of the experiment was to analyze RNA sequences bound by the Zinc Finger Antiviral Protein (ZAP). ZAP:RNA complexes were extracted and purified from MT4 cells, reversed transcribed and analysed by NGS. Two biological replicates are included.
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| Contributor(s) |
Goncalves-Carneiro D, Bieniasz P |
| Citation missing |
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| Submission date |
Aug 12, 2024 |
| Last update date |
Sep 01, 2024 |
| Contact name |
Daniel Goncalves-Carneiro |
| E-mail(s) |
d.goncalves-carneiro@imperial.ac.uk
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| Organization name |
Imperial College London
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| Street address |
Sir Alexander Fleming Building, Imperial College Rd
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| City |
London |
| ZIP/Postal code |
SW7 2AZ |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA1147239 |
