Integrative analysis of nanopore direct RNA sequencing data reveals a role of PUS7-dependent pseudouridylation in regulation of m6A and m5C modifications Article Swipe
Mohit Bansal
,
Anirban Kundu
,
Anamika Gupta
,
Jane Ding
,
Andrew Gibson
,
Sanjay Varma RudraRaju
,
Sunil Sudarshan
,
Han-Fei Ding
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.01.31.578250
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.01.31.578250
Understanding the interactions between different RNA modifications is essential for unraveling their biological functions. Here, we report NanoPsiPy, a computational pipeline that employs nanopore direct RNA sequencing to identify pseudouridine (Ψ) sites and quantify their levels at single-nucleotide resolution. We validated NanoPsiPy by transcriptome-wide profiling of PUS7-dependent Ψ sites in poly-A RNA and rRNA. NanoPsiPy leverages Ψ-induced U-to-C basecalling errors in nanopore sequencing data, allowing detection of both low and high stoichiometric Ψ sites. We identified 8,624 PUS7-dependent Ψ sites in 1,246 mRNAs encoding proteins associated with ribosome biogenesis, translation, and energy metabolism. Importantly, integrative analysis revealed that PUS7 knockdown increases global mRNA N 6 -methyladenosine (m 6 A) and 5-methylcytosine (m 5 C) levels, suggesting an antagonistic relationship between Ψ and these modifications. Our study underscores the potential of nanopore direct RNA sequencing in revealing the co-regulation of RNA modifications and the capacity of NanoPsiPy in analyzing pseudouridylation and its impact on other RNA modifications.
Related Topics
Concepts
Nanopore sequencing
Nanopore
Profiling (computer programming)
Transcriptome
Computational biology
RNA
RNA-Seq
Biology
Computer science
Genome
Nanotechnology
Genetics
Gene expression
Gene
Materials science
Operating system
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2024.01.31.578250
- https://www.biorxiv.org/content/biorxiv/early/2024/02/01/2024.01.31.578250.1.full.pdf
- OA Status
- green
- Cited By
- 7
- References
- 31
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4391428858
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4391428858Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2024.01.31.578250Digital Object Identifier
- Title
-
Integrative analysis of nanopore direct RNA sequencing data reveals a role of PUS7-dependent pseudouridylation in regulation of m6A and m5C modificationsWork title
- Type
-
preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2024Year of publication
- Publication date
-
2024-02-01Full publication date if available
- Authors
-
Mohit Bansal, Anirban Kundu, Anamika Gupta, Jane Ding, Andrew Gibson, Sanjay Varma RudraRaju, Sunil Sudarshan, Han-Fei DingList of authors in order
- Landing page
-
https://doi.org/10.1101/2024.01.31.578250Publisher landing page
- PDF URL
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https://www.biorxiv.org/content/biorxiv/early/2024/02/01/2024.01.31.578250.1.full.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://www.biorxiv.org/content/biorxiv/early/2024/02/01/2024.01.31.578250.1.full.pdfDirect OA link when available
- Concepts
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Nanopore sequencing, Nanopore, Profiling (computer programming), Transcriptome, Computational biology, RNA, RNA-Seq, Biology, Computer science, Genome, Nanotechnology, Genetics, Gene expression, Gene, Materials science, Operating systemTop concepts (fields/topics) attached by OpenAlex
- Cited by
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7Total citation count in OpenAlex
- Citations by year (recent)
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2025: 5, 2024: 1, 2022: 1Per-year citation counts (last 5 years)
- References (count)
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31Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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