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Cited by 7Genetics and Neurodevelopmental DisordersRNA Research and SplicingCancer-related molecular mechanisms research

Molecular interactome of HNRNPU reveals regulatory networks in neuronal differentiation and DNA methylation

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Oksanen, Marika, Mastropasqua, Francesca, Mazan-Mamczarz, Krystyna, Martindale, Jennifer L, Ye, Xuan, Arora, Abishek, Banskota, Nirad, Gorospe, Myriam +1 more·2026·Nucleic Acids Research
DOI 10.1093/nar/gkag107PMC PMC12895067

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Abstract

HNRNPU is an RNA-binding protein with diverse roles in transcriptional and post-transcriptional regulation. Pathogenic genetic variants of HNRNPU cause a severe neurodevelopmental disorder (NDD), but the underlying molecular mechanisms are unclear. Here, we comprehensively investigate the HNRNPU molecular interactome by integrating protein-protein interaction (PPI) mapping, RNA target identification, and genome-wide DNA methylation profiling in human neuroepithelial stem cells and differentiating neural cells. We identified extensive HNRNPU-centered networks, including an association with the mammalian SWI/SNF chromatin-remodeling complex, and uncovered a previously unrecognized role in translation. We present evidence that HNRNPU associates with messenger RNAs (mRNAs) encoding proteins important for neuronal development, including several linked to NDDs. Silencing HNRNPU reprogrammed methylation dynamics at regulatory regions, particularly at active and bivalent promoters of neurodevelopmental transcription factors. Integrative analysis across PPI, RNA, and methylome datasets identified 19 converging genes at all three molecular levels, including NDD genes within the SWI/SNF complex, SMARCA4 and SMARCC2, and RNA-processing machinery such as SYNCRIP. Together, these data showcase HNRNPU as a central coordinator of RNA metabolism and epigenetic remodeling during neural differentiation, linking RNA-binding, chromatin organization, and DNA methylation to the pathogenesis of HNRNPU-related NDDs.

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  • Variations in NIPBL and HNRNPU can trigger large-scale transcriptional network rearrangements, resulting in multisystem developmental abnormalities and brain structural alterations.

    “Variations in these genes can trigger large-scale transcriptional network rearrangements, resulting in multisystem developmental abnormalities and brain structural alterations (Oksanen et al., 2026).”

    From Biological hierarchy from genotype to phenotype in syndromic and non-syndromic autism spectrum disorder (2026) · cites this paper as Oksanen et al., 2026

    The Introduction links HNRNPU haploinsufficiency to developmental delay and other neurodevelopmental features, while the Discussion reports molecular regulatory changes and notes cortex-development defects in Hnrnpu knockout mice. The paper does not establish the claim for NIPBL, nor does it show that large-scale transcriptional network rearrangements cause multisystem abnormalities and brain structural alterations in affected individuals. (LLM, conf=0.85)

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Cited by

Sorted by citations

Authors
Oksanen, M., Mastropasqua, F., Mazan-Mamczarz, K., Martindale, J. L., Ye, X., Arora, A., Banskota, N., Gorospe, M., & Tammimies, K.
Affiliations
  • National Institutes of Health (US)
  • Karolinska University Hospital (SE)
Corresponding author
Tammimies, Kristiina
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2026-02-05
Volume
54
Issue
4
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkag107
PMC
PMC12895067
OpenAlex
W7128709615
Cited by
7
References
1
Citations by year
2026: 6 · 2025: 1
FWCI
24.02
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by)
Funders
  • National Academic Infrastructure for Supercomputing in Sweden
  • UPPMAX
  • Swedish Research Council (2022-06725, 2017-01660, 2023-02111)
  • Swedish Foundation for Strategic Research (FFL18-0104)
  • Swedish Brain Foundation–Hjärnfonden
  • NIH
  • Osk. Huttunen Foundation
  • H.K.H. Kronprinsessan Lovisas förening för barnasjukvård och Stiftelsen Axel Tielmans minnesfond (2020-00573, 2021-00617, 2023-00784, 2024-032)
  • Strategic Research Area Neuroscience
  • Karolinska Institutet
  • KI Foundations
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
Keywords
HNRNPU, RNA-binding proteins, neuronal differentiation, DNA methylation, neurodevelopmental disorders, SWI/SNF chromatin remodeling, SMARCA4, SMARCC2, SYNCRIP, translation (biology), RNA metabolism, epigenetic regulation, neuroepithelial stem cells, bivalent promoters
MeSH terms
Cell Differentiation, Chromosomal Proteins, Non-Histone, DNA Helicases, Humans, Neurons, Nuclear Proteins, Promoter Regions, Genetic, RNA, Messenger, Transcription Factors, DNA Methylation, Heterogeneous-Nuclear Ribonucleoprotein U, Chromatin Assembly and Disassembly, Epigenesis, Genetic, Gene Regulatory Networks, Neurogenesis, Neural Stem Cells, Protein Interaction Maps, Neurodevelopmental Disorders

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