Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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HNRNPU RNA targets and DNA methylation changes during neural differentiation


ABSTRACT: This study investigates the molecular mechanisms by which the DNA/RNA-binding protein HNRNPU regulates gene expression during early human neural development. Pathogenic variants in HNRNPU cause a severe neurodevelopmental disorder, but the underlying mechanisms remain poorly understood. To explore the role of HNRNPU in transcriptional and epigenetic regulation, we used human induced pluripotent stem cell (hiPSC)-derived neuroepithelial stem cells (NES) and differentiating neural cells as model systems. We performed formaldehyde crosslinking and ribonucleoprotein immunoprecipitation followed by RNA sequencing (fRIP-seq) to identify RNA targets bound by HNRNPU, whole-genome bisulfite sequencing (WGBS) to assess the impact of HNRNPU silencing on DNA methylation landscapes, and CUT&RUN profiling to map chromatin marks at regulatory regions. Together, these datasets provide a comprehensive view of HNRNPU’s interactions with RNA, and its influence on the epigenetic state of key developmental genes. The data can be used to study RNA–protein interactions, DNA methylation dynamics, and chromatin regulation during neural differentiation. Mass spectrometry data was deposited to PRIDE under accession number PXD061718.

INSTRUMENT(S): Illumina NovaSeq X, NextSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Marika Oksanen 

PROVIDER: E-MTAB-14910 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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