The HNRNPU Knockout HAP1 Polyclonal Cells are a CRISPR/Cas9-edited polyclonal knockout cell population designed for the study of heterogeneous nuclear ribonucleoprotein U (HNRNPU) function. This loss-of-function model is generated by disrupting the HNRNPU gene in the HAP1 parental cell line, enabling researchers to dissect the roles of this multifunctional RNA-binding protein in pre-mRNA processing, chromatin organization, transcriptional regulation, and DNA damage responses.
The HAP1 cell line is a near-haploid, fibroblast-like cell line derived from the KBM-7 chronic myeloid leukemia (CML) cell line. As a BCR-ABL-positive and near-haploid model, HAP1 cells are widely employed in genetic screening and cancer biology research due to the ease of generating single-gene knockouts and the reduced genetic redundancy. The male origin and adherent morphology further contribute to its utility as a robust host system for functional genomics studies.
HNRNPU is a scaffolding nuclear protein that binds RNA and matrix attachment region DNA, acting as a key regulator of chromatin architecture and RNA metabolism. Mechanistically, HNRNPU is activated by ATM kinase-mediated phosphorylation in response to DNA damage and integrates signals from the PI3K/AKT pathway via CDK1. It interacts with PARP1, CTCF, RNA polymerase II, and chromatin remodelers such as SMARCA4 (BRG1) to coordinate transcriptional regulation and splicing. HNRNPU directly binds and modulates the function of XIST RNA, thereby contributing to X-chromosome inactivation, while also regulating the expression of MYC and CCND1 mRNAs and the activity of splicing factors like RBFOX2 and SRSF1. Knockout of HNRNPU disrupts these interactions, causing aberrant splicing, altered chromatin looping, impaired DNA repair, and dysregulation of circadian and X-inactivation pathways.
In the HAP1 context, HNRNPU knockout provides a powerful tool to investigate the intersection of RNA biology and chromatin dynamics in a leukemia-relevant background. The near-haploid nature minimizes functional compensation by homologous alleles, ensuring that observed phenotypes are directly attributable to HNRNPU loss. This model is particularly valuable for exploring how HNRNPU-dependent DNA repair defects contribute to genomic instability in BCR-ABL-positive leukemias and for identifying synthetic lethal interactions that may open new therapeutic avenues. Additionally, the role of HNRNPU in neurodevelopmental disorders and glioblastoma can be probed using this cell system.
Typical research applications include functional genomics screens, RNA splicing analyses via RNA-seq and RT-qPCR, chromatin immunoprecipitation (ChIP-qPCR) for chromatin binding studies, and DNA repair investigations using ??H2AX flow cytometry or comet assays. The cells are also suitable for immunofluorescence localization studies, RNA immunoprecipitation to identify HNRNPU-bound RNAs, and XIST RNA FISH to assess X-inactivation status. These polyclonal knockout cells support a wide range of experimental workflows in cancer biology, RNA biology, and chromatin research. For further information, please contact Ascent Research.
