Similar Datasets
Project description:Genome-wide distribution of ZHX3 in human fibroblast cells.
| PRJNA767336 | ENA
Project description:ChIP-seq analysis of NSD2 in IMR-90 cells. We found that NSD2 is enriched at gene bodies of actively transcribed genes and required for maintenace of H3K36me3 levels at these loci.
2020-09-22 | GSE138065 | GEO
Project description:ZHX3 is a transcriptional factor whose role in human pancreatic beta cells is not well understood. In attempt to identify the genes that ZHX3 regulates in beta cells, we KO ZHX3 using CRISPR in EndoC-βH1 cells and performed RNA-Seq. We have only identified 36 and 31 genes that were significantly up and downregulated respectively. This is in concordance with our functional data whereby the KO of ZHX3 in EndoC-βH1 did not affect its insulin secretory function. Overall, we conclude that the KO of ZHX3 did not result in major perturbations in EndoC-βH1 cells.
2025-02-26 | GSE236102 | GEO
Project description:The aim of this RNA-Seq analysis was to identify target genes of the transcription repressor ZHX3 in HepG2 cells. To do so, four stable lines were generated in HepG2 using three different ZHX3-targeting CRISPR constructs and an empty vector construct. Bulk RNA-Seq analysis was performed on these four lines. Sequencing was done by NovogeneAIT Genomics using the Illumina® NovaSeq6000-PE150 platform and 63-82 million base pairs were sequenced per sample. A total of 47 and 156 genes were found to be consistently upregulated and downregulated (fold change ≥ 2 and FDR < 0.05), respectively, in all three KO lines as compared to the empty control line. Functional enrichment analysis of the 156 upregulated genes using g:profiler revealed the enrichment of two biological processess, urate transport and urate metabolic process. qPCR analysis validated the upregulation of uric acid transporter gene SLC17A1.
2025-02-26 | GSE193872 | GEO
Project description:DNA integration is a defining step in the retroviral life cycle and the basis of stable gene transfer in retrovirus-based gene therapy. Previous studies of integration by HIV-based vectors have shown that integration is not random, but favored in active transcription units. Studies to date have focused on HIV integration in dividing cells, leaving open the question of whether integration target site selection might differ in nondividing cells. According to one idea, division of the host cell might be required for favored integration in transcription units, possibly as a result of chromatin remodeling during DNA replication. Here we have investigated this issue by comparing integration in dividing IMR-90 primary lung fibroblasts to integration in nondividing IMR-90 cells arrested in G1 by serum starvation and contact inhibition. We identified several differences in integration site selection in arrested versus dividing cells, including the frequency of integration in transcription units and in gene-rich regions. However, integration in nondividing cells was in fact more favored in transcription units, contrary to the idea that cell division was important for this bias. These data provide the first view of lentiviral integration in nondividing cells and help constrain models for the mechanism of favored integration in genes. Keywords: comparative genomic analysis, dividing versus non-dividing cells.
2005-11-10 | GSE3555 | GEO
Project description:ZHX3, which encodes for a transcriptional repressor, is associated with fasting blood glucose (FBG) levels and increased type 2 diabetes (T2D) risk but its role in cell types involved in glucose metabolism is not well understood. Here, we show that the deletion of ZHX3 in the human pancreatic β cell line EndoC-βH1 did not impair glucose-stimulated insulin secretion (GSIS) nor perturb its transcriptome. On the other hand, we found that ZHX3 represses the expression of gluconeogenic genes PCK1 and G6PC1 in the human hepatoma line HepG2. Transcriptomic analysis of ZHX3-deficient HepG2 cells revealed that the uric acid transporter gene SLC17A1 was upregulated, which consequentially led to increased uric acid secretion. High levels of uric acid could then impair GSIS in EndoC-βH1 cells. Subsequently, in-depth co-immunoprecipitation followed by mass spectrometry analysis of ZHX3 in HepG2 cells identified transcription factor CEBPB as its binding partner, required to repress the transcription of PCK1, G6PC1 and partially SLC17A1 in HepG2 cells. Overall, our study uncovered the role of ZHX3 in regulating glucose metabolism in hepatocytes, thereby influencing FBG levels and its association with T2D risk.
2026-04-27 | PXD046714 | Pride
Project description:Transcriptomic analysis of ZHX3-depleted HepG2 cells
| PRJNA798264 | ENA
Project description:Long non-coding RNAs (lncRNAs) play pivotal regulatory roles in mammalian male gametogenesis. Advances in high-throughput technologies have demonstrated that lncRNAs orchestrate robust, flexible, and context-specific gene regulatory networks through dynamic interactions with proteins, DNA, and RNA, modulating transcriptional and post-transcriptional processes. However, the mechanistic role of in situ lncRNA-mRNA interactions in spermatogonial stem cell (SSC) differentiation remains poorly understood. In this study, we employed RIC-seq (RNA in situ conformation sequencing) and LongRNA-seq to systematically identify a functional interaction between lncRNA Gm16751 and Zhx3 mRNA during SSC differentiation, which was further visualized via a Circos plot. Mechanistically, we demonstrated that Gm16751 enhances the mRNA stability of Zhx3, thereby promoting SSC differentiation. Furthermore, mass spectrometry analysis revealed that RPS3 (Ribosomal Protein S3) serves as a critical RNA-binding protein (RBP) that bridges the interaction between Gm16751 and Zhx3, ultimately stabilizing Zhx3 mRNA and modulating SSC differentiation. Our findings provide novel mechanistic insights into the lncRNA-mRNA regulatory axis in SSC differentiation and establish a foundation for understanding the molecular etiology of male germ cell developmental disorders and spermatogenic dysfunction.
2026-06-10 | GSE296666 | GEO
Project description:Long non-coding RNAs (lncRNAs) play pivotal regulatory roles in mammalian male gametogenesis. Advances in high-throughput technologies have demonstrated that lncRNAs orchestrate robust, flexible, and context-specific gene regulatory networks through dynamic interactions with proteins, DNA, and RNA, modulating transcriptional and post-transcriptional processes. However, the mechanistic role of in situ lncRNA-mRNA interactions in spermatogonial stem cell (SSC) differentiation remains poorly understood. In this study, we employed RIC-seq (RNA in situ conformation sequencing) and LongRNA-seq to systematically identify a functional interaction between lncRNA Gm16751 and Zhx3 mRNA during SSC differentiation, which was further visualized via a Circos plot. Mechanistically, we demonstrated that Gm16751 enhances the mRNA stability of Zhx3, thereby promoting SSC differentiation. Furthermore, mass spectrometry analysis revealed that RPS3 (Ribosomal Protein S3) serves as a critical RNA-binding protein (RBP) that bridges the interaction between Gm16751 and Zhx3, ultimately stabilizing Zhx3 mRNA and modulating SSC differentiation. Our findings provide novel mechanistic insights into the lncRNA-mRNA regulatory axis in SSC differentiation and establish a foundation for understanding the molecular etiology of male germ cell developmental disorders and spermatogenic dysfunction.
2026-06-10 | GSE296667 | GEO