Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

LncRNA-operated stem cell fate control: RPS3 organizes the in situ Gm16751-Zhx3 interactome to program spermatogonial differentiation [Long RNA-Seq]

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE296667 | GEO | 2026/06/10

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

lncRNA-operated stem cell fate control: RPS3 organizes the in situ Gm16751-Zhx3 interactome to program spermatogonial differentiation [RIC-Seq]

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

mouse spermatogonial stem cells LC-MS

2026-06-08 | PXD063805 | Pride

Genome-wide distribution of ZHX3 in human fibroblast cells.

Project description:ChIP-seq analysis of ZHX3 in IMR-90 cells. We found that ZHX3 is enriched at the promoter site of target genes.

2022-01-01 | GSE184992 | GEO

Effect of deletion of ZHX3 on gene expression in human pancreatic beta cells EndoC-BH1

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

LncRNA Sequencing Analysis of Mouse spermatogonial stem cells during retinoic acid treatment

Project description:Retinoic acid triggers differentiation of spermatogonial stem cells by activating the expression of differentiating genes. Long noncoding RNAs (lncRNA) are transcripts longer than 200 nucleotides that do not code for proteins, providing a new perspective of RNA species in gene regulation. However, the function of lncRNAs in determining SSC differentiation has not been investigated. Here, we used high-throughput sequencing to profile all lncRNAs in SSCs, and report the dataset of lncRNAs during SSC differentiation.

2017-05-23 | GSE99147 | GEO

Transcriptomic analysis of ZHX3-depleted HepG2 cells

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

ZHX3 interacts with CEBPB to repress hepatic gluconeogenic gene expression and uric acid secretion

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

Transcriptomic analysis of ZHX3-depleted HepG2 cells

Project description:Transcriptomic analysis of ZHX3-depleted HepG2 cells

| PRJNA798264 | ENA

NP Cell line vs control cell

Project description:Background: Stem cells were often used for intervertebral disc degeneration (IDD) regeneration. The underlying mechanisms remain to be explored. LncRNAs were found to be related to the physiological process such as apoptosis and differentiation. Many studies focus on the messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) between normal nucleus pulposus and degeneration nucleus pulposus. However, few studies have shed light on the different expression of lncRNA and mRNA in the differentiation. In the present study, we aimed to determine mRNAs and lncRNAs, which are differentially expressed during in human adipose-derived mesenchymal stem cells (hADSCs) differentiation process into np-like cell types and to explore the related signaling pathways and the regulatory networks. Methods: hADSCs were induced to differentiation into np-like cell under the cytokine circumstance. The mark genes of np-like cell were determined by PCR and immunology staining. Then RNA-seq was used to analysis the expression of lncRNA and mRNA in the differentiation of hADSCs into np-like cell types. The significant genes were confirmed by Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Results: We found 14 lncRNAs and 601 mRNAs were significantly differentially expressed in hADSCs differentiation. The RNA-seq data were confirmed by real-time PCR. Furthermore, we found Gene Ontology terms were upregulated, and downregulated and significantly enriched pathways. Moreover, gene network shows significant differentially expressed genes. Meanwhile, the relationship of significantly changed mRNAs and lncRNAs were revealed by mRNA-lncRNA co-expression network. Conclusion: Our results first explore differentially expressed lncRNAs and mRNAs in the differentiation of hADSCs into np-like cell types. These may supply useful information for better understanding of stem cell therapy and IDD regeneration.

2025-08-18 | E-MTAB-15403 | biostudies-arrayexpress

Genome-wide distribution of ZHX3 in human fibroblast cells.

Project description:Genome-wide distribution of ZHX3 in human fibroblast cells.

| PRJNA767336 | ENA