Chromatin-Associated Protein Sugp2 Involved in mRNA Alternative Splicing During Mouse Spermatogenesis

Zhan, Junfeng; Li, Jianbo; Wu, Yuerong; Wu, Panfeng; Yu, Ziqi; Cui, Peng; Zhou, Mofan; Xu, Youyong; Jin, Tingyu; Du, Ziye; Luo, Mengcheng; Liu, Cong

doi:10.3389/fvets.2021.754021

Cited by 3 publications

(2 citation statements)

References 36 publications

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“…Species-conserved TE-derived alternative promoters were not limited to the same subfamily of TEs, i.e., different TE subfamilies acted on the same gene across the three species. For example, the MIR element serves as a testis-specific promoter for SUGP2 , which mediates the alternative splicing regulatory network during spermatogenesis in the testes ( Zhan et al, 2021 ). The subfamilies of MIR were MIRb, MIR, and MIR1_Amn in pigs, mice, and humans, respectively (Supplementary Figure S9).…”

Section: Resultsmentioning

confidence: 99%

Pig H3K4me3, H3K27ac, and gene expression profiles reveal reproductive tissue-specific activity of transposable elements

Jiang,

Zhou,

Ling

et al. 2024

Zoological Research

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Regulatory sequences and transposable elements (TEs) account for a large proportion of the genomic sequences of species; however, their roles in gene transcription, especially tissue-specific expression, remain largely unknown. Pigs serve as an excellent animal model for studying genomic sequence biology due to the extensive diversity among their wild and domesticated populations. Here, we conducted an integrated analysis using H3K27ac ChIP-seq, H3K4me3 ChIP-seq, and RNA-seq data from 10 different tissues of seven fetuses and eight closely related adult pigs. We aimed to annotate the regulatory elements and TEs to elucidate their associations with histone modifications and mRNA expression across different tissues and developmental stages. Based on correlation analysis between mRNA expression and H3K27ac and H3K4me3 peak activity, results indicated that H3K27ac exhibited stronger associations with gene expression than H3K4me3. Furthermore, 1.45% of TEs overlapped with either the H3K27ac or H3K4me3 peaks, with the majority displaying tissue-specific activity. Notably, a TE subfamily (LTR4C_SS), containing binding motifs for SIX1 and SIX4, showed specific enrichment in the H3K27ac peaks of the adult and fetal ovaries. RNA-seq analysis also revealed widespread expression of TEs in the exons or promoters of genes, including 4 688 TE-containing transcripts with distinct development stage-specific and tissue-specific expression. Of note, 1 967 TE-containing transcripts were enriched in the testes. We identified a long terminal repeat (LTR), MLT1F1, acting as a testis-specific alternative promoter in SRPK2 (a cell cycle-related protein kinase) in our pig dataset. This element was also conserved in humans and mice, suggesting either an ancient integration of TEs in genes specifically expressed in the testes or parallel evolutionary patterns. Collectively, our findings demonstrate that TEs are deeply embedded in the genome and exhibit important tissue-specific biological functions, particularly in the reproductive organs.

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Section: Resultsmentioning

confidence: 99%

Pig H3K4me3, H3K27ac, and gene expression profiles reveal reproductive tissue-specific activity of transposable elements

Jiang,

Zhou,

Ling

et al. 2024

Zoological Research

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“…SMAD3 is a key transcription factor mediating the TGF-β signalling pathway, and its receptors are overexpressed in PAAD cells [47]. Moreover, there have been few studies on SUGP2, which indicate that it is mostly involved in RNA processing [48] and spermatogenesis [49]. proliferation.…”

Section: Identification Of Related Genes Interacting With Pcdh1mentioning

confidence: 99%

PCDH1, a poor prognostic biomarker and potential target for pancreatic adenocarcinoma metastatic therapy

Du,

Yi,

Zou

et al. 2023

BMC Cancer

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Background Pancreatic adenocarcinoma (PAAD) is an aggressive solid tumour characterised by few early symptoms, high mortality, and lack of effective treatment. Therefore, it is important to identify new potential therapeutic targets and prognostic biomarkers of PAAD. Methods The Cancer Genome Atlas and Genotype-Tissue Expression databases were used to identify the expression and prognostic model of protocadherin 1 (PCDH1). The prognostic performance of risk factors and diagnosis of patients with PAAD were evaluated by regression analysis, nomogram, and receiver operating characteristic curve. Paraffin sections were collected from patients for immunohistochemistry (IHC) analysis. The expression of PCDH1 in cells obtained from primary tumours or metastatic biopsies was identified using single-cell RNA sequencing (scRNA-seq). Real-time quantitative polymerase chain reaction (qPCR) and western blotting were used to verify PCDH1 expression levels and the inhibitory effects of the compounds. Results The RNA and protein levels of PCDH1 were significantly higher in PAAD cells than in normal pancreatic ductal cells, similar to those observed in tissue sections from patients with PAAD. Aberrant methylation of the CpG site cg19767205 and micro-RNA (miRNA) hsa-miR-124-1 may be important reasons for the high PCDH1 expression in PAAD. Up-regulated PCDH1 promotes pancreatic cancer cell metastasis. The RNA levels of PCDH1 were significantly down-regulated following flutamide treatment. Flutamide reduced the percentage of PCDH1 RNA level in PAAD cells Panc-0813 to < 50%. In addition, the PCDH1 protein was significantly down-regulated after Panc-0813 cells were incubated with 20 µM flutamide and proves to be a potential therapeutic intervention for PAAD. Conclusion PCDH1 is a key prognostic biomarker and promoter of PAAD metastasis. Additionally, flutamide may serve as a novel compound that down-regulates PCDH1 expression as a potential treatment for combating PAAD progression and metastasis.

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Hereditary Hemochromatosis Caused by SUGP2 and DENND3 Mutation in China: A Case Report

Qiu,

Yuan,

Guo

et al. 2024

Clinical Case Reports

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Chromatin-Associated Protein Sugp2 Involved in mRNA Alternative Splicing During Mouse Spermatogenesis

Cited by 3 publications

References 36 publications

Pig H3K4me3, H3K27ac, and gene expression profiles reveal reproductive tissue-specific activity of transposable elements

Pig H3K4me3, H3K27ac, and gene expression profiles reveal reproductive tissue-specific activity of transposable elements

PCDH1, a poor prognostic biomarker and potential target for pancreatic adenocarcinoma metastatic therapy

Hereditary Hemochromatosis Caused by SUGP2 and DENND3 Mutation in China: A Case Report

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