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A transcriptomic analysis of Nsmce1 overexpression in mouse hippocampal neuronal cell by RNA sequencing

  • Mengting Gong
  • Zhen Wang
  • Yanjun Liu
  • Wenxing Li
  • Shoudong Ye
  • Jie Zhu
  • Hui Zhang
  • Jing Wang
  • Kan HeEmail author
Original Article
  • 53 Downloads

Abstract

Mouse Nsmce1 gene is the homolog of non-structural maintenance of chromosomes element 1 (NSE1) that is mainly involved in maintenance of genome integrity, DNA damage response, and DNA repair. Defective DNA repair may cause neurological disorders such as Alzheimer’s disease (AD). So far, there is no direct evidence for the correlation between Nsmce1 and AD. In order to explore the function of Nsmce1 in the regulation of nervous system, we have overexpressed or knocked down Nsmce1 in the mouse hippocampal neuronal cells (MHNCs) HT-22 and detected its regulation of AD marker genes as well as cell proliferation. The results showed that the expression of App, Bace2, and Mapt could be inhibited by Nsmce1 overexpression and activated by the knockdown of Nsmce1. Moreover, the HT-22 cell proliferation ability could be promoted by Nsmce1 overexpression and inhibited by knockdown of Nsmce1. Furthermore, we performed a transcriptomics study by RNA sequencing (RNA-seq) to evaluate and quantify the gene expression profiles in response to the overexpression of Nsmce1 in HT-22 cells. As a result, 224 significantly dysregulated genes including 83 upregulated and 141 downregulated genes were identified by the comparison of Nsmce1 /+ to WT cells, which were significantly enriched in several Gene Ontology (GO) terms and pathways. In addition, the complexity of the alternative splicing (AS) landscape was increased by Nsmce1 overexpression in HT-22 cells. Thousands of AS events were identified to be mainly involved in the pathway of ubiquitin-mediated proteolysis (UMP) as well as 3 neurodegenerative diseases including AD. The protein-protein interaction network was reconstructed to show top 10 essential genes regulated by Nsmce1. Our sequencing data is available in the Gene Expression Omnibus (GEO) database with accession number as GSE113436. These results may provide some evidence of molecular and cellular functions of Nsmce1 in MHNCs.

Keywords

Nsmce1 HT-22 RNA-seq Alternative splicing AD 

Notes

Authors’ contributions

KH conceived and designed the study. MG, YL, WZ, and WXL performed the experiments and data analysis. MG and KH wrote the paper. SY, JZ, HZ, and JW reviewed and edited the manuscript. All authors read and approved the manuscript.

Funding information

This study received financial supports by the Natural Science Foundation Project of Anhui Province (1508085QC63 and 1908085MC87), Key University Science Research Project of Anhui Province (KJ2017A021), and the Scientific Research Foundation and Academic & Technology Leaders Introduction Project, and 211 Project of Anhui University (10117700023), and the Student Research Training Program of Anhui University (J10118516042).

Compliance with ethical standards

Competing interests

The authors declare that they have no competing interests.

Supplementary material

10142_2019_728_MOESM1_ESM.xls (808 kb)
Table S1. The full information of DEGs in response to the overexpression ofNsmce1in the hippocampus neuron HT22 cells. Based on the analysis of differentially expressed genes (DEGs), we have identified 224 significantly dysregulated genes with FC more than 2 and p value less than 0.05, including 83 up-regulated (in red) and 141 down-regulated (in green) genes by the comparison of Nsmce1 /+ group to WT group. The full information of each DEG contains Ensembl ID, Gene symbol, gene expression profiles in each sample, average expression value in the WT group (G1), average expression value in the Nsmce1 /+ group (G2), log2 of Fold change by the comparison of Nsmce1 /+ group to WT group, significance level p value, false discovery rate (FDR), involved Gene Ontology (GO) terms including three categories of biological process (BP), cellular component (CC) and molecular function (MF) as well as KEGG pathways. (XLS 808 kb).
10142_2019_728_MOESM2_ESM.xls (142 kb)
Table S2. The enriched GO terms in response to the overexpression ofNsmce1in HT22 cells. There were totally 320 GO terms for BP, 24 GO terms for CC as well as 98 GO terms for MF significantly enriched in the regulation of Nsmce1 in HT-22 cells.The information of each GO term contains ID in Gene Ontology database, the name of GO terms, the category, the number of involved genes (annotated), the number of identified DEGs (significant), the gene symbol of involved DEGs and the significance. (XLS 142 kb).
10142_2019_728_MOESM3_ESM.xls (24 kb)
Table S3. The enriched KEGG pathways in response to the overexpression ofNsmce1in HT22 cells. There were 17 KEGG pathways were identified to be significantly enriched in the regulation of Nsmce1 in HT-22 cells. The information of each KEGG pathway contains ID in KEGG database, the name of KEGG pathway, the pathway class, the number of involved genes (annotated), the number of identified DEGs (significant), the gene symbol of involved DEGs and the significance. (XLS 23 kb).

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Mengting Gong
    • 1
  • Zhen Wang
    • 2
  • Yanjun Liu
    • 3
  • Wenxing Li
    • 4
    • 5
  • Shoudong Ye
    • 1
    • 3
  • Jie Zhu
    • 3
  • Hui Zhang
    • 3
  • Jing Wang
    • 3
  • Kan He
    • 1
    • 3
    Email author
  1. 1.Center for Stem Cell and Translational Medicine, School of Life SciencesAnhui UniversityHefeiChina
  2. 2.Department of GeneticsAlbert Einstein College of MedicineBronxUSA
  3. 3.Department of Biostatistics, School of Life SciencesAnhui UniversityHefeiChina
  4. 4.State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
  5. 5.Kunming College of Life ScienceUniversity of Chinese Academy of SciencesKunmingChina

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