Open Access

Determination of long non‑coding RNAs associated with EZH2 in neuroblastoma by RIP‑seq, RNA‑seq and ChIP‑seq

  • Authors:
    • Mujie Ye
    • Lulu Xie
    • Jingjing Zhang
    • Baihui Liu
    • Xiangqi Liu
    • Jiajun He
    • Duan Ma
    • Kuiran Dong
  • View Affiliations

  • Published online on: July 13, 2020     https://doi.org/10.3892/ol.2020.11862
  • Article Number: 1
  • Copyright: © Ye et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

Neuroblastoma (NB) is the most common type of extracranial solid tumor found in children. Despite several treatment options, patients with advanced stage disease have a poor prognosis. Previous studies have reported that enhancer of zeste homolog 2 (EZH2) and long non‑coding RNAs (lncRNAs) have abnormal expression levels in NB and participate in tumorigenesis and NB development. However, the association between EZH2 and lncRNAs remain unclear. In the present study, RNA immunoprecipitation‑sequencing (RIP‑seq) was used to analyze the lncRNAs binding to EZH2. Following EZH2 knockdown via short hairpin RNA, RNA‑seq was performed in shEZH2 and control groups in SH‑SY5Y cells. Chromatin IP (ChIP)‑seq was used to determine the genes that may be regulated by EZH2. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to identify the signaling pathways involved in NB. The results from RIP‑seq identified 94 lncRNAs, including SNHG7, SNHG22, KTN‑AS1 and Linc00843. Furthermore, results from RNA‑seq demonstrated that, following EZH2 knockdown, 448 genes were up‑ and 571 genes were downregulated, with 32 lncRNAs up‑ and 35 downregulated and differentially expressed compared with control groups. Certain lncRNAs, including MALAT1, H19, Linc01021 and SNHG5, were differentially expressed in EZH2‑knockdown group compared with the control group. ChIP‑seq identified EZH2 located in the promoter region of 138 lncRNAs including CASC16, CASC15, LINC00694 and TBX5‑AS1. In summary, the present study demonstrated that certain lncRNAs directly bound EZH2 and regulated EZH2 expression levels. A number of these lncRNAs that are associated with EZH2 may participate in NB tumorigenesis.
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October-2020
Volume 20 Issue 4

Print ISSN: 1792-1074
Online ISSN:1792-1082

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Spandidos Publications style
Ye M, Xie L, Zhang J, Liu B, Liu X, He J, Ma D and Dong K: Determination of long non‑coding RNAs associated with EZH2 in neuroblastoma by RIP‑seq, RNA‑seq and ChIP‑seq. Oncol Lett 20: 1, 2020
APA
Ye, M., Xie, L., Zhang, J., Liu, B., Liu, X., He, J. ... Dong, K. (2020). Determination of long non‑coding RNAs associated with EZH2 in neuroblastoma by RIP‑seq, RNA‑seq and ChIP‑seq. Oncology Letters, 20, 1. https://doi.org/10.3892/ol.2020.11862
MLA
Ye, M., Xie, L., Zhang, J., Liu, B., Liu, X., He, J., Ma, D., Dong, K."Determination of long non‑coding RNAs associated with EZH2 in neuroblastoma by RIP‑seq, RNA‑seq and ChIP‑seq". Oncology Letters 20.4 (2020): 1.
Chicago
Ye, M., Xie, L., Zhang, J., Liu, B., Liu, X., He, J., Ma, D., Dong, K."Determination of long non‑coding RNAs associated with EZH2 in neuroblastoma by RIP‑seq, RNA‑seq and ChIP‑seq". Oncology Letters 20, no. 4 (2020): 1. https://doi.org/10.3892/ol.2020.11862