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HOTAIRM1, an enhancer lncRNA, promotes glioma proliferation by regulating long-range chromatin interactions within HOXA cluster genes

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Abstract

The long noncoding RNA HOTAIRM1 reportedly plays important roles in acute myeloid leukemia, gastric cancer and colorectal cancer. Here, we analyzed potential function of HOTAIRM1 in glioma and asked whether it participates in long-range chromatin interactions. We monitored expression of HOTAIRM1 in glioma tissues and correlated levels with patient survival using the TCGA dataset. HOTAIRM1 was highly expressed in glioma tissue, with high levels associated with shortened patient survival time. We then suppressed HOTAIRM1 activity in the human glioblastoma U251 line using CRISPR-cas9 to knock in a truncating polyA fragment. Reporter analysis of these and control cells confirmed that the HOTAIRM1 locus serves as an active enhancer. We then performed Capture-C analysis to identify target genes of that locus and applied RNA antisense purification to assess chromatin interactions between the HOTAIRM1 locus and HOXA cluster genes. HOTAIRM1 knockdown in glioma cells decreased proliferation and reduced expression of HOXA cluster genes. HOTAIRM1 regulates long-range interactions between the HOTAIRM1 locus and HOXA genes. Our work suggests a new mechanism by which HOTAIRM1 regulates glioma progression by regulating high-order chromatin structure and could suggest novel therapeutic targets to treat an intractable cancer.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (Grant Nos. 31701129, 81772687, 31530027) and the Natural Science Foundation of Tianjin City of China (Grant No. 18JCQNJC10100).

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Authors and Affiliations

  1. State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China

    Tengfei Shi, Dianhao Guo, Heming Xu, Guangsong Su, Jun Chen, Zhongfang Zhao, Jiandang Shi, Lei Zhang & Wange Lu

  2. Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA

    Michelle Wedemeyer & Frank Attenello

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  1. Tengfei Shi
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Contributions

WL, LZ, and TS conceived the projects. TS, HX, GS, JC, ZZ, and JS performed the experiments. DG contributed to sequencing and bioinformatics analysis. TS, LZ, FA, and MW wrote the manuscript.

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Correspondence to Lei Zhang or Wange Lu.

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11033_2020_5371_MOESM1_ESM.pdf

Supplementary Fig. 1— HOTAIRM1 downregulation inhibits glioma proliferation. A Kaplan-Meir survival curve of patients with high versus low HOTAIRM1 expression. Bars indicate s.e.m., ***p < 0.001. B Schematic of CRISPR-Cas9-mediated HOTAIRM1 polyA knock-in. C Efficiency of HOTAIRM1 knock-down in two glioma lines (KI-1 and KI-2). D Proliferation of indicated glioma lines, as determined by an MTS assay. E, G Colony formation assays of indicated lines. F,H Flow cytometry analysis of the cell cycle indicates that HOTAIRM1 knockdown is associated with a decreased number of cells in S and an increase in the number of cells in G1 or G2. Bars indicate s.e.m., ***p<0.001 (PDF 294 kb)

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Shi, T., Guo, D., Xu, H. et al. HOTAIRM1, an enhancer lncRNA, promotes glioma proliferation by regulating long-range chromatin interactions within HOXA cluster genes. Mol Biol Rep 47, 2723–2733 (2020). https://doi.org/10.1007/s11033-020-05371-0

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