Enhancer RNA commits osteogenesis via microRNA-3129 expression in human bone marrow-derived mesenchymal stem cells

Anh Phuong Nguyen; Kaoru Yamagata; Shigeru Iwata; Gulzhan Trimova; Tong Zhang; Yu Shan; Mai-Phuong Nguyen; Koshiro Sonomoto; Shingo Nakayamada; Shigeaki Kato; Yoshiya Tanaka

doi:10.1186/s41232-022-00228-4

Enhancer RNA commits osteogenesis via microRNA-3129 expression in human bone marrow-derived mesenchymal stem cells

Inflamm Regen. 2022 Sep 16;42(1):43. doi: 10.1186/s41232-022-00228-4.

Authors

Affiliations

¹ The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Japan, 1-1 Iseigaoka, Yahata-nishi, Kitakyushu, 807-8555, Japan.
² Endocrinology and Diabetes Department, Bach Mai Hospital, Hanoi, Vietnam.
³ Department of Clinical Subjects, High School of Medicine, Faculty of Medicine and Health Care, Al-Farabi Kazakh National University, Almaty, Kazakhstan.
⁴ Department of Basic Pathology, School of Medicine/School of Graduate Education, Fukushima Medical University, Fukushima, Japan.
⁵ Graduate School of Life Science and Engineering, Iryo Sosei University, Iwaki, Fukushima, Japan.
⁶ The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Japan, 1-1 Iseigaoka, Yahata-nishi, Kitakyushu, 807-8555, Japan. tanaka@med.uoeh-u.ac.jp.

Abstract

Background: Highly regulated gene expression program underlies osteogenesis of mesenchymal stem cells (MSCs), but the regulators in the program are not entirely identified. As enhancer RNAs (eRNAs) have recently emerged as a key regulator in gene expression, we assume a commitment of an eRNA in osteogenesis.

Methods: We performed in silico analysis to identify potential osteogenic microRNA (miRNA) gene predicted to be regulated by super-enhancers (SEs). SE inhibitor treatment and eRNA knocking-down were used to confirm the regulational mechanism of eRNA. miRNA function in osteogenesis was elucidated by miR mimic and inhibitor transfection experiments.

Results: miR-3129 was found to be located adjacent in a SE (osteoblast-specific SE_46171) specifically activated in osteoblasts by in silico analysis. A RT-quantitative PCR analysis of human bone marrow-derived MSC (hBMSC) cells showed that eRNA_2S was transcribed from the SE with the expression of miR-3129. Knockdown of eRNA_2S by locked nucleic acid as well as treatment of SE inhibitors JQ1 or THZ1 resulted in low miR-3129 levels. Overexpression of miR-3129 promoted hBMSC osteogenesis, while knockdown of miR-3129 inhibited hBMSC osteogenesis. Solute carrier family 7 member 11 (SLC7A11), encoding a bone formation suppressor, was upregulated following miR-3129-5p inhibition and identified as a target gene for miR-3129 during differentiation of hBMSCs into osteoblasts.

Conclusions: miR-3129 expression is regulated by SEs via eRNA_2S and this miRNA promotes hBMSC differentiation into osteoblasts through downregulating the target gene SLC7A11. Thus, the present study uncovers a commitment of an eRNA via a miR-3129/SLC7A11 regulatory pathway during osteogenesis of hBMSCs.

Keywords: Enhancer RNA; Mesenchymal stem cells; Osteogenesis; Super-enhancer; miR-3129.