Computational identification of miRNAs that modulate the differentiation of mesenchymal stem cells to osteoblasts
MicroRNAs (miRNAs) are small endogenous noncoding RNAs that play an instrumental role in post-transcriptional modulation of gene expression. Genes related to osteogenesis (i.e., RUNX2, COL1A1 and OSX) is important in controlling the differentiation of mesenchymal stem cells (MSCs) to bone tissues. T...
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doaj-7e85af21bca7495eb54c71dd95f177cd2020-11-24T22:59:53ZengPeerJ Inc.PeerJ2167-83592016-04-014e197610.7717/peerj.1976Computational identification of miRNAs that modulate the differentiation of mesenchymal stem cells to osteoblastsKanokwan Seenprachawong0Pornlada Nuchnoi1Chanin Nantasenamat2Virapong Prachayasittikul3Aungkura Supokawej4Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Bangkok, ThailandCenter for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, ThailandCenter of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, ThailandDepartment of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, ThailandDepartment of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Bangkok, ThailandMicroRNAs (miRNAs) are small endogenous noncoding RNAs that play an instrumental role in post-transcriptional modulation of gene expression. Genes related to osteogenesis (i.e., RUNX2, COL1A1 and OSX) is important in controlling the differentiation of mesenchymal stem cells (MSCs) to bone tissues. The regulated expression level of miRNAs is critically important for the differentiation of MSCs to preosteoblasts. The understanding of miRNA regulation in osteogenesis could be applied for future applications in bone defects. Therefore, this study aims to shed light on the mechanistic pathway underlying osteogenesis by predicting miRNAs that may modulate this pathway. This study investigates RUNX2, which is a major transcription factor for osteogenesis that drives MSCs into preosteoblasts. Three different prediction tools were employed for identifying miRNAs related to osteogenesis using the 3’UTR of RUNX2 as the target gene. Of the 1,023 miRNAs, 70 miRNAs were found by at least two of the tools. Candidate miRNAs were then selected based on their free energy values, followed by assessing the probability of target accessibility. The results showed that miRNAs 23b, 23a, 30b, 143, 203, 217, and 221 could regulate the RUNX2 gene during the differentiation of MSCs to preosteoblasts.https://peerj.com/articles/1976.pdfmiRNAsMicroRNAsOsteogenesisMesenchymal stem cellsBioinformaticsRUNX2 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Kanokwan Seenprachawong Pornlada Nuchnoi Chanin Nantasenamat Virapong Prachayasittikul Aungkura Supokawej |
spellingShingle |
Kanokwan Seenprachawong Pornlada Nuchnoi Chanin Nantasenamat Virapong Prachayasittikul Aungkura Supokawej Computational identification of miRNAs that modulate the differentiation of mesenchymal stem cells to osteoblasts PeerJ miRNAs MicroRNAs Osteogenesis Mesenchymal stem cells Bioinformatics RUNX2 |
author_facet |
Kanokwan Seenprachawong Pornlada Nuchnoi Chanin Nantasenamat Virapong Prachayasittikul Aungkura Supokawej |
author_sort |
Kanokwan Seenprachawong |
title |
Computational identification of miRNAs that modulate the differentiation of mesenchymal stem cells to osteoblasts |
title_short |
Computational identification of miRNAs that modulate the differentiation of mesenchymal stem cells to osteoblasts |
title_full |
Computational identification of miRNAs that modulate the differentiation of mesenchymal stem cells to osteoblasts |
title_fullStr |
Computational identification of miRNAs that modulate the differentiation of mesenchymal stem cells to osteoblasts |
title_full_unstemmed |
Computational identification of miRNAs that modulate the differentiation of mesenchymal stem cells to osteoblasts |
title_sort |
computational identification of mirnas that modulate the differentiation of mesenchymal stem cells to osteoblasts |
publisher |
PeerJ Inc. |
series |
PeerJ |
issn |
2167-8359 |
publishDate |
2016-04-01 |
description |
MicroRNAs (miRNAs) are small endogenous noncoding RNAs that play an instrumental role in post-transcriptional modulation of gene expression. Genes related to osteogenesis (i.e., RUNX2, COL1A1 and OSX) is important in controlling the differentiation of mesenchymal stem cells (MSCs) to bone tissues. The regulated expression level of miRNAs is critically important for the differentiation of MSCs to preosteoblasts. The understanding of miRNA regulation in osteogenesis could be applied for future applications in bone defects. Therefore, this study aims to shed light on the mechanistic pathway underlying osteogenesis by predicting miRNAs that may modulate this pathway. This study investigates RUNX2, which is a major transcription factor for osteogenesis that drives MSCs into preosteoblasts. Three different prediction tools were employed for identifying miRNAs related to osteogenesis using the 3’UTR of RUNX2 as the target gene. Of the 1,023 miRNAs, 70 miRNAs were found by at least two of the tools. Candidate miRNAs were then selected based on their free energy values, followed by assessing the probability of target accessibility. The results showed that miRNAs 23b, 23a, 30b, 143, 203, 217, and 221 could regulate the RUNX2 gene during the differentiation of MSCs to preosteoblasts. |
topic |
miRNAs MicroRNAs Osteogenesis Mesenchymal stem cells Bioinformatics RUNX2 |
url |
https://peerj.com/articles/1976.pdf |
work_keys_str_mv |
AT kanokwanseenprachawong computationalidentificationofmirnasthatmodulatethedifferentiationofmesenchymalstemcellstoosteoblasts AT pornladanuchnoi computationalidentificationofmirnasthatmodulatethedifferentiationofmesenchymalstemcellstoosteoblasts AT chaninnantasenamat computationalidentificationofmirnasthatmodulatethedifferentiationofmesenchymalstemcellstoosteoblasts AT virapongprachayasittikul computationalidentificationofmirnasthatmodulatethedifferentiationofmesenchymalstemcellstoosteoblasts AT aungkurasupokawej computationalidentificationofmirnasthatmodulatethedifferentiationofmesenchymalstemcellstoosteoblasts |
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