Differential Expression Profiling of Long Noncoding RNA and mRNA during Osteoblast Differentiation in Mouse
Long noncoding RNAs (lncRNAs) are emerging as an important controller affecting metabolic tissue development, signaling, and function. However, little is known about the function and profile of lncRNAs in osteoblastic differentiation in mice. Here, we analyzed the RNA-sequencing (RNA-Seq) datasets o...
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| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2018-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2018/7691794 |
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| author | Minjung Kim Youngseok Yu Ji-Hoi Moon InSong Koh Jae-Hyung Lee |
| author_facet | Minjung Kim Youngseok Yu Ji-Hoi Moon InSong Koh Jae-Hyung Lee |
| author_sort | Minjung Kim |
| collection | DOAJ |
| description | Long noncoding RNAs (lncRNAs) are emerging as an important controller affecting metabolic tissue development, signaling, and function. However, little is known about the function and profile of lncRNAs in osteoblastic differentiation in mice. Here, we analyzed the RNA-sequencing (RNA-Seq) datasets obtained for 18 days in two-day intervals from neonatal mouse calvarial pre-osteoblast-like cells. Over the course of osteoblast differentiation, 4058 mRNAs and 3948 lncRNAs were differentially expressed, and they were grouped into 12 clusters according to the expression pattern by fuzzy c-means clustering. Using weighted gene coexpression network analysis, we identified 9 modules related to the early differentiation stage (days 2–8) and 7 modules related to the late differentiation stage (days 10–18). Gene ontology and KEGG pathway enrichment analysis revealed that the mRNA and lncRNA upregulated in the late differentiation stage are highly associated with osteogenesis. We also identified 72 mRNA and 89 lncRNAs as potential markers including several novel markers for osteoblast differentiation and activation. Our findings provide a valuable resource for mouse lncRNA study and improves our understanding of the biology of osteoblastic differentiation in mice. |
| format | Article |
| id | doaj-art-180c01d9581046208bf62ea6faff7723 |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2018-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-180c01d9581046208bf62ea6faff77232025-02-03T06:12:18ZengWileyInternational Journal of Genomics2314-436X2314-43782018-01-01201810.1155/2018/76917947691794Differential Expression Profiling of Long Noncoding RNA and mRNA during Osteoblast Differentiation in MouseMinjung Kim0Youngseok Yu1Ji-Hoi Moon2InSong Koh3Jae-Hyung Lee4Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of KoreaDepartment of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of KoreaDepartment of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of KoreaDepartment of Physiology, College of Medicine, Hanyang University, Seoul, Republic of KoreaDepartment of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of KoreaLong noncoding RNAs (lncRNAs) are emerging as an important controller affecting metabolic tissue development, signaling, and function. However, little is known about the function and profile of lncRNAs in osteoblastic differentiation in mice. Here, we analyzed the RNA-sequencing (RNA-Seq) datasets obtained for 18 days in two-day intervals from neonatal mouse calvarial pre-osteoblast-like cells. Over the course of osteoblast differentiation, 4058 mRNAs and 3948 lncRNAs were differentially expressed, and they were grouped into 12 clusters according to the expression pattern by fuzzy c-means clustering. Using weighted gene coexpression network analysis, we identified 9 modules related to the early differentiation stage (days 2–8) and 7 modules related to the late differentiation stage (days 10–18). Gene ontology and KEGG pathway enrichment analysis revealed that the mRNA and lncRNA upregulated in the late differentiation stage are highly associated with osteogenesis. We also identified 72 mRNA and 89 lncRNAs as potential markers including several novel markers for osteoblast differentiation and activation. Our findings provide a valuable resource for mouse lncRNA study and improves our understanding of the biology of osteoblastic differentiation in mice.http://dx.doi.org/10.1155/2018/7691794 |
| spellingShingle | Minjung Kim Youngseok Yu Ji-Hoi Moon InSong Koh Jae-Hyung Lee Differential Expression Profiling of Long Noncoding RNA and mRNA during Osteoblast Differentiation in Mouse International Journal of Genomics |
| title | Differential Expression Profiling of Long Noncoding RNA and mRNA during Osteoblast Differentiation in Mouse |
| title_full | Differential Expression Profiling of Long Noncoding RNA and mRNA during Osteoblast Differentiation in Mouse |
| title_fullStr | Differential Expression Profiling of Long Noncoding RNA and mRNA during Osteoblast Differentiation in Mouse |
| title_full_unstemmed | Differential Expression Profiling of Long Noncoding RNA and mRNA during Osteoblast Differentiation in Mouse |
| title_short | Differential Expression Profiling of Long Noncoding RNA and mRNA during Osteoblast Differentiation in Mouse |
| title_sort | differential expression profiling of long noncoding rna and mrna during osteoblast differentiation in mouse |
| url | http://dx.doi.org/10.1155/2018/7691794 |
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