Comparative analysis of osteoblast gene expression profiles and Runx2 genomic occupancy of mouse and human osteoblasts in vitro.
Gene
; 626: 119-131, 2017 Aug 30.
Article
em En
| MEDLINE
| ID: mdl-28502869
ABSTRACT
Fast progress of the next generation sequencing (NGS) technology has allowed global transcriptional profiling and genome-wide mapping of transcription factor binding sites in various cellular contexts. However, limited number of replicates and high amount of data processing may weaken the significance of the findings. Comparative analyses of independent data sets acquired in the different laboratories would greatly increase the validity of the data. Runx2 is the key transcription factor regulating osteoblast differentiation and bone formation. We performed a comparative analysis of three published Runx2 data sets of chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) analysis in osteoblasts from mouse and human origin. Moreover, we assessed the similarity of the corresponding transcription data of these studies available online. The ChIP-seq data analysis confirmed general features of Runx2 binding, including location at genic vs intergenic regions and abundant Runx2 binding on promoters of the highly expressed genes. We also found high frequency of Runx2 DNA binding without a consensus Runx2 motif at the binding site. Importantly, mouse and human Runx2 showed moderately similar binding patterns in terms of peak-associated closest genes and their associated genomic ontology (GO) pathways. Accordingly, the gene expression profiles were highly similar and osteoblastic phenotype was prominent in the differentiated stage in both species. In conclusion, ChIP-seq method shows good reproducibility in the context of mature osteoblasts, and mouse and human osteoblast models resemble each other closely in Runx2 binding and in gene expression profiles, supporting the use of these models as adequate tools in studying osteoblast differentiation.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Osteoblastos
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Cromatina
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Subunidade alfa 1 de Fator de Ligação ao Core
Tipo de estudo:
Prognostic_studies
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Systematic_reviews
Limite:
Animals
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Humans
Idioma:
En
Revista:
Gene
Ano de publicação:
2017
Tipo de documento:
Article
País de afiliação:
Finlândia
País de publicação:
HOLANDA
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HOLLAND
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NETHERLANDS
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NL
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PAISES BAJOS
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THE NETHERLANDS