Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation

Bone continuously undergoes remodeling by a tightly regulated process that involves osteoblast differentiation from Mesenchymal Stem Cells (MSC). However, commitment of MSC to osteoblastic lineage is a poorly understood process. Chromatin organization functions as a molecular gatekeeper of DNA funct...

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Bibliographic Details
Published in:PloS one 2016-02, Vol.11 (2), p.e0148619-e0148619
Main Authors: Thompson, Bethtrice, Varticovski, Lyuba, Baek, Songjoon, Hager, Gordon L
Format: Article
Language:English
Subjects:
Adipocytes
Adipogenesis - genetics
Analysis
Binding Sites
Biocompatibility
Biology
Biology and Life Sciences
Bone remodeling
Cell Cycle - genetics
Cell Differentiation - genetics
Cell Line
Cellular communication
Chromatin
Chromatin - genetics
Chromatin - metabolism
Chromatin Immunoprecipitation
Cluster Analysis
Computational Biology - methods
Correlation analysis
Cues
Cytokines
Deoxyribonuclease
Deoxyribonucleic acid
Differentiation
DNA
Enhancers
Extracellular matrix
Gene expression
Gene Expression Profiling
Gene Expression Regulation
Gene sequencing
Genetic regulation
Genome-wide association studies
Genome-Wide Association Study - methods
Genomes
High-Throughput Nucleotide Sequencing
Hormones
Humans
Hypersensitivity
Laboratories
Medicine and Health Sciences
Mesenchyme
Molecular Sequence Annotation
Mutation
Nucleotide Motifs
Osteoblastogenesis
Osteoblasts
Osteoblasts - cytology
Osteoblasts - metabolism
Osteogenesis
Osteogenesis - physiology
Osteoporosis
Pathways
Promoters
Protein Binding
Regulatory Sequences, Ribonucleic Acid
Signal Transduction
Stem cells
Temperature
Transcription factors
Transcription Factors - metabolism
Transcriptome
Wnt protein
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Description
Summary:Bone continuously undergoes remodeling by a tightly regulated process that involves osteoblast differentiation from Mesenchymal Stem Cells (MSC). However, commitment of MSC to osteoblastic lineage is a poorly understood process. Chromatin organization functions as a molecular gatekeeper of DNA functions. Detection of sites that are hypersensitive to Dnase I has been used for detailed examination of changes in response to hormones and differentiation cues. To investigate the early steps in commitment of MSC to osteoblasts, we used a model human temperature-sensitive cell line, hFOB. When shifted to non-permissive temperature, these cells undergo "spontaneous" differentiation that takes several weeks, a process that is greatly accelerated by osteogenic induction media. We performed Dnase I hypersensitivity assays combined with deep sequencing to identify genome-wide potential regulatory events in cells undergoing early steps of commitment to osteoblasts. Massive reorganization of chromatin occurred within hours of differentiation. Whereas ~30% of unique DHS sites were located in the promoters, the majority was outside of the promoters, designated as enhancers. Many of them were at novel genomic sites and need to be confirmed experimentally. We developed a novel method for identification of cellular networks based solely on DHS enhancers signature correlated to gene expression. The analysis of enhancers that were unique to differentiating cells led to identification of bone developmental program encompassing 147 genes that directly or indirectly participate in osteogenesis. Identification of these pathways provided an unprecedented view of genomic regulation during early steps of differentiation and changes related to WNT, AP-1 and other pathways may have therapeutic implications.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0148619