Open Access Highly Accessed Research article

Genome-wide map of quantified epigenetic changes during in vitro chondrogenic differentiation of primary human mesenchymal stem cells

Sarah R Herlofsen1*, Jan Christian Bryne2, Torill Høiby1, Li Wang3, Robbyn Issner3, Xiaolan Zhang3, Michael J Coyne3, Patrick Boyle3, Hongcang Gu3, Leonardo A Meza-Zepeda2, Philippe Collas4, Tarjei S Mikkelsen35 and Jan E Brinchmann14

Author Affiliations

1 Institute of Immunology and Norwegian Center for Stem Cell Research, Oslo University Hospital Rikshospitalet, Oslo 0424, Norway

2 Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo 0424, Norway

3 Broad Institute of MIT and Harvard, Massachusetts 02142, USA

4 Institute of Basic Medical Sciences, Department of Biochemistry, University of Oslo, Oslo 0317, Norway

5 Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA

For all author emails, please log on.

BMC Genomics 2013, 14:105  doi:10.1186/1471-2164-14-105

Published: 15 February 2013



For safe clinical application of engineered cartilage made from mesenchymal stem cells (MSCs), molecular mechanisms for chondrogenic differentiation must be known in detail. Changes in gene expression and extracellular matrix synthesis have been extensively studied, but the epigenomic modifications underlying these changes have not been described. To this end we performed whole-genome chromatin immunoprecipitation and deep sequencing to quantify six histone modifications, reduced representation bisulphite sequencing to quantify DNA methylation and mRNA microarrays to quantify gene expression before and after 7 days of chondrogenic differentiation of MSCs in an alginate scaffold. To add to the clinical relevance of our observations, the study is based on primary bone marrow-derived MSCs from four donors, allowing us to investigate inter-individual variations.


We see two levels of relationship between epigenetic marking and gene expression. First, a large number of genes ontogenetically linked to MSC properties and the musculoskeletal system are epigenetically prepatterned by moderate changes in H3K4me3 and H3K9ac near transcription start sites. Most of these genes remain transcriptionally unaltered. Second, transcriptionally upregulated genes, more closely associated with chondrogenesis, are marked by H3K36me3 in gene bodies, highly increased H3K4me3 and H3K9ac on promoters and 5' end of genes, and increased H3K27ac and H3K4me1 marking in at least one enhancer region per upregulated gene. Within the 7-day time frame, changes in promoter DNA methylation do not correlate significantly with changes in gene expression. Inter-donor variability analysis shows high level of similarity between the donors for this data set.


Histone modifications, rather than DNA methylation, provide the primary epigenetic control of early differentiation of MSCs towards the chondrogenic lineage.