Identification of differentially methylated regions in new genes associated with knee osteoarthritis

Carolina A. Bonin, Eric A. Lewallen, Saurabh Baheti, Elizabeth Bradley, Michael J. Stuart, Daniel J. Berry, Andre J van Wijnen, Jennifer J Westendorf

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Epigenetic changes in articular chondrocytes are associated with osteoarthritis (OA) disease progression. Numerous studies have identified differentially methylated cytosines in OA tissues; however, the consequences of altered CpG methylation at single nucleotides on gene expression and phenotypes are difficult to predict. With the objective of detecting novel genes relevant to OA, we conducted a genome-wide assessment of differentially methylated sites (DMSs) and differentially methylated regions (DMRs). DNA was extracted from visually damaged and normal appearing, non-damaged human knee articular cartilage from the same joint and then subjected to reduced representation bisulfite sequencing. DMRs were identified using a genome-wide systematic bioinformatics approach. A sliding-window of 500. bp was used for screening the genome for regions with clusters of DMSs. Gene expression levels were assessed and cell culture demethylation experiments were performed to further examine top candidate genes associated with damaged articular cartilage. More than 1000 DMRs were detected in damaged osteoarthritic cartilage. Nineteen of these contained five or more DMSs and were located in gene promoters or first introns and exons. Gene expression assessment revealed that hypermethylated DMRs in damaged samples were more consistently associated with gene repression than hypomethylated DMRs were with gene activation. Accordingly, a demethylation agent induced expression of most hypermethylated genes in chondrocytes. Our study revealed the utility of a systematic DMR search as an alternative to focusing on single nucleotide data. In particular, this approach uncovered promising candidates for functional studies such as the hypermethylated protein-coding genes FOXP4 and SHROOM1, which appear to be linked to OA pathology in humans and warrant further investigation.

Original languageEnglish (US)
JournalGene
DOIs
StateAccepted/In press - Sep 22 2015

Fingerprint

Knee Osteoarthritis
Osteoarthritis
Genes
Articular Cartilage
Genome
Chondrocytes
Gene Expression
Nucleotides
Joints
Cytosine
Computational Biology
Epigenomics
Introns
Methylation
Transcriptional Activation
Cartilage
Disease Progression
Exons
Knee
Cell Culture Techniques

Keywords

  • Articular cartilage
  • Differentially methylated regions
  • DNA methylation
  • FOXP4
  • SHROOM1

ASJC Scopus subject areas

  • Genetics

Cite this

Identification of differentially methylated regions in new genes associated with knee osteoarthritis. / Bonin, Carolina A.; Lewallen, Eric A.; Baheti, Saurabh; Bradley, Elizabeth; Stuart, Michael J.; Berry, Daniel J.; van Wijnen, Andre J; Westendorf, Jennifer J.

In: Gene, 22.09.2015.

Research output: Contribution to journalArticle

Bonin, Carolina A. ; Lewallen, Eric A. ; Baheti, Saurabh ; Bradley, Elizabeth ; Stuart, Michael J. ; Berry, Daniel J. ; van Wijnen, Andre J ; Westendorf, Jennifer J. / Identification of differentially methylated regions in new genes associated with knee osteoarthritis. In: Gene. 2015.
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