SOX9 regulates multiple genes in chondrocytes, including genes encoding ECM proteins, ECM modification enzymes, receptors, and transporters

PLoS One. 2014 Sep 17;9(9):e107577. doi: 10.1371/journal.pone.0107577. eCollection 2014.

Abstract

The transcription factor SOX9 plays an essential role in determining the fate of several cell types and is a master factor in regulation of chondrocyte development. Our aim was to determine which genes in the genome of chondrocytes are either directly or indirectly controlled by SOX9. We used RNA-Seq to identify genes whose expression levels were affected by SOX9 and used SOX9 ChIP-Seq to identify those genes that harbor SOX9-interaction sites. For RNA-Seq, the RNA expression profile of primary Sox9flox/flox mouse chondrocytes infected with Ad-CMV-Cre was compared with that of the same cells infected with a control adenovirus. Analysis of RNA-Seq data indicated that, when the levels of Sox9 mRNA were decreased more than 8-fold by infection with Ad-CMV-Cre, 196 genes showed a decrease in expression of at least 4-fold. These included many cartilage extracellular matrix (ECM) genes and a number of genes for ECM modification enzymes (transferases), membrane receptors, transporters, and others. In ChIP-Seq, 75% of the SOX9-interaction sites had a canonical inverted repeat motif within 100 bp of the top of the peak. SOX9-interaction sites were found in 55% of the genes whose expression was decreased more than 8-fold in SOX9-depleted cells and in somewhat fewer of the genes whose expression was reduced more than 4-fold, suggesting that these are direct targets of SOX9. The combination of RNA-Seq and ChIP-Seq has provided a fuller understanding of the SOX9-controlled genetic program of chondrocytes.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites
  • Chondrocytes / metabolism*
  • Chromatin Immunoprecipitation
  • Extracellular Matrix Proteins / genetics*
  • Extracellular Matrix Proteins / metabolism*
  • Gene Expression
  • Gene Expression Profiling
  • Gene Expression Regulation*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Mice
  • Mice, Knockout
  • Nucleotide Motifs
  • Position-Specific Scoring Matrices
  • Protein Binding
  • Protein Transport
  • SOX9 Transcription Factor / genetics
  • SOX9 Transcription Factor / metabolism*

Substances

  • Extracellular Matrix Proteins
  • SOX9 Transcription Factor