Identification of Putative Target Genes of the Transcription Factor RUNX2

Comparisons of the genomes of Neandertals and Denisovans with present-day human genomes have suggested that the gene RUNX2, which encodes a transcription factor, may have been positively selected during early human evolution. Here, we overexpress RUNX2 in ten human cell lines and identify genes that are directly or indirectly affected by RUNX2 expression. We find a number of genes not previously known to be affected by RUNX2 expression, in particular BIRC3, genes encoded on the mitochondrial genome, and several genes involved in bone and tooth formation. These genes are likely to provide inroads into pathways affected by RUNX2 and potentially by the evolutionary changes that affected RUNX2 in modern humans.

• Publication year

  2013

• Venue

  PLoS ONE

• Publication date

  2013-12-12

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1371/journal.pone.0083218PMID 24349465PMCID 3861491
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• R: A language and environment for statistical computing.

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  2011influential reference
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  2010influential reference
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  2010cited by this paper
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