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This article is part of the supplement: Selected articles from the Twelfth Asia Pacific Bioinformatics Conference (APBC 2014): Genomics

Open Access Proceedings

Accumulation of CTCF-binding sites drives expression divergence between tandemly duplicated genes in humans

Ben-Yang Liao* and Andrew Ying-Fei Chang

  • * Corresponding author: Ben-Yang Liao

Author Affiliations

Division of Biostatistics & Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County 350, Taiwan, R.O.C

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BMC Genomics 2014, 15(Suppl 1):S8  doi:10.1186/1471-2164-15-S1-S8

Published: 24 January 2014



During eukaryotic genome evolution, tandem gene duplication is the most frequent event giving rise to clustered gene families. However, how expression divergence between tandemly duplicated genes has emerged and maintained remain unclear. In particular, it is unknown if epigenetic regulators have been involved in the process.


We demonstrate that CCCTC-binding factor (CTCF), the master epigenetic regulator and the only known insulator protein in humans, has played a predominant role in generating divergence in both expression profiles and expression levels between adjacent paralogs in the human genome. This phenomenon was not observed for non-paralogous adjacent genes. After tandem duplication events, CTCF-binding sites gradually accumulate between paralogs. This trend was more prominent for genes involved in particular functions.


The accumulation of CTCF-binding sites drives expression divergence of tandemly duplicated genes. This process is likely targeted by natural selection. Our study reveals the importance of CTCF to the evolution of animal diversity and complexity.

epigenetics; DNA methylation; genome architecture; ChIP-seq; RNA-seq