HOXC9 directly regulates distinct sets of genes to coordinate diverse cellular processes during neuronal differentiation

Xiangwei Wang, Jeong-Hyeon Choi, Jane Ding, Liqun Yang, Lambert C. Ngoka, Eun J. Lee, Yunhong Zha, Ling Mao, Bilian Jin, Mingqiang Ren, John Kenneth Cowell, Shuang Huang, Huidong Shi, Hongjuan Cui, Hanfei Ding

Research output: Contribution to journalArticlepeer-review

21 Scopus citations


Background: Cellular differentiation is characterized by the acquisition of specialized structures and functions, cell cycle exit, and global attenuation of the DNA damage response. It is largely unknown how these diverse cellular events are coordinated at the molecular level during differentiation. We addressed this question in a model system of neuroblastoma cell differentiation induced by HOXC9.Results: We conducted a genome-wide analysis of the HOXC9-induced neuronal differentiation program. Microarray gene expression profiling revealed that HOXC9-induced differentiation was associated with transcriptional regulation of 2,370 genes, characterized by global upregulation of neuronal genes and downregulation of cell cycle and DNA repair genes. Remarkably, genome-wide mapping by ChIP-seq demonstrated that HOXC9 bound to 40% of these genes, including a large number of genes involved in neuronal differentiation, cell cycle progression and the DNA damage response. Moreover, we showed that HOXC9 interacted with the transcriptional repressor E2F6 and recruited it to the promoters of cell cycle genes for repressing their expression.Conclusions: Our results demonstrate that HOXC9 coordinates diverse cellular processes associated with differentiation by directly activating and repressing the transcription of distinct sets of genes.

Original languageEnglish (US)
Article number830
JournalBMC Genomics
Issue number1
StatePublished - Nov 25 2013


  • Cell cycle arrest
  • DNA damage response
  • E2F6
  • HOXC9
  • Neuroblastoma
  • Neuronal differentiation

ASJC Scopus subject areas

  • Biotechnology
  • Genetics


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