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Open Access Research

Myc and Miz-1 have coordinate genomic functions including targeting Hox genes in human embryonic stem cells

Natalia Varlakhanova123, Rebecca Cotterman123, Keith Bradnam2, Ian Korf24 and Paul S Knoepfler123*

Author Affiliations

1 Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Sacramento, CA, USA

2 Genome Center, University of California Davis School of Medicine, Sacramento, CA, USA

3 Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, Sacramento, CA, USA

4 Department of Molecular and Cell Biology, University of California Davis School of Medicine, Sacramento, CA, USA

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Epigenetics & Chromatin 2011, 4:20  doi:10.1186/1756-8935-4-20

Published: 4 November 2011

Abstract

Background

A proposed role for Myc in maintaining mouse embryonic stem (ES) cell pluripotency is transcriptional repression of key differentiation-promoting genes, but detail of the mechanism has remained an important open topic.

Results

To test the hypothesis that the zinc finger protein Miz-1 plays a central role, in the present work we conducted chromatin immunoprecipitation/microarray (ChIP-chip) analysis of Myc and Miz-1 in human ES cells, finding homeobox (Hox) genes as the most significant functional class of Miz-1 direct targets. Miz-1 differentiation-associated target genes specifically lack acetylated lysine 9 and trimethylated lysine 4 of histone H3 (AcH3K9 and H3K4me3) 9 histone marks, consistent with a repressed transcriptional state. Almost 30% of Miz-1 targets are also bound by Myc and these cobound genes are mostly factors that promote differentiation including Hox genes. Knockdown of Myc increased expression of differentiation genes directly bound by Myc and Miz-1, while a subset of the same genes is downregulated by Miz-1 loss-of-function. Myc and Miz-1 proteins interact with each other and associate with several corepressor factors in ES cells, suggesting a mechanism of repression of differentiation genes.

Conclusions

Taken together our data indicate that Miz-1 and Myc maintain human ES cell pluripotency by coordinately suppressing differentiation genes, particularly Hox genes. These data also support a new model of how Myc and Miz-1 function on chromatin.