Research Highlights

Nature Reports Stem Cells
Published online: 19 June 2008 | doi:10.1038/stemcells.2008.94

Two networks of pluripotency

Monya Baker¹

An analysis of transcription factor binding sites finds clusters that clarify cooperative binding

The list of factors that contribute to pluripotency is long and growing, but the diagram of how these proteins interact with the genome and with each other is far from complete. Publishing in Cell, researchers led by Chia-Lin Wei and Huck-Hui Ng at the Genome Institute of Singapore probed these interactions by analyzing where and how a baker's dozen of transcription factors bind in the genome.

Pluripotency transcription factors bind DNA in clusters

Huck-Hui Ng at the Genome Institute of Singapore

To conduct their investigation, the researchers applied a recently reported technique called ChIP-seq to transcription factors well known for their roles in mouse embryonic stem (ES) cells. ChIP-seq combines a technique that collects the DNA fragments to which transcription factors bind (chromatin immunoprecipitation) with ultra-high-throughput sequencing. This method can search out genetic sites to which particular transcription factors bind in particular cell types. Michael Teitell, an ES scientist at the University of California, Los Angeles, says more labs are adopting this method, partly because other techniques can be biased to particular segments of the genome. "The main reason to be excited is that there is no limitation to the areas of the genome that can be interrogated and the depth to which it can be covered by sequencing."

Wei and Ng's analysis describes the transcription factors as "wired into the genome" in two clusters whose binding sites often overlap extensively. The first cluster contains an all-star cast including Nanog, Oct4, Sox2, Smad1 and Stat3. The second, smaller cluster consists of c-Myc (an oncogene that boosts reprogramming efficiency), n-Myc, Zfx and E2f1.

The analysis also sheds light on how the factors bind cooperatively. For example, the binding sequences for Sox2 and Oct4 often occurred together as a motif, supporting the idea that a heterodimer of those proteins is the functional binding unit. In another experiment to explore cooperative binding, the researchers found that depleting Oct4 lowered the binding rates for Smad1 and Stat3, but Oct4 binding was undisturbed by disruptions to these pathways. Researchers also found regions of the genome that were co-occupied by multiple transcription factors within ES cells, providing both further evidence of their interaction and insights.

Earlier this year, a study led by Stuart Orkin used a different technique to analyze the binding sites of a slightly different set of nine transcription factors. Ng and Wei speculate that future work integrating these data sets will prove useful in identifying the essentials of gene-regulatory networks necessary to the ES-cell state.²

Monya Baker is editor of Nature Reports Stem Cells.