Genomic and Proteomic Analyses of Prdm5 Reveal Interactions with Insulator Binding Proteins in Embryonic Stem Cells

Abstract

PRDM proteins belong to the SET domain protein family, which is involved in the regulation of gene expression. Although few PRDM members possess histone methyltransferase activity, the molecular mechanisms by which the other members exert transcriptional regulation remain to be delineated. In this study, we find that Prdm5 is highly expressed in mouse embryonic stem (mES) cells and exploit this cellular system to characterize molecular functions of Prdm5. By combining proteomics and next-generation sequencing technologies, we identify Prdm5 interaction partners and genomic occupancy. We demonstrate that although Prdm5 is dispensable for mES cell maintenance, it directly targets genomic regions involved in early embryonic development and affects the expression of a subset of developmental regulators during cell differentiation. Importantly, Prdm5 interacts with Ctcf, cohesin, and TFIIIC and cooccupies genomic loci. In summary, our data indicate how Prdm5 modulates transcription by interacting with factors involved in genome organization in mouse embryonic stem cells.

SUPPLEMENTAL MATERIAL

Supplemental material for this article may be found at http://dx.doi.org/10.1128/MCB.00545-13.

ACKNOWLEDGMENTS

We are grateful to Anita Friismose and Cord Brakebusch for assistance in the transgenic core facility. We acknowledge Bettina Mentz and Maddalena Arigoni for excellent technical assistance and Klaus Hansen for suggestions and help with biochemical experiments.

Work in our laboratories was supported by the Danish National Research Foundation, the Danish National Advanced Technology Foundation, the Novo Nordisk Foundation, European Commission (EC) FP7 programs (ONCOMIRS, grant agreement number 201102, and APO-SYS), the Lundbeck Foundation, and the Danish Cancer Society. G.G.G. is supported by an American-Italian Cancer Foundation postdoctoral research fellowship. C.F. is supported by a Marie Curie IEF and EMBO long-term fellowship.

This publication reflects only the authors' views. The EC is not liable for any use that may be made of the information herein.