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

Abstract

c 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 nextgeneration 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.

Towards a predictive model of chromatin 3D organization

“…Furthermore, YY1 is enriched with CTCF at TAD borders [21]. As is the case in Drosophila , TFIIIC colocalizes with CTCF, cohesin, and the DNA-binding tumor suppressor protein Prdm5 at many locations of the mammalian genome [22–24]. The POZ-Zn finger transcription factor Kaiso interacts with CTCF but its genome-wide distribution or possible role in 3D organization has not been explored in detail [25].…”

Architectural proteins: regulators of 3D genome organization in cell fate

“…Recent experiments showing that tRNA genes can block enhancer function and that TFIIIC co-localizes with CTCF at many ETC loci through the mouse and human genomes suggest a conservation in the function of TFIIIC as an architectural protein from yeast to humans [14]. Other proteins shown to co-localize or directly interact with CTCF in vertebrates include YY1, Kaiso, chromodomain helicase DNA-binding protein 8 (CHD8), PARP1, MYC-associated zinc-finger protein (MAZ), JUND, zinc-finger protein 143 (ZNF143), PR domain zinc-finger protein 5 (PRDM5) and nucleophosmin [15-17]. Drosophila has also been a rich source of information aimed at understanding the structure and organization of this class of proteins.…”

TFIIIC binding to Alu elements controls gene expression via chromatin looping and histone acetylation

“…We then asked how TFIIIC could promote chromatin looping with CTCF, which is enriched at promoter regions 22 , and interacts with TFIIIC 23 . Notably, CTCF occupancy at TGAPs was significantly higher compared to a random set of promoters ( fig.…”