Genome-wide targeting of the epigenetic regulatory protein CTCF to gene promoters by the transcription factor TFII-I

• Published in: Proceedings of the National Academy of Sciences - PNAS 2015-02, Vol.112 (7), p.E677-E686
• Main Authors: Peña-Hernández, Rodrigo, Marques, Maud, Hilmi, Khalid, Zhao, Teijun, Saad, Amine, Alaoui-Jamali, Moulay A., del Rincon, Sonia V., Ashworth, Todd, Roy, Ananda L., Emerson, Beverly M., Witcher, Michael
• Format: Article
• Language: English
• Subjects: Biological Sciences; CCCTC-Binding Factor; Cell Line, Tumor; Chromatin; Deoxyribonucleic acid; DNA; Epigenesis, Genetic; Epigenetics; Fractionation; Gene Knockdown Techniques; Genome, Human; Genotype & phenotype; Humans; Mass spectrometry; Phosphorylation; PNAS Plus; Promoter Regions, Genetic; Proteins; Repressor Proteins - genetics; RNA polymerase; Transcription Factors - physiology
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1416674112

Significance CCCTC-binding factor (CTCF) is an epigenetic regulatory protein that is not only functionally diverse, but is also targeted to highly diverse DNA binding sites. CTCF cooperates with accessory proteins to achieve various functional outputs. Further evidence in Drosophila shows that CTCF may also be targeted to chromatin via accessory proteins. The identity of such mammalian proteins remains elusive. Herein, we describe evidence that the transcription factor general transcription factor II-I (TFII-I) targets CTCF binding to metabolism-related genes across the genome. We find that TFII-I regulates the transcription of genes within this network on the level of initiation via RNA polymerase II phosphorylation. These results provide a starting point for understanding a biological network communicating information between chromatin architecture, transcription, and metabolism. CCCTC-binding factor (CTCF) is a key regulator of nuclear chromatin structure and gene regulation. The impact of CTCF on transcriptional output is highly varied, ranging from repression to transcriptional pausing and transactivation. The multifunctional nature of CTCF may be directed solely through remodeling chromatin architecture. However, another hypothesis is that the multifunctional nature of CTCF is mediated, in part, through differential association with protein partners having unique functions. Consistent with this hypothesis, our mass spectrometry analyses of CTCF interacting partners reveal a previously undefined association with the transcription factor general transcription factor II-I (TFII-I). Biochemical fractionation of CTCF indicates that a distinct CTCF complex incorporating TFII-I is assembled on DNA. Unexpectedly, we found that the interaction between CTCF and TFII-I is essential for directing CTCF to the promoter proximal regulatory regions of target genes across the genome, particularly at genes involved in metabolism. At genes coregulated by CTCF and TFII-I, we find knockdown of TFII-I results in diminished CTCF binding, lack of cyclin-dependent kinase 8 (CDK8) recruitment, and an attenuation of RNA polymerase II phosphorylation at serine 5. Phenotypically, knockdown of TFII-I alters the cellular response to metabolic stress. Our data indicate that TFII-I directs CTCF binding to target genes, and in turn the two proteins cooperate to recruit CDK8 and enhance transcription initiation.