Modulation of NF-κB-dependent gene transcription using programmable DNA minor groove binders

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 109; no. 4; pp. 1023 - 1028
• Main Authors: Raskatov, Jevgenij A, Meier, Jordan L, Puckett, James W, Yang, Fei, Ramakrishnan, Parameswaran, Dervan, Peter B
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 24.01.2012; National Acad Sciences
• Subjects: Antagonists; Biological Sciences; Cancer; Cell death; Cell Line, Tumor; Chromatin; Chromatin Immunoprecipitation; Differentiation; DNA; DNA - metabolism; Gene Expression Profiling; Gene Expression Regulation - drug effects; Gene Expression Regulation - physiology; genes; Heterocyclic Compounds, 3-Ring; Humans; Immune response; Immunoprecipitation; Interleukin 6; Interleukin 8; Interleukin-6 - genetics; Interleukin-6 - metabolism; Interleukin-8 - genetics; Interleukin-8 - metabolism; Microscopy, Confocal; NF- Kappa B protein; NF-kappa B - antagonists & inhibitors; NF-kappa B - metabolism; Nucleic Acid Denaturation; Nylons - metabolism; Nylons - pharmacology; Physical Sciences; Plasminogen Activator Inhibitor 1 - metabolism; polyamides; Promoters; Pyridines; Real-Time Polymerase Chain Reaction; reverse transcriptase polymerase chain reaction; transcription (genetics); Transcription factors; Transcription, Genetic - physiology
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1118506109

Nuclear factor κB (NF-κB) is a transcription factor that regulates various aspects of immune response, cell death, and differentiation as well as cancer. In this study we introduce the Py-Im polyamide 1 that binds preferentially to the sequences 5'-WGGWWW-3' and 5'GGGWWW-3'. The compound is capable of binding to κB sites and reducing the expression of various NF-κB–driven genes including IL6 and IL8 by qRT-PCR. Chromatin immunoprecipitation experiments demonstrate a reduction of p65 occupancy within the proximal promoters of those genes. Genome-wide expression analysis by RNA-seq compares the DNA-binding polyamide with the well-characterized NF-κB inhibitor PS1145, identifies overlaps and differences in affected gene groups, and shows that both affect comparable numbers of TNF-α–inducible genes. Inhibition of NF-κB DNA binding via direct displacement of the transcription factor is a potential alternative to the existing antagonists.