Using synthetic genome readers/regulators to interrogate chromatin processes: A brief review

• Published in: Methods (San Diego, Calif.) Calif.), 2024-05, Vol.225, p.20-27
• Main Authors: Philips, Steven J., Danda, Adithi, Ansari, Aseem Z.
• Format: Article
• Language: English
• Subjects: Animals; chemistry; Chromatin - genetics; Chromatin - metabolism; Chromatin Assembly and Disassembly - drug effects; Chromatin Assembly and Disassembly - genetics; COSMIC; CSI; DiSEL; gene expression; Gene Expression Regulation - drug effects; genes; Genome-targeting; genomics; Genomics - methods; Humans; medicine; Nucleosome; nucleosomes; Nucleosomes - genetics; Nucleosomes - metabolism; Nylons - chemistry; Nylons - pharmacology; Polyamide; SEL; SynGR; Synthetic transcription factors; therapeutics; Transcription
• ISSN: 1046-2023; 1095-9130; 1095-9130
• DOI: 10.1016/j.ymeth.2024.03.001

•Cognate Site Identification (CSI) studies reveal the full spectrum of DNA sequences bound by specific SynGRs.•Specificity and Binding Energy Landscapes (SELs) display the entire spectrum of binding sites of a natural or synthetic DNA binder.•Crosslinking of Small Molecules to Isolate Chromatin (COSMIC) allows for direct interrogation of polyamide-DNA interactions in live cells.•Using the SynGR platform and “601” nucleosomes, we can now biochemically and biophysically interrogate the crosstalk of chromatin marks and the nature of chromatin organization.•SynTEF1, a prototype SynGR, provides evidence that SynGRs can be used to target nucleosomes in vitro and repressive heterochromatin in vivo. Aberrant gene expression underlies numerous human ailments. Hence, developing small molecules to target and remedy dysfunctional gene regulation has been a long-standing goal at the interface of chemistry and medicine. A major challenge for designing small molecule therapeutics aimed at targeting desired genomic loci is the minimization of widescale disruption of genomic functions. To address this challenge, we rationally design polyamide-based multi-functional molecules, i.e., Synthetic Genome Readers/Regulators (SynGRs), which, by design, target distinct sequences in the genome. Herein, we briefly review how SynGRs access chromatin-bound and chromatin-free genomic sites, then highlight the methods for the study of chromatin processes using SynGRs on positioned nucleosomes in vitro or disease-causing repressive genomic loci in vivo.