C2H2 zinc finger proteins greatly expand the human regulatory lexicon

• Published in: Nature biotechnology 2015-05, Vol.33 (5), p.555-562
• Main Authors: Najafabadi, Hamed S, Mnaimneh, Sanie, Schmitges, Frank W, Garton, Michael, Lam, Kathy N, Yang, Ally, Albu, Mihai, Weirauch, Matthew T, Radovani, Ernest, Kim, Philip M, Greenblatt, Jack, Frey, Brendan J, Hughes, Timothy R
• Format: Article
• Language: English
• Subjects: 13/106; 13/44; 38/23; 38/77; 42/47; 631/114/2114; 631/208/191; 631/208/200; 82/80; Agriculture; Amino acids; Binding sites; Bioinformatics; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Carrier Proteins - genetics; Carrier Proteins - metabolism; Chromatin - metabolism; Deoxyribonucleic acid; DNA; DNA-Binding Proteins - genetics; Gene Expression Regulation; Genome, Human; Genomes; Humans; Life Sciences; Nuclear Proteins - genetics; Nuclear Proteins - metabolism; Properties; Protein Binding; Protein research; Proteins; Regulatory Sequences, Nucleic Acid; Repressor Proteins - genetics; Repressor Proteins - metabolism; resource; Retroelements - genetics; Transcription factors
• ISSN: 1087-0156; 1546-1696
• DOI: 10.1038/nbt.3128

Comprehensive analysis of the binding specificities of C2H2 zinc finger proteins reveals their DNA recognition code. Cys2-His2 zinc finger (C2H2-ZF) proteins represent the largest class of putative human transcription factors. However, for most C2H2-ZF proteins it is unknown whether they even bind DNA or, if they do, to which sequences. Here, by combining data from a modified bacterial one-hybrid system with protein-binding microarray and chromatin immunoprecipitation analyses, we show that natural C2H2-ZFs encoded in the human genome bind DNA both in vitro and in vivo , and we infer the DNA recognition code using DNA-binding data for thousands of natural C2H2-ZF domains. In vivo binding data are generally consistent with our recognition code and indicate that C2H2-ZF proteins recognize more motifs than all other human transcription factors combined. We provide direct evidence that most KRAB-containing C2H2-ZF proteins bind specific endogenous retroelements (EREs), ranging from currently active to ancient families. The majority of C2H2-ZF proteins, including KRAB proteins, also show widespread binding to regulatory regions, indicating that the human genome contains an extensive and largely unstudied adaptive C2H2-ZF regulatory network that targets a diverse range of genes and pathways.