ZNF410 Uniquely Activates the NuRD Component CHD4 to Silence Fetal Hemoglobin Expression

• Published in: Molecular cell Vol. 81; no. 2; pp. 239 - 254.e8
• Main Authors: Lan, Xianjiang, Ren, Ren, Feng, Ruopeng, Ly, Lana C., Lan, Yemin, Zhang, Zhe, Aboreden, Nicholas, Qin, Kunhua, Horton, John R., Grevet, Jeremy D., Mayuranathan, Thiyagaraj, Abdulmalik, Osheiza, Keller, Cheryl A., Giardine, Belinda, Hardison, Ross C., Crossley, Merlin, Weiss, Mitchell J., Cheng, Xiaodong, Shi, Junwei, Blobel, Gerd A.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 21.01.2021
• Subjects: Animals; Binding Sites; CHD4; Chlorocebus aethiops; COS Cells; CRISPR screen; CRISPR-Cas Systems; DNA - genetics; DNA - metabolism; erythroid biology; Erythroid Precursor Cells - cytology; Erythroid Precursor Cells - metabolism; Erythroid Precursor Cells - transplantation; Fetal Blood - cytology; Fetal Blood - metabolism; fetal hemoglobin; Fetal Hemoglobin - genetics; Fetal Hemoglobin - metabolism; Fetus; Gene Editing; HEK293 Cells; hemoglobin switching; Heterografts; Humans; Mi-2 Nucleosome Remodeling and Deacetylase Complex - chemistry; Mi-2 Nucleosome Remodeling and Deacetylase Complex - genetics; Mi-2 Nucleosome Remodeling and Deacetylase Complex - metabolism; Mice; Models, Molecular; Mouse Embryonic Stem Cells - cytology; NuRD; Protein Binding; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand; Protein Interaction Domains and Motifs; sickle cell disease; transcription; transcription factor; Transcription Factors - chemistry; Transcription Factors - genetics; Transcription Factors - metabolism; Transcriptional Activation; ZNF410; transcription factor; fetal hemoglobin; transcription; hemoglobin switching; CRISPR screen; erythroid biology; CHD4; NuRD; ZNF410; sickle cell disease
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2020.11.006

Metazoan transcription factors typically regulate large numbers of genes. Here we identify via a CRISPR-Cas9 genetic screen ZNF410, a pentadactyl DNA-binding protein that in human erythroid cells directly activates only a single gene, the NuRD component CHD4. Specificity is conveyed by two highly evolutionarily conserved clusters of ZNF410 binding sites near the CHD4 gene with no counterparts elsewhere in the genome. Loss of ZNF410 in adult-type human erythroid cell culture systems and xenotransplantation settings diminishes CHD4 levels and derepresses the fetal hemoglobin genes. While previously known to be silenced by CHD4, the fetal globin genes are exposed here as among the most sensitive to reduced CHD4 levels. In vitro DNA binding assays and crystallographic studies reveal the ZNF410-DNA binding mode. ZNF410 is a remarkably selective transcriptional activator in erythroid cells, and its perturbation might offer new opportunities for treatment of hemoglobinopathies. [Display omitted] •A CRISPR screen implicates ZNF410 in fetal globin gene repression•The CHD4 gene is the singular direct ZNF410 target in erythroid cells•Fetal globin genes are exquisitely sensitive to CHD4 levels•Five C2H2 zinc fingers of ZNF410 recognize the major groove of a 14-bp sequence Lan et al. show that the transcription factor ZNF410 has a single direct target gene, the NuRD component CHD4, through which it silences the fetal-type β-globin genes in adult erythroid cells. The exquisite specificity of ZNF410 could be exploited therapeutically for treatment of hemoglobinopathies.