Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch

• Published in: Cell Vol. 173; no. 2; pp. 430 - 442.e17
• Main Authors: Liu, Nan, Hargreaves, Victoria V., Zhu, Qian, Kurland, Jesse V., Hong, Jiyoung, Kim, Woojin, Sher, Falak, Macias-Trevino, Claudio, Rogers, Julia M., Kurita, Ryo, Nakamura, Yukio, Yuan, Guo-Cheng, Bauer, Daniel E., Xu, Jian, Bulyk, Martha L., Orkin, Stuart H.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 05.04.2018
• Subjects: Base Sequence; BCL11A; beta-Globins - genetics; beta-Thalassemia - genetics; beta-Thalassemia - pathology; Binding Sites; Carrier Proteins - genetics; Carrier Proteins - metabolism; Cell Line; Chromatin - metabolism; Clustered Regularly Interspaced Short Palindromic Repeats - genetics; CUT&RUN; digital genomic footprinting; DNA binding; Erythroid Cells - cytology; Erythroid Cells - metabolism; Fetal Hemoglobin - genetics; gamma-Globins - genetics; Gene Editing; hemoglobin; Humans; Nuclear Proteins - genetics; Nuclear Proteins - metabolism; Promoter Regions, Genetic; Protein Isoforms - genetics; Protein Isoforms - metabolism; protein-binding microarray; repression; Repressor Proteins; zinc finger; Zinc Fingers - genetics; digital genomic footprinting; BCL11A; protein-binding microarray; CUT&RUN; repression; zinc finger; gene editing; hemoglobin; DNA binding
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2018.03.016

Fetal hemoglobin (HbF, α2γ2) level is genetically controlled and modifies severity of adult hemoglobin (HbA, α2β2) disorders, sickle cell disease, and β-thalassemia. Common genetic variation affects expression of BCL11A, a regulator of HbF silencing. To uncover how BCL11A supports the developmental switch from γ- to β- globin, we use a functional assay and protein binding microarray to establish a requirement for a zinc-finger cluster in BCL11A in repression and identify a preferred DNA recognition sequence. This motif appears in embryonic and fetal-expressed globin promoters and is duplicated in γ-globin promoters. The more distal of the duplicated motifs is mutated in individuals with hereditary persistence of HbF. Using the CUT&RUN approach to map protein binding sites in erythroid cells, we demonstrate BCL11A occupancy preferentially at the distal motif, which can be disrupted by editing the promoter. Our findings reveal that direct γ-globin gene promoter repression by BCL11A underlies hemoglobin switching. [Display omitted] •BCL11A recognizes TGACCA motif in vitro and in vivo through zinc-finger domain•BCL11A acts at distal TGACCA in human γ-globin promoters to silence expression•TGACCA motif is mutated in individuals with HPFH syndrome•Editing the distal TGACCA prevents BCL11A binding and reactivates γ-globin expression The developmental transition between fetal and adult hemoglobin is controlled by a repressor that acts directly at the γ-globin gene promoter, suggesting a simplified control mechanism that could be manipulated in treatment of γ-hemoglobin disorders.