Transcription factor competition at the γ-globin promoters controls hemoglobin switching

Nan Liu; Shuqian Xu; Qiuming Yao; Qian Zhu; Yan Kai; Jonathan Y Hsu; Phraew Sakon; Luca Pinello; Guo-Cheng Yuan; Daniel E Bauer; Stuart H Orkin

doi:10.1038/s41588-021-00798-y

Transcription factor competition at the γ-globin promoters controls hemoglobin switching

Nat Genet. 2021 Apr;53(4):511-520. doi: 10.1038/s41588-021-00798-y. Epub 2021 Mar 1.

Authors

Nan Liu^#¹, Shuqian Xu^#^{1

2}, Qiuming Yao^{1

3}, Qian Zhu⁴, Yan Kai⁴, Jonathan Y Hsu³, Phraew Sakon¹, Luca Pinello³, Guo-Cheng Yuan^{4

5}, Daniel E Bauer¹, Stuart H Orkin^{6

7}

Affiliations

¹ Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
² Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.
³ Molecular Pathology Unit & Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
⁴ Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
⁵ Department of Genetics and Genomic Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
⁶ Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA. [email protected].
⁷ Howard Hughes Medical Institute, Boston, MA, USA. [email protected].

^# Contributed equally.

Abstract

BCL11A, the major regulator of fetal hemoglobin (HbF, α₂γ₂) level, represses γ-globin expression through direct promoter binding in adult erythroid cells in a switch to adult hemoglobin (HbA, α₂β₂). To uncover how BCL11A initiates repression, we used CRISPR-Cas9, dCas9, dCas9-KRAB and dCas9-VP64 screens to dissect the γ-globin promoters and identified an activator element near the BCL11A-binding site. Using CUT&RUN and base editing, we demonstrate that a proximal CCAAT box is occupied by the activator NF-Y. BCL11A competes with NF-Y binding through steric hindrance to initiate repression. Occupancy of NF-Y is rapidly established following BCL11A depletion, and precedes γ-globin derepression and locus control region (LCR)-globin loop formation. Our findings reveal that the switch from fetal to adult globin gene expression within the >50-kb β-globin gene cluster is initiated by competition between a stage-selective repressor and a ubiquitous activating factor within a remarkably discrete region of the γ-globin promoters.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Base Sequence
Binding Sites
Binding, Competitive
CCAAT-Binding Factor / chemistry*
CCAAT-Binding Factor / genetics
CCAAT-Binding Factor / metabolism
Erythropoiesis / genetics
Fetal Hemoglobin / genetics*
Fetal Hemoglobin / metabolism
Gene Editing / methods
Gene Expression Regulation
HEK293 Cells
Hemoglobin A / genetics*
Hemoglobin A / metabolism
Humans
Models, Molecular
Primary Cell Culture
Promoter Regions, Genetic*
Protein Binding
Protein Conformation, alpha-Helical
Protein Conformation, beta-Strand
Protein Interaction Domains and Motifs
Repressor Proteins / chemistry*
Repressor Proteins / genetics
Repressor Proteins / metabolism
Stem Cells
beta-Globins / chemistry
beta-Globins / genetics
beta-Globins / metabolism
gamma-Globins / chemistry*
gamma-Globins / genetics
gamma-Globins / metabolism

Substances

BCL11A protein, human
CCAAT-Binding Factor
Repressor Proteins
beta-Globins
gamma-Globins
Hemoglobin A
Fetal Hemoglobin

Abstract

Publication types

MeSH terms

Substances

Grants and funding