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Qin K, Lan X, Huang P, Saari MS, Khandros E, Keller CA, Giardine B, Abdulmalik O, Shi J, Hardison RC, Blobel GA. Molecular basis of polycomb group protein-mediated fetal hemoglobin repression. Blood 2023; 141:2756-2770. [PMID: 36893455 PMCID: PMC10273169 DOI: 10.1182/blood.2022019578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/15/2023] [Accepted: 03/01/2023] [Indexed: 03/11/2023] Open
Abstract
The switch from fetal hemoglobin (HbF) to adult hemoglobin (HbA) is a paradigm for developmental gene expression control with relevance to sickle cell disease and β-thalassemia. Polycomb repressive complex (PRC) proteins regulate this switch, and an inhibitor of PRC2 has entered a clinical trial for HbF activation. Yet, how PRC complexes function in this process, their target genes, and relevant subunit composition are unknown. Here, we identified the PRC1 subunit BMI1 as a novel HbF repressor. We uncovered the RNA binding proteins LIN28B, IGF2BP1, and IGF2BP3 genes as direct BMI1 targets, and demonstrate that they account for the entirety of BMI1's effect on HbF regulation. BMI1 functions as part of the canonical PRC1 (cPRC1) subcomplex as revealed by the physical and functional dissection of BMI1 protein partners. Lastly, we demonstrate that BMI1/cPRC1 acts in concert with PRC2 to repress HbF through the same target genes. Our study illuminates how PRC silences HbF, highlighting an epigenetic mechanism involved in hemoglobin switching.
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Affiliation(s)
- Kunhua Qin
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Xianjiang Lan
- Department of Systems Biology for Medicine, School of Basic Medical Sciences, Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Peng Huang
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Megan S. Saari
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Eugene Khandros
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Cheryl A. Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, State College, PA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, State College, PA
| | - Osheiza Abdulmalik
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ross C. Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, State College, PA
| | - Gerd A. Blobel
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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Vermunt MW, Luan J, Zhang Z, Thrasher AJ, Huang A, Saari MS, Khandros E, Beagrie RA, Zhang S, Vemulamada P, Brilleman M, Lee K, Yano JA, Giardine BM, Keller CA, Hardison RC, Blobel GA. Gene silencing dynamics are modulated by transiently active regulatory elements. Mol Cell 2023; 83:715-730.e6. [PMID: 36868189 PMCID: PMC10719944 DOI: 10.1016/j.molcel.2023.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 12/05/2022] [Accepted: 02/03/2023] [Indexed: 03/05/2023]
Abstract
Transcriptional enhancers have been extensively characterized, but cis-regulatory elements involved in acute gene repression have received less attention. Transcription factor GATA1 promotes erythroid differentiation by activating and repressing distinct gene sets. Here, we study the mechanism by which GATA1 silences the proliferative gene Kit during murine erythroid cell maturation and define stages from initial loss of activation to heterochromatinization. We find that GATA1 inactivates a potent upstream enhancer but concomitantly creates a discrete intronic regulatory region marked by H3K27ac, short noncoding RNAs, and de novo chromatin looping. This enhancer-like element forms transiently and serves to delay Kit silencing. The element is ultimately erased via the FOG1/NuRD deacetylase complex, as revealed by the study of a disease-associated GATA1 variant. Hence, regulatory sites can be self-limiting by dynamic co-factor usage. Genome-wide analyses across cell types and species uncover transiently active elements at numerous genes during repression, suggesting that modulation of silencing kinetics is widespread.
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Affiliation(s)
- Marit W Vermunt
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Jing Luan
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhe Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Pennsylvania, Philadelphia, PA 19104, USA
| | - A Josephine Thrasher
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Anran Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Megan S Saari
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Eugene Khandros
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Robert A Beagrie
- Chromatin and Disease Group, Wellcome Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Shiping Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pranay Vemulamada
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Matilda Brilleman
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kiwon Lee
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jennifer A Yano
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Belinda M Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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Qin K, Huang P, Feng R, Keller CA, Peslak SA, Khandros E, Saari MS, Lan X, Mayuranathan T, Doerfler PA, Abdulmalik O, Giardine B, Chou ST, Shi J, Hardison RC, Weiss MJ, Blobel GA. Publisher Correction: Dual function NFI factors control fetal hemoglobin silencing in adult erythroid cells. Nat Genet 2022; 54:906. [PMID: 35650318 DOI: 10.1038/s41588-022-01112-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kunhua Qin
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Peng Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ruopeng Feng
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Scott A Peslak
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Hematology/Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Eugene Khandros
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Megan S Saari
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xianjiang Lan
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | | | - Phillip A Doerfler
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Osheiza Abdulmalik
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Stella T Chou
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Qin K, Huang P, Feng R, Keller CA, Peslak SA, Khandros E, Saari MS, Lan X, Mayuranathan T, Doerfler PA, Abdulmalik O, Giardine B, Chou ST, Shi J, Hardison RC, Weiss MJ, Blobel GA. Dual function NFI factors control fetal hemoglobin silencing in adult erythroid cells. Nat Genet 2022; 54:874-884. [PMID: 35618846 PMCID: PMC9203980 DOI: 10.1038/s41588-022-01076-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 04/08/2022] [Indexed: 12/13/2022]
Abstract
The mechanisms by which the fetal-type β-globin-like genes HBG1 and HBG2 are silenced in adult erythroid precursor cells remain a fundamental question in human biology and have therapeutic relevance to sickle cell disease (SCD) and β-thalassemia. Here, we identify via a CRISPR-Cas9 genetic screen two members of the NFI transcription factor family – NFIA and NFIX – as HBG1/2 repressors. NFIA and NFIX are expressed at elevated levels in adult erythroid cells compared to fetal cells, and function cooperatively to repress HBG1/2 in cultured cells and in human-to-mouse xenotransplants. Genomic profiling, genome editing, and DNA binding assays demonstrate that the potent concerted activity of NFIA and NFIX is explained in part by their ability to stimulate the expression of BCL11A, a known silencer of the HBG1/2 genes, and in part by directly repressing the HBG1/2 genes. Thus, NFI factors emerge as versatile regulators of the fetal-to-adult switch in β-globin production.
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Affiliation(s)
- Kunhua Qin
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Peng Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ruopeng Feng
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Scott A Peslak
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Hematology/Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Eugene Khandros
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Megan S Saari
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xianjiang Lan
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | | | - Phillip A Doerfler
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Osheiza Abdulmalik
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Stella T Chou
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Abstract
The occurrence of secondary haemorrhage after traumatic hyphaema was studied in 239 patients treated in the Department of Ophthalmology, Tampere Central Hospital during the years 1972 to 1980. From 1972 to 1976, 126 patients with traumatic hyphaema were confined to bed and treated without antifibrinolytic agents; nine (7.1%) of these patients developed secondary haemorrhage. From 1977 to 1980, none of 58 patients with traumatic hyphema treated with tranexamic acid developed secondary haemorrhage which was seen in 3 (5.5%) of 55 patients treated without antifibrinolytic agents; the activities of these patients were not restricted and the eyes were not patched. The resorption of the hyphaema was significantly delayed in the tranexamic acid treated patients. It is concluded that tranexamic acid delays resorption of the blood-clot sealing the damaged vessel and preventing secondary haemorrhage after traumatic hyphaema without bed-rest and binocular patching.
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