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Luo H, Zhu G, Xu J, Lai Q, Yan B, Guo Y, Fung TK, Zeisig BB, Cui Y, Zha J, Cogle C, Wang F, Xu B, Yang FC, Li W, So CWE, Qiu Y, Xu M, Huang S. HOTTIP lncRNA Promotes Hematopoietic Stem Cell Self-Renewal Leading to AML-like Disease in Mice. Cancer Cell 2019; 36:645-659.e8. [PMID: 31786140 PMCID: PMC6917035 DOI: 10.1016/j.ccell.2019.10.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 08/30/2019] [Accepted: 10/24/2019] [Indexed: 01/04/2023]
Abstract
Long non-coding RNAs (lncRNAs) are critical for regulating HOX genes, aberration of which is a dominant mechanism for leukemic transformation. How HOX gene-associated lncRNAs regulate hematopoietic stem cell (HSC) function and contribute to leukemogenesis remains elusive. We found that HOTTIP is aberrantly activated in acute myeloid leukemia (AML) to alter HOXA-driven topologically associated domain (TAD) and gene expression. HOTTIP loss attenuates leukemogenesis of transplanted mice, while reactivation of HOTTIP restores leukemic TADs, transcription, and leukemogenesis in the CTCF-boundary-attenuated AML cells. Hottip aberration in mice abnormally promotes HSC self-renewal leading to AML-like disease by altering the homeotic/hematopoietic gene-associated chromatin signature and transcription program. Hottip aberration acts as an oncogenic event to perturb HSC function by reprogramming leukemic-associated chromatin and gene transcription.
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Affiliation(s)
- Huacheng Luo
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Ganqian Zhu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Jianfeng Xu
- Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qian Lai
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; Department of Hematology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China
| | - Bowen Yan
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Ying Guo
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136; Department of Cell System & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Tsz Kan Fung
- School of Cancer and Pharmaceutical Science, King's College London, London SE5 9NU, UK
| | - Bernd B Zeisig
- School of Cancer and Pharmaceutical Science, King's College London, London SE5 9NU, UK
| | - Ya Cui
- Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Jie Zha
- Department of Hematology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China
| | - Christopher Cogle
- Division of Hematology/Oncology, Department of Medicine, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Fei Wang
- Department of Hematology and Oncology, The Affiliated Zhongda Hospital, Southeast University Medical School, Nanjing 210009, China
| | - Bing Xu
- Department of Hematology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China
| | - Feng-Chun Yang
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136; Department of Cell System & Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Wei Li
- Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Chi Wai Eric So
- School of Cancer and Pharmaceutical Science, King's College London, London SE5 9NU, UK.
| | - Yi Qiu
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL 32610, USA.
| | - Mingjiang Xu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136; Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
| | - Suming Huang
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; Penn State Cancer Institute, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
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DNA·RNA triple helix formation can function as a cis-acting regulatory mechanism at the human β-globin locus. Proc Natl Acad Sci U S A 2019; 116:6130-6139. [PMID: 30867287 DOI: 10.1073/pnas.1900107116] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We have identified regulatory mechanisms in which an RNA transcript forms a DNA duplex·RNA triple helix with a gene or one of its regulatory elements, suggesting potential auto-regulatory mechanisms in vivo. We describe an interaction at the human β-globin locus, in which an RNA segment embedded in the second intron of the β-globin gene forms a DNA·RNA triplex with the HS2 sequence within the β-globin locus control region, a major regulator of globin expression. We show in human K562 cells that the triplex is stable in vivo. Its formation causes displacement from HS2 of major transcription factors and RNA Polymerase II, and consequently in loss of factors and polymerase that bind to the human ε- and γ-globin promoters, which are activated by HS2 in K562 cells. This results in reduced expression of these genes. These effects are observed when a small length of triplex-forming RNA is introduced into cells, or when a full-length intron-containing human β-globin transcript is expressed. Related results are obtained in human umbilical cord blood-derived erythroid progenitor-2 cells, in which β-globin expression is similarly affected by triplex formation. These results suggest a model in which RNAs conforming to the strict sequence rules for DNA·RNA triplex formation may participate in feedback regulation of genes in cis.
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Li Y, Schulz VP, Deng C, Li G, Shen Y, Tusi BK, Ma G, Stees J, Qiu Y, Steiner LA, Zhou L, Zhao K, Bungert J, Gallagher PG, Huang S. Setd1a and NURF mediate chromatin dynamics and gene regulation during erythroid lineage commitment and differentiation. Nucleic Acids Res 2016; 44:7173-88. [PMID: 27141965 PMCID: PMC5009724 DOI: 10.1093/nar/gkw327] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 04/15/2016] [Indexed: 01/08/2023] Open
Abstract
The modulation of chromatin structure is a key step in transcription regulation in mammalian cells and eventually determines lineage commitment and differentiation. USF1/2, Setd1a and NURF complexes interact to regulate chromatin architecture in erythropoiesis, but the mechanistic basis for this regulation is hitherto unknown. Here we showed that Setd1a and NURF complexes bind to promoters to control chromatin structural alterations and gene activation in a cell context dependent manner. In human primary erythroid cells USF1/2, H3K4me3 and the NURF complex were significantly co-enriched at transcription start sites of erythroid genes, and their binding was associated with promoter/enhancer accessibility that resulted from nucleosome repositioning. Mice deficient for Setd1a, an H3K4 trimethylase, in the erythroid compartment exhibited reduced Ter119/CD71 positive erythroblasts, peripheral blood RBCs and hemoglobin levels. Loss of Setd1a led to a reduction of promoter-associated H3K4 methylation, inhibition of gene transcription and blockade of erythroid differentiation. This was associated with alterations in NURF complex occupancy at erythroid gene promoters and reduced chromatin accessibility. Setd1a deficiency caused decreased associations between enhancer and promoter looped interactions as well as reduced expression of erythroid genes such as the adult β-globin gene. These data indicate that Setd1a and NURF complexes are specifically targeted to and coordinately regulate erythroid promoter chromatin dynamics during erythroid lineage differentiation.
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Affiliation(s)
- Ying Li
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL 32610, USA Macau Institute for Applied Research in Medicine and Health, State Key laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau 519020, China
| | - Vincent P Schulz
- Department of Pediatrics, Pathology, and Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Changwang Deng
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Guangyao Li
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Yong Shen
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Betsabeh K Tusi
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Gina Ma
- Public Health Studies, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jared Stees
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Yi Qiu
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL 32610, USA Genetics Institute, University of Florida, Gainesville, FL 32610, USA UF health Cancer center, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Laurie A Steiner
- Department of Pediatrics, University of Rochester, Rochester, NY 14642, USA
| | - Lei Zhou
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL 32610, USA Genetics Institute, University of Florida, Gainesville, FL 32610, USA UF health Cancer center, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Keji Zhao
- Systems Biology Center, NHLBI, National Institute of Health, Bethesda, MD 20814, USA
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL 32610, USA Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Patrick G Gallagher
- Department of Pediatrics, Pathology, and Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Suming Huang
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL 32610, USA Macau Institute for Applied Research in Medicine and Health, State Key laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau 519020, China Genetics Institute, University of Florida, Gainesville, FL 32610, USA UF health Cancer center, University of Florida College of Medicine, Gainesville, FL 32610, USA
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Qi L, Higgins CE, Higgins SP, Law BK, Simone TM, Higgins PJ. The basic helix-loop-helix/leucine zipper transcription factor USF2 integrates serum-induced PAI-1 expression and keratinocyte growth. J Cell Biochem 2015; 115:1840-7. [PMID: 24905330 DOI: 10.1002/jcb.24861] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 05/30/2014] [Indexed: 01/30/2023]
Abstract
Plasminogen activator inhibitor type-1 (PAI-1), a major regulator of the plasmin-dependent pericellular proteolytic cascade, is prominently expressed during the tissue response to injury although the factors that impact PAI-1 induction and their role in the repair process are unclear. Kinetic modeling using established biomarkers of cell cycle transit (c-MYC; cyclin D1; cyclin A) in synchronized human (HaCaT) keratinocytes, and previous cytometric assessments, indicated that PAI-1 transcription occurred early after serum-stimulation of quiescent (G0) cells and prior to G1 entry. It was established previously that differential residence of USF family members (USF1→USF2 switch) at the PE2 region E box (CACGTG) characterized the G0 → G1 transition period and the transcriptional status of the PAI-1 gene. A consensus PE2 E box motif (5'-CACGTG-3') at nucleotides -566 to -561 was required for USF/E box interactions and serum-dependent PAI-1 transcription. Site-directed CG → AT substitution at the two central nucleotides inhibited formation of USF/probe complexes and PAI-1 promoter-driven reporter expression. A dominant-negative USF (A-USF) construct or double-stranded PE2 "decoy" attenuated serum- and TGF-β1-stimulated PAI-1 synthesis. Tet-Off induction of an A-USF insert reduced both PAI-1 and PAI-2 transcripts while increasing the fraction of Ki-67(+) cells. Conversely, overexpression of USF2 or adenoviral-delivery of a PAI-1 vector inhibited HaCaT colony expansion indicating that the USF1 → USF2 transition and subsequent PAI-1 transcription are critical events in the epithelial go-or-grow response. Collectively, these data suggest that USF2, and its target gene PAI-1, regulate serum-stimulated keratinocyte growth, and likely the cadence of cell cycle progression in replicatively competent cells as part of the injury repair program.
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Affiliation(s)
- Li Qi
- Center for Cell Biology & Cancer Research, Albany Medical College, Albany, New York, 12208
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5
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Barrow JJ, Li Y, Hossain M, Huang S, Bungert J. Dissecting the function of the adult β-globin downstream promoter region using an artificial zinc finger DNA-binding domain. Nucleic Acids Res 2014; 42:4363-74. [PMID: 24497190 PMCID: PMC3985677 DOI: 10.1093/nar/gku107] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Developmental stage-specific expression of the β-type globin genes is regulated by many cis- and trans-acting components. The adult β-globin gene contains an E-box located 60 bp downstream of the transcription start site that has been shown to bind transcription factor upstream stimulatory factor (USF) and to contribute to efficient in vitro transcription. We expressed an artificial zinc finger DNA-binding domain (ZF-DBD) targeting this site (+60 ZF-DBD) in murine erythroleukemia cells. Expression of the +60 ZF-DBD reduced the recruitment and elongation of RNA polymerase II (Pol II) at the adult β-globin gene and at the same time increased the binding of Pol II at locus control region (LCR) element HS2, suggesting that Pol II is transferred from the LCR to the globin gene promoters. Expression of the +60 ZF-DBD also reduced the frequency of interactions between the LCR and the adult β-globin promoter. ChIP-exonuclease-sequencing revealed that the +60ZF-DBD was targeted to the adult β-globin downstream promoter and that the binding of the ZF-DBD caused alterations in the association of USF2 containing protein complexes. The data demonstrate that targeting a ZF-DBD to the adult β-globin downstream promoter region interferes with the LCR-mediated recruitment and activity of Pol II.
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Affiliation(s)
- Joeva J Barrow
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Shands Cancer Center, Powell-Gene Therapy Center, University of Florida, Gainesville, 32610, FL, USA
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Cytoplasmic poly(A) binding protein C4 serves a critical role in erythroid differentiation. Mol Cell Biol 2014; 34:1300-9. [PMID: 24469397 DOI: 10.1128/mcb.01683-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The expression of an mRNA is strongly impacted by its 3' poly(A) tail and associated poly(A)-binding proteins (PABPs). Vertebrates encode six PABP isoforms that vary in abundance, distribution, developmental control, and subcellular localization. Here we demonstrate that the minor PABP isoform PABPC4 is expressed in erythroid cells and impacts the steady-state expression of a subset of erythroid mRNAs. Motif analyses reveal a high-value AU-rich motif in the 3' untranslated regions (UTRs) of PABPC4-impacted mRNAs. This motif enhances the association of PABPC4 with mRNAs containing critically shortened poly(A) tails. This association may serve to protect a subset of mRNAs from accelerated decay. Finally, we demonstrate that selective depletion of PABPC4 in an erythroblast cell line inhibits terminal erythroid maturation with corresponding alterations in the erythroid gene expression. These observations lead us to conclude that PABPC4 plays an essential role in posttranscriptional control of a major developmental pathway.
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Rosenberg M, Fan AX, Lin IJ, Liang SY, Bungert J. Cell-cycle specific association of transcription factors and RNA polymerase ii with the human β-globin gene locus. J Cell Biochem 2013; 114:1997-2006. [PMID: 23519692 DOI: 10.1002/jcb.24542] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 03/05/2013] [Indexed: 12/28/2022]
Abstract
The human β-globin genes are regulated by a locus control region (LCR) and are expressed at extremely high levels in erythroid cells. How transcriptional fidelity of highly expressed genes is regulated and maintained during the cell cycle is not completely understood. Here, we analyzed the association of transcription factor USF, the co-activator CBP, topoisomerase I (Topo I), basal transcription factor TFIIB, and RNA polymerase II (Pol II) with the β-globin gene locus at specific cell-cycle stages. The data demonstrate that while association of Pol II with globin locus associated chromatin decreased in mitotically arrested cells, it remained bound at lower levels at the γ-globin gene promoter. During early S-phase, association of CBP, USF, and Pol II with the globin gene locus decreased. The re-association of CBP and USF2 with the LCR preceded re-association of Pol II, suggesting that these proteins together mediate recruitment of Pol II to the β-globin gene locus during S-phase. Finally, we analyzed the association of Topo I with the globin gene locus during late S-phase. In general, Topo I association correlated with the binding of Pol II. Inhibition of Topo I activity reduced Pol II binding at the LCR and intergenic regions but not at the γ-globin gene promoter. The data demonstrate dynamic associations of transcription factors with the globin gene locus during the cell cycle and support previous results showing that specific components of transcription complexes remain associated with highly transcribed genes during mitosis.
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Affiliation(s)
- Michael Rosenberg
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, Florida, 32610
| | - Alex Xiucheng Fan
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, Florida, 32610
| | - I-Ju Lin
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, Florida, 32610
| | - Shermi Y Liang
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, Florida, 32610
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, Florida, 32610
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Deng C, Li Y, Liang S, Cui K, Salz T, Yang H, Tang Z, Gallagher PG, Qiu Y, Roeder R, Zhao K, Bungert J, Huang S. USF1 and hSET1A mediated epigenetic modifications regulate lineage differentiation and HoxB4 transcription. PLoS Genet 2013; 9:e1003524. [PMID: 23754954 PMCID: PMC3675019 DOI: 10.1371/journal.pgen.1003524] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 04/09/2013] [Indexed: 01/25/2023] Open
Abstract
The interplay between polycomb and trithorax complexes has been implicated in embryonic stem cell (ESC) self-renewal and differentiation. It has been shown recently that WRD5 and Dpy-30, specific components of the SET1/MLL protein complexes, play important roles during ESC self-renewal and differentiation of neural lineages. However, not much is known about how and where specific trithorax complexes are targeted to genes involved in self-renewal or lineage-specification. Here, we report that the recruitment of the hSET1A histone H3K4 methyltransferase (HMT) complex by transcription factor USF1 is required for mesoderm specification and lineage differentiation. In undifferentiated ESCs, USF1 maintains hematopoietic stem/progenitor cell (HS/PC) associated bivalent chromatin domains and differentiation potential. Furthermore, USF1 directed recruitment of the hSET1A complex to the HoxB4 promoter governs the transcriptional activation of HoxB4 gene and regulates the formation of early hematopoietic cell populations. Disruption of USF or hSET1A function by overexpression of a dominant-negative AUSF1 mutant or by RNA-interference-mediated knockdown, respectively, led to reduced expression of mesoderm markers and inhibition of lineage differentiation. We show that USF1 and hSET1A together regulate H3K4me3 modifications and transcription preinitiation complex assembly at the hematopoietic-associated HoxB4 gene during differentiation. Finally, ectopic expression of USF1 in ESCs promotes mesoderm differentiation and enforces the endothelial-to-hematopoietic transition by inducing hematopoietic-associated transcription factors, HoxB4 and TAL1. Taken together, our findings reveal that the guided-recruitment of the hSET1A histone methyltransferase complex and its H3K4 methyltransferase activity by transcription regulator USF1 safeguards hematopoietic transcription programs and enhances mesoderm/hematopoietic differentiation. Embryonic stem cells (ESCs) are capable of differentiating into any type of cell or tissue of the body. It is important to understand how developmental genes are controlled during differentiation of ESCs into specific cell types. The hSET1/MLL histone modifying protein complexes add methyl groups to lysine 4 on the N-terminal tails of the DNA associated protein histone H3 and activate gene expression. Although the hSET1/MLL enzymatic complexes play a role in activating genes involved in ESC growth and differentiation, how and where these activities are targeted to remains unclear. In this report, we demonstrate that DNA binding factor USF1 interacts with and brings the hSET1A enzymatic complex to its target gene, HoxB4, during blood cell specification and differentiation. Consistent with the function of HoxB4 in early blood cell formation, we found that the inactivation of USF1 or hSET1A activities leads to a block in the differentiation of blood cells and causes reductions in methylation levels of H3K4 and expression of HoxB4, without impairing the self-renewal capability of ESCs. Taken together, our findings reveal that the collaboration between the hSET1A enzymatic complex and DNA binding regulator USF1 activates developmental genes that control cellular differentiation programs during development.
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Affiliation(s)
- Changwang Deng
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Ying Li
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Shermi Liang
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Kairong Cui
- Systems Biology Center, NHLBI, NIH, Bethesda, Maryland, United States of America
| | - Tal Salz
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Hui Yang
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Zhanyun Tang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York, United States of America
| | - Patrick G. Gallagher
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Yi Qiu
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Robert Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York, United States of America
| | - Keji Zhao
- Systems Biology Center, NHLBI, NIH, Bethesda, Maryland, United States of America
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, United States of America
- Genetics Institute, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Suming Huang
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, United States of America
- Genetics Institute, University of Florida College of Medicine, Gainesville, Florida, United States of America
- * E-mail:
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Neutralizing the function of a β-globin-associated cis-regulatory DNA element using an artificial zinc finger DNA-binding domain. Proc Natl Acad Sci U S A 2012; 109:17948-53. [PMID: 23074246 DOI: 10.1073/pnas.1207677109] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gene expression is primarily regulated by cis-regulatory DNA elements and trans-interacting proteins. Transcription factors bind in a DNA sequence-specific manner and recruit activities that modulate the association and activity of transcription complexes at specific genes. Often, transcription factors belong to families of related proteins that interact with similar DNA sequences. Furthermore, genes are regulated by multiple, sometimes redundant, cis-regulatory elements. Thus, the analysis of the role of a specific DNA regulatory sequence and the interacting proteins in the context of intact cells is challenging. In this study, we designed and functionally characterized an artificial DNA-binding domain that neutralizes the function of a cis-regulatory DNA element associated with adult β-globin gene expression. The zinc finger DNA-binding domain (ZF-DBD), comprising six ZFs, interacted specifically with a CACCC site located 90 bp upstream of the transcription start site (-90 β-ZF-DBD), which is normally occupied by KLF1, a major regulator of adult β-globin gene expression. Stable expression of the -90 β-ZF-DBD in mouse erythroleukemia cells reduced the binding of KLF1 with the β-globin gene, but not with locus control region element HS2, and led to reduced transcription. Transient transgenic embryos expressing the -90 β-ZF-DBD developed normally but revealed reduced expression of the adult β-globin gene. These results demonstrate that artificial DNA-binding proteins lacking effector domains are useful tools for studying and modulating the function of cis-regulatory DNA elements.
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Chromatin boundaries require functional collaboration between the hSET1 and NURF complexes. Blood 2011; 118:1386-94. [PMID: 21653943 DOI: 10.1182/blood-2010-11-319111] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Chromatin insulators protect erythroid genes from being silenced during erythropoiesis, and the disruption of barrier insulator function in erythroid membrane gene loci results in mild or severe anemia. We showed previously that the USF1/2-bound 5'HS4 insulator mediates chromatin barrier activity in the erythroid-specific chicken β-globin locus. It is currently not known how insulators establish such a barrier. To understand the function of USF1, we purified USF1-associated protein complexes and found that USF1 forms a multiprotein complex with hSET1 and NURF, thus exhibiting histone H3K4 methyltransferase- and ATP-dependent nucleosome remodeling activities, respectively. Both SET1 and NURF are recruited to the 5'HS4 insulator by USF1 to retain the active chromatin structure in erythrocytes. Knock-down of NURF resulted in a rapid loss of barrier activity accompanied by an alteration of nucleosome positioning, increased occupancy of the nucleosome-free linker region at the insulator site, and increased repressive H3K27me3 levels in the vicinity of the HS4 insulator. Furthermore, suppression of SET1 reduced barrier activity, decreased H3K4me2 and acH3K9/K14, and diminished the recruitment of BPTF at several erythroid-specific barrier insulator sites. Therefore, our data reveal a synergistic role of hSET1 and NURF in regulating the USF-bound barrier insulator to prevent erythroid genes from encroachment of heterochromatin.
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Role of helix-loop-helix proteins during differentiation of erythroid cells. Mol Cell Biol 2011; 31:1332-43. [PMID: 21282467 DOI: 10.1128/mcb.01186-10] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Helix-loop-helix (HLH) proteins play a profound role in the process of development and cellular differentiation. Among the HLH proteins expressed in differentiating erythroid cells are the ubiquitous proteins Myc, USF1, USF2, and TFII-I, as well as the hematopoiesis-specific transcription factor Tal1/SCL. All of these HLH proteins exhibit distinct functions during the differentiation of erythroid cells. For example, Myc stimulates the proliferation of erythroid progenitor cells, while the USF proteins and Tal1 regulate genes that specify the differentiated phenotype. This minireview summarizes the known activities of Myc, USF, TFII-I, and Tal11/SCL and discusses how they may function sequentially, cooperatively, or antagonistically in regulating expression programs during the differentiation of erythroid cells.
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Zhou Z, Li X, Deng C, Ney PA, Huang S, Bungert J. USF and NF-E2 cooperate to regulate the recruitment and activity of RNA polymerase II in the beta-globin gene locus. J Biol Chem 2010; 285:15894-905. [PMID: 20236933 DOI: 10.1074/jbc.m109.098376] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The human beta-globin gene is expressed at high levels in erythroid cells and regulated by proximal and distal cis-acting DNA elements, including promoter, enhancer, and a locus control region (LCR). Transcription complexes are recruited not only to the globin gene promoters but also to the LCR. Previous studies have implicated the ubiquitously expressed transcription factor USF and the tissue-restricted activator NF-E2 in the recruitment of transcription complexes to the beta-globin gene locus. Here we demonstrate that although USF is required for the efficient association of RNA polymerase II (Pol II) with immobilized LCR templates, USF and NF-E2 together regulate the association of Pol II with the adult beta-globin gene promoter. Recruitment of Pol II to the LCR occurs in undifferentiated murine erythroleukemia cells, but phosphorylation of LCR-associated Pol II at serine 5 of the C-terminal domain is mediated by erythroid differentiation and requires the activity of NF-E2. Furthermore, we provide evidence showing that USF interacts with NF-E2 in erythroid cells. The data provide mechanistic insight into how ubiquitous and tissue-restricted transcription factors cooperate to regulate the recruitment and activity of transcription complexes in a tissue-specific chromatin domain.
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Affiliation(s)
- Zhuo Zhou
- Department of Biochemistry and Molecular Biology, Powell Gene Therapy Center, Center for Epigenetics, and Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
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H4R3 methylation facilitates beta-globin transcription by regulating histone acetyltransferase binding and H3 acetylation. Blood 2010; 115:2028-37. [PMID: 20068219 DOI: 10.1182/blood-2009-07-236059] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Histone modifications play an important role in the process of transcription. However, in contrast to lysine methylation, the role of arginine methylation in chromatin structure and transcription has been underexplored. The globin genes are regulated by a highly organized chromatin structure that juxtaposes the locus control region (LCR) with downstream globin genes. We report here that the targeted recruitment of asymmetric dimethyl H4R3 catalyzed by PRMT1 (protein arginine methyltransferase 1) facilitates histone H3 acetylation on Lys9/Lys14. Dimethyl H4R3 provides a binding surface for P300/CBP-associated factor (PCAF) and directly enhances histone H3 acetylation in vitro. We show that these active modifications are essential for efficient interactions between the LCR and the beta(maj)-promoter as well as transcription of the beta-globin gene. Furthermore, knockdown (KD) of PRMT1 by RNA interference in erythroid progenitor cells prevents histone acetylation, enhancer and promoter interaction, and recruitment of transcription complexes to the active beta-globin promoter. Reintroducing rat PRMT1 into the PRMT1 KD MEL cells rescues PRMT1 binding, beta-globin transcription, and erythroid differentiation. Taken together, our data suggest that PRMT1-mediated dimethyl H4R3 facilitates histone acetylation and enhancer/promoter communications, which lead to the efficient recruitment of transcription preinitiation complexes to active promoters.
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