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Cheng IH, Pi WC, Hsu CH, Guo Y, Lai JL, Wang GG, Chung BC, Roeder RG, Chen WY. TAF2, within the TFIID complex, regulates the expression of a subset of protein-coding genes. Cell Death Discov 2024; 10:244. [PMID: 38773077 PMCID: PMC11109217 DOI: 10.1038/s41420-024-02017-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/23/2024] Open
Abstract
TFIID, one of the general transcription factor (GTF), regulates transcriptional initiation of protein-coding genes through direct binding to promoter elements and subsequent recruitment of other GTFs and RNA polymerase II. Although generally required for most protein-coding genes, accumulated studies have also demonstrated promoter-specific functions for several TFIID subunits in gene activation. Here, we report that TBP-associated factor 2 (TAF2) specifically regulates TFIID binding to a small subset of protein-coding genes and is essential for cell growth of multiple cancer lines. Co-immunoprecipitation assays revealed that TAF2 may be sub-stoichiometrically associated with the TFIID complex, thus indicating a minor fraction of TAF2-containing TFIID in cells. Consistently, integrated genome-wide profiles show that TAF2 binds to and regulates only a small subset of protein-coding genes. Furthermore, through the use of an inducible TAF2 degradation system, our results reveal a reduction of TBP/TFIID binding to several ribosomal genes upon selective ablation of TAF2. In addition, depletion of TAF2, as well as the TAF2-regulated ribosomal protein genes RPL30 and RPL39, decreases ribosome assembly and global protein translation. Collectively, this study suggests that TAF2 within the TFIID complex is of functional importance for TBP/TFIID binding to and expression of a small subset of protein-coding genes, thus establishing a previously unappreciated promoter-selective function for TAF2.
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Affiliation(s)
- I-Hsin Cheng
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Wen-Chieh Pi
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chung-Hao Hsu
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yiran Guo
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Cancer Institute, Durham, NC, 27710, USA
| | - Jun-Lin Lai
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Gang G Wang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Cancer Institute, Durham, NC, 27710, USA
| | - Bon-Chu Chung
- Insitute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biomedical Sciences, Neuroscience and Brain Disease Center, China Medical University, Taichung, Taiwan
- National Laboratory Animal Center, National Applied Research Laboratories, Taipei, Taiwan
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, 10065, USA
| | - Wei-Yi Chen
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan.
- Cancer and Immunology Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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2
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Lv X, Murphy K, Murphy Z, Getman M, Rahman N, Nakamura Y, Blanc L, Gallagher PG, Palis J, Mohandas N, Steiner LA. HEXIM1 is an essential transcription regulator during human erythropoiesis. Blood 2023; 142:2198-2215. [PMID: 37738561 PMCID: PMC10733840 DOI: 10.1182/blood.2022019495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 08/17/2023] [Accepted: 08/19/2023] [Indexed: 09/24/2023] Open
Abstract
ABSTRACT Regulation of RNA polymerase II (RNAPII) activity is an essential process that governs gene expression; however, its contribution to the fundamental process of erythropoiesis remains unclear. hexamethylene bis-acetamide inducible 1 (HEXIM1) regulates RNAPII activity by controlling the location and activity of positive transcription factor β. We identified a key role for HEXIM1 in controlling erythroid gene expression and function, with overexpression of HEXIM1 promoting erythroid proliferation and fetal globin expression. HEXIM1 regulated erythroid proliferation by enforcing RNAPII pausing at cell cycle check point genes and increasing RNAPII occupancy at genes that promote cycle progression. Genome-wide profiling of HEXIM1 revealed that it was increased at both repressed and activated genes. Surprisingly, there were also genome-wide changes in the distribution of GATA-binding factor 1 (GATA1) and RNAPII. The most dramatic changes occurred at the β-globin loci, where there was loss of RNAPII and GATA1 at β-globin and gain of these factors at γ-globin. This resulted in increased expression of fetal globin, and BGLT3, a long noncoding RNA in the β-globin locus that regulates fetal globin expression. GATA1 was a key determinant of the ability of HEXIM1 to repress or activate gene expression. Genes that gained both HEXIM1 and GATA1 had increased RNAPII and increased gene expression, whereas genes that gained HEXIM1 but lost GATA1 had an increase in RNAPII pausing and decreased expression. Together, our findings reveal a central role for universal transcription machinery in regulating key aspects of erythropoiesis, including cell cycle progression and fetal gene expression, which could be exploited for therapeutic benefit.
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Affiliation(s)
- Xiurui Lv
- Center for Child Health Research, University of Rochester, Rochester, NY
| | - Kristin Murphy
- Center for Child Health Research, University of Rochester, Rochester, NY
| | - Zachary Murphy
- Center for Child Health Research, University of Rochester, Rochester, NY
| | - Michael Getman
- Center for Child Health Research, University of Rochester, Rochester, NY
| | - Nabil Rahman
- Center for Child Health Research, University of Rochester, Rochester, NY
| | - Yukio Nakamura
- Rikagaku Kenkyūjyo (RIKEN) BioResource Research Center, Tsukuba Campus, Ibaraki, Japan
| | - Lionel Blanc
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY
| | | | - James Palis
- Center for Child Health Research, University of Rochester, Rochester, NY
| | - Narla Mohandas
- Red Cell Physiology Laboratory, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY
| | - Laurie A. Steiner
- Center for Child Health Research, University of Rochester, Rochester, NY
- Center for RNA Biology, University of Rochester, Rochester, NY
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3
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Felício D, du Mérac TR, Amorim A, Martins S. Functional implications of paralog genes in polyglutamine spinocerebellar ataxias. Hum Genet 2023; 142:1651-1676. [PMID: 37845370 PMCID: PMC10676324 DOI: 10.1007/s00439-023-02607-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/22/2023] [Indexed: 10/18/2023]
Abstract
Polyglutamine (polyQ) spinocerebellar ataxias (SCAs) comprise a group of autosomal dominant neurodegenerative disorders caused by (CAG/CAA)n expansions. The elongated stretches of adjacent glutamines alter the conformation of the native proteins inducing neurotoxicity, and subsequent motor and neurological symptoms. Although the etiology and neuropathology of most polyQ SCAs have been extensively studied, only a limited selection of therapies is available. Previous studies on SCA1 demonstrated that ATXN1L, a human duplicated gene of the disease-associated ATXN1, alleviated neuropathology in mice models. Other SCA-associated genes have paralogs (i.e., copies at different chromosomal locations derived from duplication of the parental gene), but their functional relevance and potential role in disease pathogenesis remain unexplored. Here, we review the protein homology, expression pattern, and molecular functions of paralogs in seven polyQ dominant ataxias-SCA1, SCA2, MJD/SCA3, SCA6, SCA7, SCA17, and DRPLA. Besides ATXN1L, we highlight ATXN2L, ATXN3L, CACNA1B, ATXN7L1, ATXN7L2, TBPL2, and RERE as promising functional candidates to play a role in the neuropathology of the respective SCA, along with the parental gene. Although most of these duplicates lack the (CAG/CAA)n region, if functionally redundant, they may compensate for a partial loss-of-function or dysfunction of the wild-type genes in SCAs. We aim to draw attention to the hypothesis that paralogs of disease-associated genes may underlie the complex neuropathology of dominant ataxias and potentiate new therapeutic strategies.
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Affiliation(s)
- Daniela Felício
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal
- Instituto Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313, Porto, Portugal
| | - Tanguy Rubat du Mérac
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal
- Faculty of Science, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007, Porto, Portugal
| | - Sandra Martins
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal.
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal.
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4
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Hisler V, Bardot P, Detilleux D, Stierle M, Sanchez EG, Richard C, Arab LH, Ehrhard C, Morlet B, Hadzhiev Y, Jung M, Gras SL, Négroni L, Müller F, Tora L, Vincent SD. RNA polymerase II transcription with partially assembled TFIID complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.27.567046. [PMID: 38076793 PMCID: PMC10705246 DOI: 10.1101/2023.11.27.567046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
The recognition of core promoter sequences by the general transcription factor TFIID is the first step in the process of RNA polymerase II (Pol II) transcription initiation. Metazoan holo-TFIID is composed of the TATA binding protein (TBP) and of 13 TBP associated factors (TAFs). Inducible Taf7 knock out (KO) results in the formation of a Taf7-less TFIID complex, while Taf10 KO leads to serious defects within the TFIID assembly pathway. Either TAF7 or TAF10 depletions correlate with the detected TAF occupancy changes at promoters, and with the distinct phenotype severities observed in mouse embryonic stem cells or mouse embryos. Surprisingly however, under either Taf7 or Taf10 deletion conditions, TBP is still associated to the chromatin, and no major changes are observed in nascent Pol II transcription. Thus, partially assembled TFIID complexes can sustain Pol II transcription initiation, but cannot replace holo-TFIID over several cell divisions and/or development.
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Affiliation(s)
- Vincent Hisler
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Paul Bardot
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Dylane Detilleux
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Matthieu Stierle
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Emmanuel Garcia Sanchez
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Claire Richard
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Lynda Hadj Arab
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Cynthia Ehrhard
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Bastien Morlet
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
- Proteomics platform
| | - Yavor Hadzhiev
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Matthieu Jung
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
- GenomEast
| | - Stéphanie Le Gras
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
- GenomEast
| | - Luc Négroni
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
- Proteomics platform
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - László Tora
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Stéphane D. Vincent
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
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5
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Wells M, Steiner L. Epigenetic and Transcriptional Control of Erythropoiesis. Front Genet 2022; 13:805265. [PMID: 35330735 PMCID: PMC8940284 DOI: 10.3389/fgene.2022.805265] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/16/2022] [Indexed: 12/21/2022] Open
Abstract
Erythropoiesis is a process of enormous magnitude, with the average person generating two to three million red cells every second. Erythroid progenitors start as large cells with large nuclei, and over the course of three to four cell divisions they undergo a dramatic decrease in cell size accompanied by profound nuclear condensation, which culminates in enucleation. As maturing erythroblasts are undergoing these dramatic phenotypic changes, they accumulate hemoglobin and express high levels of other erythroid-specific genes, while silencing much of the non-erythroid transcriptome. These phenotypic and gene expression changes are associated with distinct changes in the chromatin landscape, and require close coordination between transcription factors and epigenetic regulators, as well as precise regulation of RNA polymerase II activity. Disruption of these processes are associated with inherited anemias and myelodysplastic syndromes. Here, we review the epigenetic mechanisms that govern terminal erythroid maturation, and their role in human disease.
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Affiliation(s)
- Maeve Wells
- Department of Pediatrics, University of Rochester, Rochester, NY, United States
| | - Laurie Steiner
- Department of Pediatrics, University of Rochester, Rochester, NY, United States
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6
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What do Transcription Factors Interact With? J Mol Biol 2021; 433:166883. [PMID: 33621520 DOI: 10.1016/j.jmb.2021.166883] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 12/11/2022]
Abstract
Although we have made significant progress, we still possess a limited understanding of how genomic and epigenomic information directs gene expression programs through sequence-specific transcription factors (TFs). Extensive research has settled on three general classes of TF targets in metazoans: promoter accessibility via chromatin regulation (e.g., SAGA), assembly of the general transcription factors on promoter DNA (e.g., TFIID), and recruitment of RNA polymerase (Pol) II (e.g., Mediator) to establish a transcription pre-initiation complex (PIC). Here we discuss TFs and their targets. We also place this in the context of our current work with Saccharomyces (yeast), where we find that promoters typically lack an architecture that supports TF function. Moreover, yeast promoters that support TF binding also display interactions with cofactors like SAGA and Mediator, but not TFIID. It is unknown to what extent all genes in metazoans require TFs and their cofactors.
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7
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Wang Z, Wang P, Li Y, Peng H, Zhu Y, Mohandas N, Liu J. Interplay between cofactors and transcription factors in hematopoiesis and hematological malignancies. Signal Transduct Target Ther 2021; 6:24. [PMID: 33468999 PMCID: PMC7815747 DOI: 10.1038/s41392-020-00422-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/16/2020] [Accepted: 10/26/2020] [Indexed: 02/07/2023] Open
Abstract
Hematopoiesis requires finely tuned regulation of gene expression at each stage of development. The regulation of gene transcription involves not only individual transcription factors (TFs) but also transcription complexes (TCs) composed of transcription factor(s) and multisubunit cofactors. In their normal compositions, TCs orchestrate lineage-specific patterns of gene expression and ensure the production of the correct proportions of individual cell lineages during hematopoiesis. The integration of posttranslational and conformational modifications in the chromatin landscape, nucleosomes, histones and interacting components via the cofactor–TF interplay is critical to optimal TF activity. Mutations or translocations of cofactor genes are expected to alter cofactor–TF interactions, which may be causative for the pathogenesis of various hematologic disorders. Blocking TF oncogenic activity in hematologic disorders through targeting cofactors in aberrant complexes has been an exciting therapeutic strategy. In this review, we summarize the current knowledge regarding the models and functions of cofactor–TF interplay in physiological hematopoiesis and highlight their implications in the etiology of hematological malignancies. This review presents a deep insight into the physiological and pathological implications of transcription machinery in the blood system.
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Affiliation(s)
- Zi Wang
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, 410011, ChangSha, Hunan, China. .,Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China.
| | - Pan Wang
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China
| | - Yanan Li
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China
| | - Hongling Peng
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, 410011, ChangSha, Hunan, China
| | - Yu Zhu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China
| | - Narla Mohandas
- Red Cell Physiology Laboratory, New York Blood Center, New York, NY, USA
| | - Jing Liu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China.
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8
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Papadopoulos P, Kafasi A, De Cuyper IM, Barroca V, Lewandowski D, Kadri Z, Veldthuis M, Berghuis J, Gillemans N, Benavente Cuesta CM, Grosveld FG, van Zwieten R, Philipsen S, Vernet M, Gutiérrez L, Patrinos GP. Mild dyserythropoiesis and β-like globin gene expression imbalance due to the loss of histone chaperone ASF1B. Hum Genomics 2020; 14:39. [PMID: 33066815 PMCID: PMC7566067 DOI: 10.1186/s40246-020-00283-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/10/2020] [Indexed: 01/09/2023] Open
Abstract
The expression of the human β-like globin genes follows a well-orchestrated developmental pattern, undergoing two essential switches, the first one during the first weeks of gestation (ε to γ), and the second one during the perinatal period (γ to β). The γ- to β-globin gene switching mechanism includes suppression of fetal (γ-globin, HbF) and activation of adult (β-globin, HbA) globin gene transcription. In hereditary persistence of fetal hemoglobin (HPFH), the γ-globin suppression mechanism is impaired leaving these individuals with unusual elevated levels of fetal hemoglobin (HbF) in adulthood. Recently, the transcription factors KLF1 and BCL11A have been established as master regulators of the γ- to β-globin switch. Previously, a genomic variant in the KLF1 gene, identified by linkage analysis performed on twenty-seven members of a Maltese family, was found to be associated with HPFH. However, variation in the levels of HbF among family members, and those from other reported families carrying genetic variants in KLF1, suggests additional contributors to globin switching. ASF1B was downregulated in the family members with HPFH. Here, we investigate the role of ASF1B in γ- to β-globin switching and erythropoiesis in vivo. Mouse-human interspecies ASF1B protein identity is 91.6%. By means of knockdown functional assays in human primary erythroid cultures and analysis of the erythroid lineage in Asf1b knockout mice, we provide evidence that ASF1B is a novel contributor to steady-state erythroid differentiation, and while its loss affects the balance of globin expression, it has no major role in hemoglobin switching.
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Affiliation(s)
- Petros Papadopoulos
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands.
- Department of Hematology, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain.
| | - Athanassia Kafasi
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, AMC, UvA, Amsterdam, The Netherlands
| | - Iris M De Cuyper
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, AMC, UvA, Amsterdam, The Netherlands
| | - Vilma Barroca
- UMR Stabilité Génétique Cellules Souches et Radiations, Université de Paris and Université de Paris-Saclay, CEA, 18 route du Panorama, 92260, Fontenay-aux-Roses, France
- U1274, Inserm, 18 route du Panorama, 92260, Fontenay-aux-Roses, France
| | - Daniel Lewandowski
- UMR Stabilité Génétique Cellules Souches et Radiations, Université de Paris and Université de Paris-Saclay, CEA, 18 route du Panorama, 92260, Fontenay-aux-Roses, France
- U1274, Inserm, 18 route du Panorama, 92260, Fontenay-aux-Roses, France
| | - Zahra Kadri
- Division of Innovative Therapies, UMR1184, Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses, France
| | - Martijn Veldthuis
- Laboratory of Red Blood Cell Diagnostics, Sanquin Diagnostics, Amsterdam, The Netherlands
| | - Jeffrey Berghuis
- Laboratory of Red Blood Cell Diagnostics, Sanquin Diagnostics, Amsterdam, The Netherlands
| | - Nynke Gillemans
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Celina María Benavente Cuesta
- Department of Hematology, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Rob van Zwieten
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, AMC, UvA, Amsterdam, The Netherlands
- Laboratory of Red Blood Cell Diagnostics, Sanquin Diagnostics, Amsterdam, The Netherlands
| | - Sjaak Philipsen
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Muriel Vernet
- UMR Stabilité Génétique Cellules Souches et Radiations, Université de Paris and Université de Paris-Saclay, CEA, 18 route du Panorama, 92260, Fontenay-aux-Roses, France
| | - Laura Gutiérrez
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
- Department of Hematology, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, AMC, UvA, Amsterdam, The Netherlands
- Platelet Research Lab -Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-, Department of Medicine -University of Oviedo-, Oviedo, Spain
| | - George P Patrinos
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, University of Patras School of Health Sciences, Patras, Greece
- Department of Pathology, College of Medicine and Health Sciences and Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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9
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Nuño-Cabanes C, Rodríguez-Navarro S. The promiscuity of the SAGA complex subunits: Multifunctional or moonlighting proteins? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194607. [PMID: 32712338 DOI: 10.1016/j.bbagrm.2020.194607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/09/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022]
Abstract
Gene expression, the decoding of DNA information into accessible instructions for protein synthesis, is a complex process in which multiple steps, including transcription, mRNA processing and mRNA export, are regulated by different factors. One of the first steps in this process involves chemical and structural changes in chromatin to allow transcription. For such changes to occur, histone tail and DNA epigenetic modifications foster the binding of transcription factors to promoter regions. The SAGA coactivator complex plays a crucial role in this process by mediating histone acetylation through Gcn5, and histone deubiquitination through Ubp8 enzymes. However, most SAGA subunits interact physically with other proteins beyond the SAGA complex. These interactions could represent SAGA-independent functions or a mechanism to widen SAGA multifunctionality. Among the different mechanisms to perform more than one function, protein moonlighting defines unrelated molecular activities for the same polypeptide sequence. Unlike pleiotropy, where a single gene can affect different phenotypes, moonlighting necessarily involves separate functions of a protein at the molecular level. In this review we describe in detail some of the alternative physical interactions of several SAGA subunits. In some cases, the alternative role constitutes a clear moonlighting function, whereas in most of them the lack of molecular evidence means that we can only define these interactions as promiscuous that require further work to verify if these are moonlighting functions.
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Affiliation(s)
- Carme Nuño-Cabanes
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC), Jaume Roig, 11, E-46010 Valencia, Spain
| | - Susana Rodríguez-Navarro
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC), Jaume Roig, 11, E-46010 Valencia, Spain.
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10
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Tuan NM, Lee CH. Role of Anillin in Tumour: From a Prognostic Biomarker to a Novel Target. Cancers (Basel) 2020; 12:E1600. [PMID: 32560530 PMCID: PMC7353083 DOI: 10.3390/cancers12061600] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/04/2020] [Accepted: 06/08/2020] [Indexed: 01/21/2023] Open
Abstract
Anillin (ANLN), an actin-binding protein, reportedly plays a vital role in cell proliferation and migration, particularly in cytokinesis. Although there have been findings pointing to a contribution of ANLN to the development of cancer, the association of ANLN to cancer remains not fully understood. Here, we gather evidence to determine the applicability of ANLN as a prognostic tool for some types of cancer, and the impact that ANLN has on the hallmarks of cancer. We searched academic repositories including PubMed and Google Scholar to find and review studies related to cancer and ANLN. The conclusion is that ANLN could be a potent target for cancer treatment, but the roles ANLN, other than in cytokinesis and its influence on tumour microenvironment remodeling in cancer development, must be further elucidated, and specific ANLN inhibitors should be found.
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Affiliation(s)
| | - Chang Hoon Lee
- College of Pharmacy, Dongguk University, Seoul 04620, Korea;
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11
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Xu Y, Milazzo JP, Somerville TDD, Tarumoto Y, Huang YH, Ostrander EL, Wilkinson JE, Challen GA, Vakoc CR. A TFIID-SAGA Perturbation that Targets MYB and Suppresses Acute Myeloid Leukemia. Cancer Cell 2018; 33:13-28.e8. [PMID: 29316427 PMCID: PMC5764110 DOI: 10.1016/j.ccell.2017.12.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/22/2017] [Accepted: 12/05/2017] [Indexed: 01/08/2023]
Abstract
Targeting of general coactivators is an emerging strategy to interfere with oncogenic transcription factors (TFs). However, coactivator perturbations often lead to pleiotropic effects by influencing numerous TFs. Here we identify TAF12, a subunit of TFIID and SAGA coactivator complexes, as a selective requirement for acute myeloid leukemia (AML) progression. We trace this dependency to a direct interaction between the TAF12/TAF4 histone-fold heterodimer and the transactivation domain of MYB, a TF with established roles in leukemogenesis. Ectopic expression of the TAF4 histone-fold fragment can efficiently squelch TAF12 in cells, suppress MYB, and regress AML in mice. Our study reveals a strategy for potent MYB inhibition in AML and highlights how an oncogenic TF can be selectively neutralized by targeting a general coactivator complex.
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Affiliation(s)
- Yali Xu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Molecular and Cellular Biology Program, Stony Brook University, New York, NY 11794, USA
| | - Joseph P Milazzo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Yusuke Tarumoto
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Yu-Han Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Elizabeth L Ostrander
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - John E Wilkinson
- ULAM/Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Grant A Challen
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
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12
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Bardot P, Vincent SD, Fournier M, Hubaud A, Joint M, Tora L, Pourquié O. The TAF10-containing TFIID and SAGA transcriptional complexes are dispensable for early somitogenesis in the mouse embryo. Development 2017; 144:3808-3818. [PMID: 28893950 DOI: 10.1242/dev.146902] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 09/02/2017] [Indexed: 01/09/2023]
Abstract
During development, tightly regulated gene expression programs control cell fate and patterning. A key regulatory step in eukaryotic transcription is the assembly of the pre-initiation complex (PIC) at promoters. PIC assembly has mainly been studied in vitro, and little is known about its composition during development. In vitro data suggest that TFIID is the general transcription factor that nucleates PIC formation at promoters. Here we show that TAF10, a subunit of TFIID and of the transcriptional co-activator SAGA, is required for the assembly of these complexes in the mouse embryo. We performed Taf10 conditional deletions during mesoderm development and show that Taf10 loss in the presomitic mesoderm (PSM) does not prevent cyclic gene transcription or PSM segmental patterning, whereas lateral plate differentiation is profoundly altered. During this period, global mRNA levels are unchanged in the PSM, with only a minor subset of genes dysregulated. Together, our data strongly suggest that the TAF10-containing canonical TFIID and SAGA complexes are dispensable for early paraxial mesoderm development, arguing against the generic role in transcription proposed for these fully assembled holo-complexes.
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Affiliation(s)
- Paul Bardot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France.,Université de Strasbourg, Illkirch 67400, France
| | - Stéphane D Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France .,Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France.,Université de Strasbourg, Illkirch 67400, France
| | - Marjorie Fournier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France.,Université de Strasbourg, Illkirch 67400, France
| | - Alexis Hubaud
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France.,Université de Strasbourg, Illkirch 67400, France
| | - Mathilde Joint
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France.,Université de Strasbourg, Illkirch 67400, France
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France.,Université de Strasbourg, Illkirch 67400, France
| | - Olivier Pourquié
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch 67400, France.,Université de Strasbourg, Illkirch 67400, France
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13
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Liu Y, Irie T, Yada T, Suzuki Y. A new computational method to predict transcriptional activity of a DNA sequence from diverse datasets of massively parallel reporter assays. Nucleic Acids Res 2017; 45:e124. [PMID: 28531296 PMCID: PMC5737609 DOI: 10.1093/nar/gkx396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 04/17/2017] [Accepted: 05/18/2017] [Indexed: 11/15/2022] Open
Abstract
In recent years, the dramatic increase in the number of applications for massively parallel reporter assay (MPRA) technology has produced a large body of data for various purposes. However, a computational model that can be applied to decipher regulatory codes for diverse MPRAs does not exist yet. Here, we propose a new computational method to predict the transcriptional activity of MPRAs, as well as luciferase reporter assays, based on the TRANScription FACtor database. We employed regression trees and multivariate adaptive regression splines to obtain these predictions and considered a feature redundancy-dependent formula for conventional regression trees to enable adaptation to diverse data. The developed method was applicable to various MPRAs despite the use of different types of transfected cells, sequence lengths, construct numbers and sequence types. We demonstrate that this method can predict the transcriptional activity of promoters in HEK293 cells through predictive functions that were estimated by independent assays in eight tumor cell lines. The prediction was generally good (Pearson's r = 0.68) which suggested that common active transcription factor binding sites across different cell types make greater contributions to transcriptional activity and that known promoter activity could confer transcriptional activity of unknown promoters in some instances, regardless of cell type.
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Affiliation(s)
- Ying Liu
- Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, Japan
| | - Takuma Irie
- Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, Japan
| | - Tetsushi Yada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, Japan
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14
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Scheenstra MR, De Cuyper IM, Branco-Madeira F, de Bleser P, Kool M, Meinders M, Hoogenboezem M, Mul E, Wolkers MC, Salerno F, Nota B, Saeys Y, Klarenbeek S, van IJcken WFJ, Hammad H, Philipsen S, van den Berg TK, Kuijpers TW, Lambrecht BN, Gutiérrez L. GATA1-Deficient Dendritic Cells Display Impaired CCL21-Dependent Migration toward Lymph Nodes Due to Reduced Levels of Polysialic Acid. THE JOURNAL OF IMMUNOLOGY 2016; 197:4312-4324. [DOI: 10.4049/jimmunol.1600103] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 09/29/2016] [Indexed: 02/05/2023]
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