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Xu J, Sivakumar C, Ryan CW, Rao RC. A novel interaction between RNA m 6A methyltransferase METTL3 and RREB1. Biochem Biophys Res Commun 2024; 733:150668. [PMID: 39278095 DOI: 10.1016/j.bbrc.2024.150668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Accepted: 09/05/2024] [Indexed: 09/17/2024]
Abstract
Regulation of gene expression is achieved through the modulation of regulatory inputs both pre- and post-transcriptionally. Methyltransferase-like 3 (METTL3) is a key player in pre-mRNA processing, actively catalyzing N6-methyladenosine (m6A). Among the most enriched mRNA targets of METTL3 is the Ras Responsive Element Binding Protein 1 (RREB1), a transcription factor which functions to govern cell fate, proliferation and DNA repair. Here, we show a novel interaction between METTL3 and RREB1. Further examination of this interaction indicates that METTL3's N-terminus is the primary interacting domain. Our findings uncover a novel interacting partner of METTL3, providing further insights into METTL3's regulatory network.
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Affiliation(s)
- Jing Xu
- Department of Ophthalmology and Visual Science, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, 48105, USA
| | - Charukesi Sivakumar
- Department of Ophthalmology and Visual Science, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, 48105, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, 48105, USA
| | - Charles W Ryan
- Medical Scientist Training Program, University of Michigan, Medical School, Ann Arbor, MI, 48105, USA
| | - Rajesh C Rao
- Department of Ophthalmology and Visual Science, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, 48105, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, 48105, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48105, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48105, USA; Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48105, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, 48105, USA; A. Alfred Taubman Medical Research Institute, University of Michigan, Ann Arbor, MI, 48105, USA; Section of Ophthalmology, Surgical Service, Veterans Administration Ann Arbor Healthcare System, Ann Arbor, MI, 48105, USA.
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2
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Wang L, Trasanidis N, Wu T, Dong G, Hu M, Bauer DE, Pinello L. Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics. Nat Methods 2023; 20:1368-1378. [PMID: 37537351 DOI: 10.1038/s41592-023-01971-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 07/05/2023] [Indexed: 08/05/2023]
Abstract
Gene regulatory networks (GRNs) are key determinants of cell function and identity and are dynamically rewired during development and disease. Despite decades of advancement, challenges remain in GRN inference, including dynamic rewiring, causal inference, feedback loop modeling and context specificity. To address these challenges, we develop Dictys, a dynamic GRN inference and analysis method that leverages multiomic single-cell assays of chromatin accessibility and gene expression, context-specific transcription factor footprinting, stochastic process network and efficient probabilistic modeling of single-cell RNA-sequencing read counts. Dictys improves GRN reconstruction accuracy and reproducibility and enables the inference and comparative analysis of context-specific and dynamic GRNs across developmental contexts. Dictys' network analyses recover unique insights in human blood and mouse skin development with cell-type-specific and dynamic GRNs. Its dynamic network visualizations enable time-resolved discovery and investigation of developmental driver transcription factors and their regulated targets. Dictys is available as a free, open-source and user-friendly Python package.
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Affiliation(s)
- Lingfei Wang
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Department of Pathology, Harvard Medical School, Boston, MA, USA
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nikolaos Trasanidis
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Department of Pathology, Harvard Medical School, Boston, MA, USA
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Ting Wu
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Guanlan Dong
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Department of Pathology, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Bioinformatics and Integrative Genomics PhD Program, Harvard Medical School, Boston, MA, USA
| | - Michael Hu
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Daniel E Bauer
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Luca Pinello
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Department of Pathology, Harvard Medical School, Boston, MA, USA.
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Ponomarenko M, Sharypova E, Drachkova I, Chadaeva I, Arkova O, Podkolodnaya O, Ponomarenko P, Kolchanov N, Savinkova L. Unannotated single nucleotide polymorphisms in the TATA box of erythropoiesis genes show in vitro positive involvements in cognitive and mental disorders. BMC MEDICAL GENETICS 2020; 21:165. [PMID: 33092544 PMCID: PMC7579878 DOI: 10.1186/s12881-020-01106-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 08/11/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Hemoglobin is a tetramer consisting of two α-chains and two β-chains of globin. Hereditary aberrations in the synthesis of one of the globin chains are at the root of thalassemia, one of the most prevalent monogenic diseases worldwide. In humans, in addition to α- and β-globins, embryonic zeta-globin and fetal γ-globin are expressed. Immediately after birth, the expression of fetal Aγ- and Gγ-globin ceases, and then adult β-globin is mostly expressed. It has been shown that in addition to erythroid cells, hemoglobin is widely expressed in nonerythroid cells including neurons of the cortex, hippocampus, and cerebellum in rodents; embryonic and adult brain neurons in mice; and mesencephalic dopaminergic brain cells in humans, mice, and rats. Lately, there is growing evidence that different forms of anemia (changes in the number and quality of blood cells) may be involved in (or may accompany) the pathogenesis of various cognitive and mental disorders, such as Alzheimer's and Parkinson's diseases, depression of various severity levels, bipolar disorders, and schizophrenia. Higher hemoglobin concentrations in the blood may lead to hyperviscosity, hypovolemia, and lung diseases, which may cause brain hypoxia and anomalies of brain function, which may also result in cognitive deficits. METHODS In this study, a search for unannotated single-nucleotide polymorphisms (SNPs) of erythroid genes was initially performed using our previously created and published SNP-TATA_Z-tester, which is a Web service for computational analysis of a given SNP for in silico estimation of its influence on the affinity of TATA-binding protein (TBP) for TATA and TATA-like sequences. The obtained predictions were finally verified in vitro by an electrophoretic mobility shift assay (EMSA). RESULTS On the basis of these experimental in vitro results and literature data, we studied TATA box SNPs influencing both human erythropoiesis and cognitive abilities. For instance, TBP-TATA affinity in the HbZ promoter decreases 6.6-fold as a result of a substitution in the TATA box (rs113180943), thereby possibly disrupting stage-dependent events of "switching" of hemoglobin genes and thus causing erythroblastosis. Therefore, rs113180943 may be a candidate marker of severe hemoglobinopathies with comorbid cognitive and mental disorders associated with cerebral blood flow disturbances. CONCLUSIONS The literature data and experimental and computations results suggest that the uncovered candidate SNP markers of erythropoiesis anomalies may also be studied in cohorts of patients with cognitive and/or mental disorders with comorbid erythropoiesis diseases in comparison to conventionally healthy volunteers. Research into the regulatory mechanisms by which the identified SNP markers contribute to the development of hemoglobinopathies and of the associated cognitive deficits will allow physicians not only to take timely and adequate measures against hemoglobinopathies but also to implement strategies preventing cognitive and mental disorders.
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Affiliation(s)
- Mikhail Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia. .,Novosibirsk State University, 1 Pirogova Street, Novosibirsk, 630090, Russia.
| | - Ekaterina Sharypova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia
| | - Irina Drachkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia
| | - Irina Chadaeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia
| | - Olga Arkova
- Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilova Street, Moscow, 119334, Russia
| | - Olga Podkolodnaya
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia
| | - Petr Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia
| | - Nikolay Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia
| | - Ludmila Savinkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Ave, Novosibirsk, 630090, Russia
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Deng YN, Xia Z, Zhang P, Ejaz S, Liang S. Transcription Factor RREB1: from Target Genes towards Biological Functions. Int J Biol Sci 2020; 16:1463-1473. [PMID: 32210733 PMCID: PMC7085234 DOI: 10.7150/ijbs.40834] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/06/2020] [Indexed: 02/05/2023] Open
Abstract
The Ras-responsive element binding protein 1(RREB1) is a member of zinc finger transcription factors, which is widely involved in biological processes including cell proliferation, transcriptional regulation and DNA damage repair. New findings reveal RREB1 functions as both transcriptional repressors and transcriptional activators for transcriptional regulation of target genes. The activation of RREB1 is regulated by MAPK pathway. We have summarized the target genes of RREB1 and discussed RREB1 roles in the cancer development. In addition, increasing evidences suggest that RREB1 is a potential risk gene for type 2 diabetes and obesity. We also review the current clinical application of RREB1 as a biomarker for melanoma detection. In conclusion, RREB1 is a promising diagnostic biomarker or new drug target for cancers and metabolic diseases.
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Affiliation(s)
- Ya-Nan Deng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, No.17, 3rd Section of People's South Road, Chengdu, 610041, P.R. China
| | - Zijing Xia
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, No.17, 3rd Section of People's South Road, Chengdu, 610041, P.R. China.,Department of Rheumatology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, P. R. China
| | - Peng Zhang
- Department of Urinary Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610041, P. R. China
| | - Samina Ejaz
- Department of Biochemistry and Biotechnology, Baghdad Campus, The Islamia University of Bahawalpur, Pakistan
| | - Shufang Liang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, No.17, 3rd Section of People's South Road, Chengdu, 610041, P.R. China
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5
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Yao J, Zhong L, Zhong P, Liu D, Yuan Z, Liu J, Yao S, Zhao Y, Chen M, Li L, Liu L, Liu B. RAS-Responsive Element-Binding Protein 1 Blocks the Granulocytic Differentiation of Myeloid Leukemia Cells. Oncol Res 2019; 27:809-818. [PMID: 30982491 PMCID: PMC7848438 DOI: 10.3727/096504018x15451301487729] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
RAS-responsive element-binding protein 1 (RREB1) is a transcription factor that is implicated in RAS signaling and multiple tumors. However, the role of RREB1 in acute myeloid leukemia has not been studied. We found that RREB1 is overexpressed in AML patients and myeloid leukemia cell lines (NB4 and HL-60), and RREB1 expression was significantly decreased during granulocytic differentiation of myeloid leukemia cells induced by all-trans retinoic acid (ATRA). Then we performed a RREB1 knockdown assay in NB4 and HL-60 cells; the results showed that knockdown of RREB1 upregulated expression of CD11b, CEBPβ, and microRNA-145 (miR-145), which hinted that knockdown of RREB1 enhanced granulocytic differentiation of myeloid leukemia cells. In addition, inhibitor of miR-145 can offset the enhanced effect on granulocytic differentiation mediated by downregulation of RREB1. These collective findings demonstrated that RREB1 blocks granulocytic differentiation of myeloid leukemia cells by inhibiting the expression of miR-145 and downstream targets of the RAS signal pathway. These may provide a promising therapeutic target for AML patients.
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Affiliation(s)
- Juanjuan Yao
- Central Laboratory of Yong Chuan Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Liang Zhong
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, P.R. China
| | - Pengqiang Zhong
- Central Laboratory of Yong Chuan Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Dongdong Liu
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, P.R. China
| | - Zhen Yuan
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, P.R. China
| | - Junmei Liu
- Central Laboratory of Yong Chuan Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Shifei Yao
- Central Laboratory of Yong Chuan Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Yi Zhao
- Central Laboratory of Yong Chuan Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Min Chen
- Central Laboratory of Yong Chuan Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Lianwen Li
- Central Laboratory of Yong Chuan Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Lu Liu
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, P.R. China
| | - Beizhong Liu
- Central Laboratory of Yong Chuan Hospital, Chongqing Medical University, Chongqing, P.R. China
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Scheps KG, Varela V, Targovnik HM. The Chaperones Involved in Hemoglobin Synthesis Take the Spotlight: Analysis of AHSP in the Argentinean Population and Review of the Literature. Hemoglobin 2018; 42:310-314. [PMID: 30558442 DOI: 10.1080/03630269.2018.1544145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Hemoglobin (Hb) synthesis is a complex, well-coordinated process that requires molecular chaperones. These intervene in different steps: regulating epigenetic mechanisms necessary for the adequate expression of the α- and β-globin clusters, binding the nascent peptides and helping them acquire their native structure, preventing oxidative damage by free globin chains and preventing the cleavage of essential erythroid transcription factors. This study analyzed the distribution of the single nucleotide polymorphism (SNP) rs4296276 in intron 1 of the α-globin chaperone α Hb-stabilizing protein (AHSP) in the Argentinean population. The risk allele was found in thalassemia patients who exhibited more severe phenotypes than expected. Future studies may help establish the role of these chaperones as modifiers in pathological states with globin chain imbalance, such as thalassemia.
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Affiliation(s)
- Karen G Scheps
- a Departamento de Microbiología , Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Inmunología, Biotecnología y Genética/Cátedra de Genética , Buenos Aires , Argentina.,b Instituto de Inmunología, Genética y Metabolismo (INIGEM) , CONICET-Universidad de Buenos Aires , Buenos Aires , Argentina
| | - Viviana Varela
- a Departamento de Microbiología , Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Inmunología, Biotecnología y Genética/Cátedra de Genética , Buenos Aires , Argentina.,b Instituto de Inmunología, Genética y Metabolismo (INIGEM) , CONICET-Universidad de Buenos Aires , Buenos Aires , Argentina
| | - Héctor M Targovnik
- a Departamento de Microbiología , Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Inmunología, Biotecnología y Genética/Cátedra de Genética , Buenos Aires , Argentina.,b Instituto de Inmunología, Genética y Metabolismo (INIGEM) , CONICET-Universidad de Buenos Aires , Buenos Aires , Argentina
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7
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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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Vierstra J, Reik A, Chang KH, Stehling-Sun S, Zhou YY, Hinkley SJ, Paschon DE, Zhang L, Psatha N, Bendana YR, O'Neill CM, Song AH, Mich A, Liu PQ, Lee G, Bauer DE, Holmes MC, Orkin SH, Papayannopoulou T, Stamatoyannopoulos G, Rebar EJ, Gregory PD, Urnov FD, Stamatoyannopoulos JA. Functional footprinting of regulatory DNA. Nat Methods 2015; 12:927-30. [PMID: 26322838 PMCID: PMC5381659 DOI: 10.1038/nmeth.3554] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 07/30/2015] [Indexed: 12/19/2022]
Abstract
Regulatory regions harbor multiple transcription factor (TF) recognition sites; however, the contribution of individual sites to regulatory function remains challenging to define. We describe an approach that exploits the error-prone nature of genome editing-induced double-strand break repair to map functional elements within regulatory DNA at nucleotide resolution. We demonstrate the approach on a human erythroid enhancer, revealing single TF recognition sites that gate the majority of downstream regulatory function.
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Affiliation(s)
- Jeff Vierstra
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | - Kai-Hsin Chang
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA
| | | | | | | | | | - L. Zhang
- Sangamo BioSciences, Pt. Richmond, CA
| | - Nikoletta Psatha
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA
| | | | | | | | | | | | - Gary Lee
- Sangamo BioSciences, Pt. Richmond, CA
| | - Daniel E. Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
| | | | - Stuart H. Orkin
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
| | | | | | | | | | | | - John A. Stamatoyannopoulos
- Department of Genome Sciences, University of Washington, Seattle, WA
- Division of Oncology, Department of Medicine, University of Washington, Seattle, WA
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9
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Pharmacological Induction of Human Fetal Globin Gene in Hydroxyurea-Resistant Primary Adult Erythroid Cells. Mol Cell Biol 2015; 35:2541-53. [PMID: 25986606 DOI: 10.1128/mcb.00035-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/06/2015] [Indexed: 11/20/2022] Open
Abstract
Pharmacological induction of the fetal γ globin gene and the consequent formation of HbF (α2/γ2) in adult erythroid cells are one feasible therapeutic strategy for sickle cell disease (SCD) and severe β-thalassemias. Hydroxyurea (HU) is the current drug of choice for SCD, but serious side effects limit its clinical use. Moreover, 30 to 50% of patients are irresponsive to HU treatment. We have used high-throughput screening to identify benzo[de]benzo[4,5]imidazo[2,1-a]isoquinolin-7-one and its derivatives (compounds I to VI) as potent γ globin inducers. Of the compounds, I to V exert superior γ globin induction and have better therapeutic potential than HU, likely because of their activation of the p38 mitogen-activated protein kinase (MAPK) signaling pathway and modulation of expression levels and/or chromosome binding of γ globin gene regulators, including BCL11A, and chromatin structure over the γ globin promoter. Unlike sodium butyrate (NaB), the global levels of acetylated histones H3 and H4 are not changed by compound II treatment. Remarkably, compound II induces the γ globin gene in HU-resistant primary human adult erythroid cells, the p38 signaling pathway of which appears to be irresponsive to HU and NaB as well as compound II. This study provides a new framework for the development of new and superior compounds for treating SCD and severe β-thalassemias.
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10
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Jjingo D, Conley AB, Wang J, Mariño-Ramírez L, Lunyak VV, Jordan IK. Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression. Mob DNA 2014; 5:14. [PMID: 25018785 PMCID: PMC4090950 DOI: 10.1186/1759-8753-5-14] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 04/10/2014] [Indexed: 11/26/2022] Open
Abstract
Background Mammalian-wide interspersed repeats (MIRs) are the most ancient family of transposable elements (TEs) in the human genome. The deep conservation of MIRs initially suggested the possibility that they had been exapted to play functional roles for their host genomes. MIRs also happen to be the only TEs whose presence in-and-around human genes is positively correlated to tissue-specific gene expression. Similar associations of enhancer prevalence within genes and tissue-specific expression, along with MIRs’ previous implication as providing regulatory sequences, suggested a possible link between MIRs and enhancers. Results To test the possibility that MIRs contribute functional enhancers to the human genome, we evaluated the relationship between MIRs and human tissue-specific enhancers in terms of genomic location, chromatin environment, regulatory function, and mechanistic attributes. This analysis revealed MIRs to be highly concentrated in enhancers of the K562 and HeLa human cell-types. Significantly more enhancers were found to be linked to MIRs than would be expected by chance, and putative MIR-derived enhancers are characterized by a chromatin environment highly similar to that of canonical enhancers. MIR-derived enhancers show strong associations with gene expression levels, tissue-specific gene expression and tissue-specific cellular functions, including a number of biological processes related to erythropoiesis. MIR-derived enhancers were found to be a rich source of transcription factor binding sites, underscoring one possible mechanistic route for the element sequences co-option as enhancers. There is also tentative evidence to suggest that MIR-enhancer function is related to the transcriptional activity of non-coding RNAs. Conclusions Taken together, these data reveal enhancers to be an important cis-regulatory platform from which MIRs can exercise a regulatory function in the human genome and help to resolve a long-standing conundrum as to the reason for MIRs’ deep evolutionary conservation.
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Affiliation(s)
- Daudi Jjingo
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Andrew B Conley
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jianrong Wang
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Leonardo Mariño-Ramírez
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA ; PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia
| | - Victoria V Lunyak
- PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia ; Buck Institute for Research on Aging, Novato, CA, USA
| | - I King Jordan
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA ; PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia
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11
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CtBP and associated LSD1 are required for transcriptional activation by NeuroD1 in gastrointestinal endocrine cells. Mol Cell Biol 2014; 34:2308-17. [PMID: 24732800 DOI: 10.1128/mcb.01600-13] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Gene expression programs required for differentiation depend on both DNA-bound transcription factors and surrounding histone modifications. Expression of the basic helix-loop-helix (bHLH) protein NeuroD1 is restricted to endocrine cells in the gastrointestinal (GI) tract, where it is important for endocrine differentiation. RREB1 (RAS-responsive element binding protein 1), identified as a component of the CtBP corepressor complex, binds to nearby DNA elements to associate with NeuroD and potentiate transcription of a NeuroD1 target gene. Transcriptional activation by RREB1 depends on recruitment of CtBP with its associated proteins, including LSD1, through its PXDLS motifs. The mechanism of transcriptional activation by CtBP has not been previously characterized. Here we found that activation was dependent on the histone H3 lysine 9 (H3K9) demethylase activity of LSD1, which removes repressive methyl marks from dimethylated H3K9 (H3K9Me2), to facilitate subsequent H3K9 acetylation by the NeuroD1-associated histone acetyltransferase, P300/CBP-associated factor (PCAF). The secretin, β-glucokinase, insulin I, and insulin II genes, four known direct targets of NeuroD1 in intestinal and pancreatic endocrine cells, all show similar promoter occupancy by CtBP-associated proteins and PCAF, with acetylation of H3K9. This work may indicate a mechanism for selective regulation of transcription by CtBP and LSD1 involving their association with specific transcription factors and cofactors to drive tissue-specific transcription.
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Ming L, Wilk R, Reed BH, Lipshitz HD. Drosophila Hindsight and mammalian RREB-1 are evolutionarily conserved DNA-binding transcriptional attenuators. Differentiation 2014; 86:159-70. [PMID: 24418439 DOI: 10.1016/j.diff.2013.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/25/2013] [Accepted: 12/05/2013] [Indexed: 12/22/2022]
Abstract
The Drosophila Hindsight (hnt) gene encodes a C2H2-type Zinc-finger protein, HNT, that plays multiple developmental roles including control of embryonic germ band retraction and regulation of retinal cell fate and morphogenesis. While the developmental functions of the human HNT homolog, RREB-1, are unknown, it has been shown to function as a transcriptional modulator of several tumor suppressor genes. Here we investigate HNT's functional motifs, target genes and its regulatory abilities. We show that the C-terminal region of HNT, containing the last five of its 14 Zinc fingers, binds in vitro to DNA elements very similar to those identified for RREB-1. We map HNT's in vivo binding sites on salivary gland polytene chromosomes and define, at high resolution, where HNT is bound to two target genes, hnt itself and nervy (nvy). Data from both loss-of-function and over-expression experiments show that HNT attenuates the transcription of these two targets in a tissue-specific manner. RREB-1, when expressed in Drosophila, binds to the same polytene chromosome sites as HNT, attenuates expression of the hnt and nvy genes, and rescues the germ band retraction phenotype. HNT's ninth Zinc finger has degenerated or been lost in the vertebrate lineage. We show that a HNT protein mutant for this finger can also attenuate target gene expression and rescue germ band retraction. Thus HNT and RREB-1 are functional homologs at the level of DNA binding, transcriptional regulation and developmental control.
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Affiliation(s)
- Liang Ming
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8.
| | - Ronit Wilk
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8.
| | - Bruce H Reed
- Department of Biology, University of Waterloo, 200 University Avenue W, Waterloo, Ontario, Canada N2L 3G1.
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8.
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Yamane T, Suzui S, Kitaura H, Takahashi-Niki K, Iguchi-Ariga SMM, Ariga H. Transcriptional activation of the cholecystokinin gene by DJ-1 through interaction of DJ-1 with RREB1 and the effect of DJ-1 on the cholecystokinin level in mice. PLoS One 2013; 8:e78374. [PMID: 24348900 PMCID: PMC3865339 DOI: 10.1371/journal.pone.0078374] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 09/19/2013] [Indexed: 01/11/2023] Open
Abstract
DJ-1 is an oncogene and also causative gene for familial Parkinson’s disease. DJ-1 has multiple functions, including transcriptional regulation. DJ-1 acts as a coactivator that binds to various transcription factors, resulting in stimulation or repression of the expression of their target genes. In this study, we found that the cholecystokinin (CCK) gene is a transcriptional target gene for DJ-1. CCK is a peptide hormone and plays roles in contraction of the gallbladder and in promotion of secretion of pancreatic fluid. CCK is co-localized with dopamine in the substantia nigra to regulate release of dopamine. Reduced expression of CCK mRNA was observed in DJ-1-knockdown cells. The Ras-responsive element (RRE) and Sp1 site were essential for promoter activity, and DJ-1 stimulated promoter activity by binding to RRE-binding protein 1 (RREBP1). The complex of DJ-1 with RREB1 but not with Sp1 bound to the RRE. Furthermore, the reduced CCK level in the serum from DJ-1-knockout mice compared to that from wild-type mice was observed. This is the first report showing that DJ-1 participates in peptide hormone synthesis.
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Affiliation(s)
- Takuya Yamane
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Sayaka Suzui
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Hirotake Kitaura
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | | | | | - Hiroyoshi Ariga
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
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Dröge J, Pande A, Englander EW, Makałowski W. Comparative genomics of neuroglobin reveals its early origins. PLoS One 2012; 7:e47972. [PMID: 23133533 PMCID: PMC3485006 DOI: 10.1371/journal.pone.0047972] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 09/24/2012] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Neuroglobin (Ngb) is a hexacoordinated globin expressed mainly in the central and peripheral nervous system of vertebrates. Although several hypotheses have been put forward regarding the role of neuroglobin, its definite function remains uncertain. Ngb appears to have a neuro-protective role enhancing cell viability under hypoxia and other types of oxidative stress. Ngb is phylogenetically ancient and has a substitution rate nearly four times lower than that of other vertebrate globins, e.g. hemoglobin. Despite its high sequence conservation among vertebrates Ngb seems to be elusive in invertebrates. PRINCIPAL FINDINGS We determined candidate orthologs in invertebrates and identified a globin of the placozoan Trichoplax adhaerens that is most likely orthologous to vertebrate Ngb and confirmed the orthologous relationship of the polymeric globin of the sea urchin Strongylocentrotus purpuratus to Ngb. The putative orthologous globin genes are located next to genes orthologous to vertebrate POMT2 similarly to localization of vertebrate Ngb. The shared syntenic position of the globins from Trichoplax, the sea urchin and of vertebrate Ngb strongly suggests that they are orthologous. A search for conserved transcription factor binding sites (TFBSs) in the promoter regions of the Ngb genes of different vertebrates via phylogenetic footprinting revealed several TFBSs, which may contribute to the specific expression of Ngb, whereas a comparative analysis with myoglobin revealed several common TFBSs, suggestive of regulatory mechanisms common to globin genes. SIGNIFICANCE Identification of the placozoan and echinoderm genes orthologous to vertebrate neuroglobin strongly supports the hypothesis of the early evolutionary origin of this globin, as it shows that neuroglobin was already present in the placozoan-bilaterian last common ancestor. Computational determination of the transcription factor binding sites repertoire provides on the one hand a set of transcriptional factors that are responsible for the specific expression of the Ngb genes and on the other hand a set of factors potentially controlling expression of a couple of different globin genes.
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Affiliation(s)
- Jasmin Dröge
- Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Muenster, Germany
| | - Amit Pande
- Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Muenster, Germany
| | - Ella W. Englander
- Department of Surgery, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Wojciech Makałowski
- Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Muenster, Germany
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