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Kawase M, Ichiyanagi K. Mouse retrotransposons: sequence structure, evolutionary age, genomic distribution and function. Genes Genet Syst 2024; 98:337-351. [PMID: 37989301 DOI: 10.1266/ggs.23-00221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Retrotransposons are transposable elements that are transposed via transcription and reverse transcription. Their copies have accumulated in the genome of mammals, occupying approximately 40% of mammalian genomic mass. These copies are often involved in numerous phenomena, such as chromatin spatial organization, gene expression, development and disease, and have been recognized as a driving force in evolution. Different organisms have gained specific retrotransposon subfamilies and retrotransposed copies, such as hundreds of Mus-specific subfamilies with diverse sequences and genomic locations. Despite this complexity, basic information is still necessary for present-day genomic and epigenomic studies. Herein, we describe the characteristics of each subfamily of Mus-specific retrotransposons in terms of sequence structure, phylogenetic relationships, evolutionary age, and preference for A or B compartments of chromatin.
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Affiliation(s)
- Masaki Kawase
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University
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2
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Jones J, Chen Y, Tiwari M, Li J, Ling J, Sen GL. KLF3 Mediates Epidermal Differentiation through the Epigenomic Writer CBP. iScience 2020; 23:101320. [PMID: 32659720 PMCID: PMC7358749 DOI: 10.1016/j.isci.2020.101320] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 06/02/2020] [Accepted: 06/24/2020] [Indexed: 12/24/2022] Open
Abstract
Impairments in the differentiation process can lead to skin diseases that can afflict ∼20% of the population. Thus, it is of utmost importance to understand the factors that promote the differentiation process. Here we identify the transcription factor KLF3 as a regulator of epidermal differentiation. Knockdown of KLF3 results in reduced differentiation gene expression and increased cell cycle gene expression. Over half of KLF3's genomic binding sites occur at active enhancers. KLF3 binds to active enhancers proximal to differentiation genes that are dependent upon KLF3 for expression. KLF3's genomic binding sites also highly overlaps with CBP, a histone acetyltransferase necessary for activating enhancers. Depletion of KLF3 causes reduced CBP localization at enhancers proximal to differentiation gene clusters, which leads to loss of enhancer activation but not priming. Our results suggest that KLF3 is necessary to recruit CBP to activate enhancers and drive epidermal differentiation gene expression.
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Affiliation(s)
- Jackson Jones
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - Yifang Chen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - Manisha Tiwari
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - Jingting Li
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - Ji Ling
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - George L Sen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA.
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Mustafin RN. The Role of Transposable Elements in the Differentiation of Stem Cells. MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY 2019. [DOI: 10.3103/s0891416819020071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Mustafin RN, Khusnutdinova EK. The role of transposable elements in the ecological morphogenesis under the influence of stress. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In natural selection, insertional mutagenesis is an important source of genome variability. Transposons are sensors of environmental stress effects, which contribute to adaptation and speciation. These effects are due to changes in the mechanisms of morphogenesis, since transposons contain regulatory sequences that have cis and trans effects on specific protein-coding genes. In variability of genomes, the horizontal transfer of transposons plays an important role, because it contributes to changing the composition of transposons and the acquisition of new properties. Transposons are capable of site-specific transpositions, which lead to the activation of stress response genes. Transposons are sources of non-coding RNA, transcription factors binding sites and protein-coding genes due to domestication, exonization, and duplication. These genes contain nucleotide sequences that interact with non-coding RNAs processed from transposons transcripts, and therefore they are under the control of epigenetic regulatory networks involving transposons. Therefore, inherited features of the location and composition of transposons, along with a change in the phenotype, play an important role in the characteristics of responding to a variety of environmental stressors. This is the basis for the selection and survival of organisms with a specific composition and arrangement of transposons that contribute to adaptation under certain environmental conditions. In evolution, the capability to transpose into specific genome sites, regulate gene expression, and interact with transcription factors, along with the ability to respond to stressors, is the basis for rapid variability and speciation by altering the regulation of ontogenesis. The review presents evidence of tissue-specific and stage-specific features of transposon activation and their role in the regulation of cell differentiation to confirm their role in ecological morphogenesis.
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Affiliation(s)
| | - E. K. Khusnutdinova
- Bashkir State Medical University;
Institute of Biochemistry and Genetics – Subdivision of the Ufa Federal Research Centre of RAS
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Mustafin RN, Khusnutdinova EK. Prospects in the Search for Peptides for Specific Regulation of Aging. ADVANCES IN GERONTOLOGY 2019. [DOI: 10.1134/s2079057019020176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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6
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Mustafin RN. Functional Dualism of Transposon Transcripts in Evolution of Eukaryotic Genomes. Russ J Dev Biol 2019. [DOI: 10.1134/s1062360418070019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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7
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Mustafin RN. The Relationship between Transposons and Transcription Factors in the Evolution of Eukaryotes. J EVOL BIOCHEM PHYS+ 2019. [DOI: 10.1134/s0022093019010022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats. Nat Genet 2017; 49:1052-1060. [PMID: 28604729 DOI: 10.1038/ng.3889] [Citation(s) in RCA: 188] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 05/03/2017] [Indexed: 12/13/2022]
Abstract
Several mechanisms of action have been proposed for DNA methyltransferase and histone deacetylase inhibitors (DNMTi and HDACi), primarily based on candidate-gene approaches. However, less is known about their genome-wide transcriptional and epigenomic consequences. By mapping global transcription start site (TSS) and chromatin dynamics, we observed the cryptic transcription of thousands of treatment-induced non-annotated TSSs (TINATs) following DNMTi and HDACi treatment. The resulting transcripts frequently splice into protein-coding exons and encode truncated or chimeric ORFs translated into products with predicted abnormal or immunogenic functions. TINAT transcription after DNMTi treatment coincided with DNA hypomethylation and gain of classical promoter histone marks, while HDACi specifically induced a subset of TINATs in association with H2AK9ac, H3K14ac, and H3K23ac. Despite this mechanistic difference, both inhibitors convergently induced transcription from identical sites, as we found TINATs to be encoded in solitary long terminal repeats of the ERV9/LTR12 family, which are epigenetically repressed in virtually all normal cells.
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Norton LJ, Hallal S, Stout ES, Funnell APW, Pearson RCM, Crossley M, Quinlan KGR. Direct competition between DNA binding factors highlights the role of Krüppel-like Factor 1 in the erythroid/megakaryocyte switch. Sci Rep 2017; 7:3137. [PMID: 28600522 PMCID: PMC5466599 DOI: 10.1038/s41598-017-03289-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 04/26/2017] [Indexed: 11/15/2022] Open
Abstract
The Krüppel-like factor (KLF) family of transcription factors play critical roles in haematopoiesis. KLF1, the founding member of the family, has been implicated in the control of both erythropoiesis and megakaryopoiesis. Here we describe a novel system using an artificial dominant negative isoform of KLF1 to investigate the role of KLF1 in the erythroid/megakaryocytic switch in vivo. We developed murine cell lines stably overexpressing a GST-KLF1 DNA binding domain fusion protein (GST-KLF1 DBD), as well as lines expressing GST only as a control. Interestingly, overexpression of GST-KLF1 DBD led to an overall reduction in erythroid features and an increase in megakaryocytic features indicative of a reduced function of endogenous KLF1. We simultaneously compared in vivo DNA occupancy of both endogenous KLF1 and GST-KLF1 DBD by ChIP qPCR. Here we found that GST-KLF1 DBD physically displaces endogenous KLF1 at a number of loci, providing novel in vivo evidence of direct competition between DNA binding proteins. These results highlight the role of KLF1 in the erythroid/megakaryocyte switch and suggest that direct competition between transcription factors with similar consensus sequences is an important mechanism in transcriptional regulation.
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Affiliation(s)
- Laura J Norton
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Samantha Hallal
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia
| | - Elizabeth S Stout
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Alister P W Funnell
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.,School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia
| | - Richard C M Pearson
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.,School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.,School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
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Mak KS, Burdach J, Norton LJ, Pearson RCM, Crossley M, Funnell APW. Erratum to: Repression of chimeric transcripts emanating from endogenous retrotransposons by a sequence-specific transcription factor. Genome Biol 2016; 17:119. [PMID: 27259285 PMCID: PMC4891914 DOI: 10.1186/s13059-016-0977-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 05/05/2016] [Indexed: 11/10/2022] Open
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Thompson PJ, Macfarlan TS, Lorincz MC. Long Terminal Repeats: From Parasitic Elements to Building Blocks of the Transcriptional Regulatory Repertoire. Mol Cell 2016; 62:766-76. [PMID: 27259207 PMCID: PMC4910160 DOI: 10.1016/j.molcel.2016.03.029] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The life cycle of endogenous retroviruses (ERVs), also called long terminal repeat (LTR) retrotransposons, begins with transcription by RNA polymerase II followed by reverse transcription and re-integration into the host genome. While most ERVs are relics of ancient integration events, "young" proviruses competent for retrotransposition-found in many mammals, but not humans-represent an ongoing threat to host fitness. As a consequence, several restriction pathways have evolved to suppress their activity at both transcriptional and post-transcriptional stages of the viral life cycle. Nevertheless, accumulating evidence has revealed that LTR sequences derived from distantly related ERVs have been exapted as regulatory sequences for many host genes in a wide range of cell types throughout mammalian evolution. Here, we focus on emerging themes from recent studies cataloging the diversity of ERV LTRs acting as important transcriptional regulatory elements in mammals and explore the molecular features that likely account for LTR exaptation in developmental and tissue-specific gene regulation.
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Affiliation(s)
- Peter J Thompson
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Todd S Macfarlan
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA.
| | - Matthew C Lorincz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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Dewi V, Kwok A, Lee S, Lee MM, Tan YM, Nicholas HR, Isono KI, Wienert B, Mak KS, Knights AJ, Quinlan KGR, Cordwell SJ, Funnell APW, Pearson RCM, Crossley M. Phosphorylation of Krüppel-like factor 3 (KLF3/BKLF) and C-terminal binding protein 2 (CtBP2) by homeodomain-interacting protein kinase 2 (HIPK2) modulates KLF3 DNA binding and activity. J Biol Chem 2015; 290:8591-605. [PMID: 25659434 DOI: 10.1074/jbc.m115.638338] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Krüppel-like factor 3 (KLF3/BKLF), a member of the Krüppel-like factor (KLF) family of transcription factors, is a widely expressed transcriptional repressor with diverse biological roles. Although there is considerable understanding of the molecular mechanisms that allow KLF3 to silence the activity of its target genes, less is known about the signal transduction pathways and post-translational modifications that modulate KLF3 activity in response to physiological stimuli. We observed that KLF3 is modified in a range of different tissues and found that the serine/threonine kinase homeodomain-interacting protein kinase 2 (HIPK2) can both bind and phosphorylate KLF3. Mass spectrometry identified serine 249 as the primary phosphorylation site. Mutation of this site reduces the ability of KLF3 to bind DNA and repress transcription. Furthermore, we also determined that HIPK2 can phosphorylate the KLF3 co-repressor C-terminal binding protein 2 (CtBP2) at serine 428. Finally, we found that phosphorylation of KLF3 and CtBP2 by HIPK2 strengthens the interaction between these two factors and increases transcriptional repression by KLF3. Taken together, our results indicate that HIPK2 potentiates the activity of KLF3.
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Affiliation(s)
- Vitri Dewi
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Alister Kwok
- the School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, 2006, Australia, and
| | - Stella Lee
- the School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, 2006, Australia, and
| | - Ming Min Lee
- the School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, 2006, Australia, and
| | - Yee Mun Tan
- the School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, 2006, Australia, and
| | - Hannah R Nicholas
- the School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, 2006, Australia, and
| | - Kyo-ichi Isono
- the RIKEN Research Center for Allergy and Immunology, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan
| | - Beeke Wienert
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Ka Sin Mak
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Alexander J Knights
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Kate G R Quinlan
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Stuart J Cordwell
- the School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, 2006, Australia, and
| | - Alister P W Funnell
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Richard C M Pearson
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Merlin Crossley
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia, the School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, 2006, Australia, and
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Upton KR, Faulkner GJ. Blood from 'junk': the LTR chimeric transcript Pu.2 promotes erythropoiesis. Mob DNA 2014; 5:15. [PMID: 24839466 PMCID: PMC4023170 DOI: 10.1186/1759-8753-5-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/02/2014] [Indexed: 11/25/2022] Open
Abstract
Transposable elements (TEs) are a prominent feature of most eukaryotic genomes. Despite rapidly accumulating evidence for the role of TE-driven insertional mutagenesis and structural variation in genome evolution, few clear examples of individual TEs impacting biology via perturbed gene regulation are available. A recent report describes the discovery of an alternative promoter for the murine erythroid transcription factor Pu.1. This promoter is located in an ORR1A0 long terminal repeat (LTR) retrotransposon intronic to Pu.1 and is regulated by the Krüppel-like factors KLF1 and KLF3. Expression of the resultant chimeric transcript, called Pu.2, spontaneously induces erythroid differentiation in vitro. These experiments illustrate how transcription factor binding sites spread by retrotransposition have the potential to impact networks encoding key biological processes in the host genome.
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Affiliation(s)
- Kyle R Upton
- Mater Research Institute - University of Queensland, TRI Building, 4102 Brisbane, QLD, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute - University of Queensland, TRI Building, 4102 Brisbane, QLD, Australia ; School of Biomedical Sciences, University of Queensland, 4072 Brisbane, QLD, Australia
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Funnell APW, Vernimmen D, Lim WF, Mak KS, Wienert B, Martyn GE, Artuz CM, Burdach J, Quinlan KGR, Higgs DR, Whitelaw E, Pearson RCM, Crossley M. Differential regulation of the α-globin locus by Krüppel-like Factor 3 in erythroid and non-erythroid cells. BMC Mol Biol 2014; 15:8. [PMID: 24885809 PMCID: PMC4033687 DOI: 10.1186/1471-2199-15-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 05/06/2014] [Indexed: 12/17/2022] Open
Abstract
Background Krüppel-like Factor 3 (KLF3) is a broadly expressed zinc-finger transcriptional repressor with diverse biological roles. During erythropoiesis, KLF3 acts as a feedback repressor of a set of genes that are activated by Krüppel-like Factor 1 (KLF1). Noting that KLF1 binds α-globin gene regulatory sequences during erythroid maturation, we sought to determine whether KLF3 also interacts with the α-globin locus to regulate transcription. Results We found that expression of a human transgenic α-globin reporter gene is markedly up-regulated in fetal and adult erythroid cells of Klf3−/− mice. Inspection of the mouse and human α-globin promoters revealed a number of canonical KLF-binding sites, and indeed, KLF3 was shown to bind to these regions both in vitro and in vivo. Despite these observations, we did not detect an increase in endogenous murine α-globin expression in Klf3−/− erythroid tissue. However, examination of murine embryonic fibroblasts lacking KLF3 revealed significant de-repression of α-globin gene expression. This suggests that KLF3 may contribute to the silencing of the α-globin locus in non-erythroid tissue. Moreover, ChIP-Seq analysis of murine fibroblasts demonstrated that across the locus, KLF3 does not occupy the promoter regions of the α-globin genes in these cells, but rather, binds to upstream, DNase hypersensitive regulatory regions. Conclusions These findings reveal that the occupancy profile of KLF3 at the α-globin locus differs in erythroid and non-erythroid cells. In erythroid cells, KLF3 primarily binds to the promoters of the adult α-globin genes, but appears dispensable for normal transcriptional regulation. In non-erythroid cells, KLF3 distinctly binds to the HS-12 and HS-26 elements and plays a non-redundant, albeit modest, role in the silencing of α-globin expression.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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