1
|
Roy AL. Role of the multifunctional transcription factor TFII-I in DNA damage repair. DNA Repair (Amst) 2021; 106:103175. [PMID: 34280590 DOI: 10.1016/j.dnarep.2021.103175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/07/2021] [Indexed: 11/27/2022]
Abstract
The multifunctional transcription factor TFII-I, encoded by the GTF2I gene, is implicated in various biological pathways, and associated with multiple human disorders. Evidence is also mounting to suggest that TFII-I is involved in DNA damage repair pathways. Here I bring together these recent observations and suggest a connection between transcriptional and DNA repair functions of TFII-I.
Collapse
Affiliation(s)
- Ananda L Roy
- National Institutes of Health, Laboratory of Molecular Biology and Immunology, Biomedical Research Center, National Institute on Aging, Baltimore, MD, United States.
| |
Collapse
|
2
|
Alesi V, Loddo S, Orlando V, Genovese S, Di Tommaso S, Liambo MT, Pompili D, Ferretti D, Calacci C, Catino G, Falasca R, Dentici ML, Novelli A, Digilio MC, Dallapiccola B. Atypical 7q11.23 deletions excluding ELN gene result in Williams-Beuren syndrome craniofacial features and neurocognitive profile. Am J Med Genet A 2020; 185:242-249. [PMID: 33098373 DOI: 10.1002/ajmg.a.61937] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/01/2020] [Accepted: 10/10/2020] [Indexed: 11/08/2022]
Abstract
Williams-Beurens syndrome (WBS) is a rare genetic disorder caused by a recurrent 7q11.23 microdeletion. Clinical characteristics include typical facial dysmorphisms, weakness of connective tissue, short stature, mild to moderate intellectual disability and distinct behavioral phenotype. Cardiovascular diseases are common due to haploinsufficiency of ELN gene. A few cases of larger or smaller deletions have been reported spanning towards the centromeric or the telomeric regions, most of which included ELN gene. We report on three patients from two unrelated families, presenting with distinctive WBS features, harboring an atypical distal deletion excluding ELN gene. Our study supports a critical role of CLIP2, GTF2IRD1, and GTF2I gene in the WBS neurobehavioral profile and in craniofacial features, highlights a possible role of HIP1 in the autism spectrum disorder, and delineates a subgroup of WBS individuals with an atypical distal deletion not associated to an increased risk of cardiovascular defects.
Collapse
Affiliation(s)
- Viola Alesi
- Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Sara Loddo
- Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
3
|
Morris DL, Sheng Y, Zhang Y, Wang YF, Zhu Z, Tombleson P, Chen L, Cunninghame Graham DS, Bentham J, Roberts AL, Chen R, Zuo X, Wang T, Wen L, Yang C, Liu L, Yang L, Li F, Huang Y, Yin X, Yang S, Rönnblom L, Fürnrohr BG, Voll RE, Schett G, Costedoat-Chalumeau N, Gaffney PM, Lau YL, Zhang X, Yang W, Cui Y, Vyse TJ. Genome-wide association meta-analysis in Chinese and European individuals identifies ten new loci associated with systemic lupus erythematosus. Nat Genet 2016; 48:940-946. [PMID: 27399966 PMCID: PMC4966635 DOI: 10.1038/ng.3603] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 06/01/2016] [Indexed: 12/14/2022]
Abstract
Systemic lupus erythematosus (SLE; OMIM 152700) is a genetically complex autoimmune disease. Genome-wide association studies (GWASs) have identified more than 50 loci as robustly associated with the disease in single ancestries, but genome-wide transancestral studies have not been conducted. We combined three GWAS data sets from Chinese (1,659 cases and 3,398 controls) and European (4,036 cases and 6,959 controls) populations. A meta-analysis of these studies showed that over half of the published SLE genetic associations are present in both populations. A replication study in Chinese (3,043 cases and 5,074 controls) and European (2,643 cases and 9,032 controls) subjects found ten previously unreported SLE loci. Our study provides further evidence that the majority of genetic risk polymorphisms for SLE are contained within the same regions across both populations. Furthermore, a comparison of risk allele frequencies and genetic risk scores suggested that the increased prevalence of SLE in non-Europeans (including Asians) has a genetic basis.
Collapse
Affiliation(s)
- David L Morris
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Yujun Sheng
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Yan Zhang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yong-Fei Wang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Zhengwei Zhu
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Philip Tombleson
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Lingyan Chen
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | | | - James Bentham
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Amy L Roberts
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Ruoyan Chen
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Xianbo Zuo
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Tingyou Wang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Leilei Wen
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Chao Yang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Lu Liu
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Lulu Yang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Feng Li
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Yuanbo Huang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Xianyong Yin
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Sen Yang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Lars Rönnblom
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Barbara G Fürnrohr
- Department of Internal Medicine 3, University of Erlangen-Nuremberg, Erlangen, Germany
- Institute for Clinical Immunology, University of Erlangen-Nuremberg, Erlangen, Germany
- Division of Genetic Epidemiology, Medical University Innsbruck, Innsbruck, Austria
- Division of Biological Chemistry, Medical University Innsbruck, Innsbruck, Austria
| | - Reinhard E Voll
- Department of Internal Medicine 3, University of Erlangen-Nuremberg, Erlangen, Germany
- Institute for Clinical Immunology, University of Erlangen-Nuremberg, Erlangen, Germany
- Department of Rheumatology, University Hospital Freiburg, Freiburg, Germany
- Department of Rheumatology and Clinical Immunology, University Hospital Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency, University Hospital Freiburg, Freiburg, Germany
| | - Georg Schett
- Department of Internal Medicine 3, University of Erlangen-Nuremberg, Erlangen, Germany
- Institute for Clinical Immunology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Nathalie Costedoat-Chalumeau
- AP-HP, Hôpital Cochin, Centre de référence maladies auto-immunes et systémiques rares, Paris, France
- Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
- The University of Hong Kong Shenzhen Hospital, Shenzhen, China
| | - Xuejun Zhang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
- Department of Dermatology, Huashan Hospital of Fudan University, Shanghai, China
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yong Cui
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Timothy J Vyse
- Division of Genetics and Molecular Medicine, King's College London, London, UK
- Division of Immunology, Infection and Inflammatory Disease, King's College London, London, UK
| |
Collapse
|
4
|
Corley SM, Canales CP, Carmona-Mora P, Mendoza-Reinosa V, Beverdam A, Hardeman EC, Wilkins MR, Palmer SJ. RNA-Seq analysis of Gtf2ird1 knockout epidermal tissue provides potential insights into molecular mechanisms underpinning Williams-Beuren syndrome. BMC Genomics 2016; 17:450. [PMID: 27295951 PMCID: PMC4907016 DOI: 10.1186/s12864-016-2801-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 05/26/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Williams-Beuren Syndrome (WBS) is a genetic disorder associated with multisystemic abnormalities, including craniofacial dysmorphology and cognitive defects. It is caused by a hemizygous microdeletion involving up to 28 genes in chromosome 7q11.23. Genotype/phenotype analysis of atypical microdeletions implicates two evolutionary-related transcription factors, GTF2I and GTF2IRD1, as prime candidates for the cause of the facial dysmorphology. RESULTS Using a targeted Gtf2ird1 knockout mouse, we employed massively-parallel sequencing of mRNA (RNA-Seq) to understand changes in the transcriptional landscape associated with inactivation of Gtf2ird1 in lip tissue. We found widespread dysregulation of genes including differential expression of 78 transcription factors or coactivators, several involved in organ development including Hey1, Myf6, Myog, Dlx2, Gli1, Gli2, Lhx2, Pou3f3, Sox2, Foxp3. We also found that the absence of GTF2IRD1 is associated with increased expression of genes involved in cellular proliferation, including growth factors consistent with the observed phenotype of extreme thickening of the epidermis. At the same time, there was a decrease in the expression of genes involved in other signalling mechanisms, including the Wnt pathway, indicating dysregulation in the complex networks necessary for epidermal differentiation and facial skin patterning. Several of the differentially expressed genes have known roles in both tissue development and neurological function, such as the transcription factor Lhx2 which regulates several genes involved in both skin and brain development. CONCLUSIONS Gtf2ird1 inactivation results in widespread gene dysregulation, some of which may be due to the secondary consequences of gene regulatory network disruptions involving several transcription factors and signalling molecules. Genes involved in growth factor signalling and cell cycle progression were identified as particularly important for explaining the skin dysmorphology observed in this mouse model. We have noted that a number of the dysregulated genes have known roles in brain development as well as epidermal differentiation and maintenance. Therefore, this study provides clues as to the underlying mechanisms that may be involved in the broader profile of WBS.
Collapse
Affiliation(s)
- Susan M Corley
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, UNSW Australia, Sydney, NSW, Australia.
| | - Cesar P Canales
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, Australia
| | - Paulina Carmona-Mora
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, Australia
| | | | | | - Edna C Hardeman
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, Australia
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, UNSW Australia, Sydney, NSW, Australia
| | - Stephen J Palmer
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, Australia
| |
Collapse
|
5
|
High-density genotyping of immune-related loci identifies new SLE risk variants in individuals with Asian ancestry. Nat Genet 2016; 48:323-30. [PMID: 26808113 PMCID: PMC4767573 DOI: 10.1038/ng.3496] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 12/23/2015] [Indexed: 01/04/2023]
Abstract
Systemic lupus erythematosus (SLE) has a strong but incompletely understood genetic architecture. We conducted an association study with replication in 4,478 SLE cases and 12,656 controls from six East Asian cohorts to identify new SLE susceptibility loci and better localize known loci. We identified ten new loci and confirmed 20 known loci with genome-wide significance. Among the new loci, the most significant locus was GTF2IRD1-GTF2I at 7q11.23 (rs73366469, Pmeta = 3.75 × 10(-117), odds ratio (OR) = 2.38), followed by DEF6, IL12B, TCF7, TERT, CD226, PCNXL3, RASGRP1, SYNGR1 and SIGLEC6. We identified the most likely functional variants at each locus by analyzing epigenetic marks and gene expression data. Ten candidate variants are known to alter gene expression in cis or in trans. Enrichment analysis highlights the importance of these loci in B cell and T cell biology. The new loci, together with previously known loci, increase the explained heritability of SLE to 24%. The new loci share functional and ontological characteristics with previously reported loci and are possible drug targets for SLE therapeutics.
Collapse
|
6
|
Carmona-Mora P, Widagdo J, Tomasetig F, Canales CP, Cha Y, Lee W, Alshawaf A, Dottori M, Whan RM, Hardeman EC, Palmer SJ. The nuclear localization pattern and interaction partners of GTF2IRD1 demonstrate a role in chromatin regulation. Hum Genet 2015; 134:1099-115. [PMID: 26275350 DOI: 10.1007/s00439-015-1591-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 08/04/2015] [Indexed: 12/11/2022]
Abstract
GTF2IRD1 is one of the three members of the GTF2I gene family, clustered on chromosome 7 within a 1.8 Mb region that is prone to duplications and deletions in humans. Hemizygous deletions cause Williams-Beuren syndrome (WBS) and duplications cause WBS duplication syndrome. These copy number variations disturb a variety of developmental systems and neurological functions. Human mapping data and analyses of knockout mice show that GTF2IRD1 and GTF2I underpin the craniofacial abnormalities, mental retardation, visuospatial deficits and hypersociability of WBS. However, the cellular role of the GTF2IRD1 protein is poorly understood due to its very low abundance and a paucity of reagents. Here, for the first time, we show that endogenous GTF2IRD1 has a punctate pattern in the nuclei of cultured human cell lines and neurons. To probe the functional relationships of GTF2IRD1 in an unbiased manner, yeast two-hybrid libraries were screened, isolating 38 novel interaction partners, which were validated in mammalian cell lines. These relationships illustrate GTF2IRD1 function, as the isolated partners are mostly involved in chromatin modification and transcriptional regulation, whilst others indicate an unexpected role in connection with the primary cilium. Mapping of the sites of protein interaction also indicates key features regarding the evolution of the GTF2IRD1 protein. These data provide a visual and molecular basis for GTF2IRD1 nuclear function that will lead to an understanding of its role in brain, behaviour and human disease.
Collapse
Affiliation(s)
- Paulina Carmona-Mora
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, 2052, Australia
| | - Jocelyn Widagdo
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Florence Tomasetig
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, 2052, Australia
| | - Cesar P Canales
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, 2052, Australia
| | - Yeojoon Cha
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, 2052, Australia
| | - Wei Lee
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, 2052, Australia
| | - Abdullah Alshawaf
- Centre for Neural Engineering, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Mirella Dottori
- Centre for Neural Engineering, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Renee M Whan
- Biomedical Imaging Facility, Mark Wainwright Analytical Centre, UNSW Australia, Sydney, NSW, 2052, Australia
| | - Edna C Hardeman
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, 2052, Australia
| | - Stephen J Palmer
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, 2052, Australia.
| |
Collapse
|
7
|
The transcription factor GTF2IRD1 regulates the topology and function of photoreceptors by modulating photoreceptor gene expression across the retina. J Neurosci 2015; 34:15356-68. [PMID: 25392503 DOI: 10.1523/jneurosci.2089-14.2014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The mechanisms that specify photoreceptor cell-fate determination, especially as regards to short-wave-sensitive (S) versus medium-wave-sensitive (M) cone identity, and maintain their nature and function, are not fully understood. Here we report the importance of general transcription factor II-I repeat domain-containing protein 1 (GTF2IRD1) in maintaining M cone cell identity and function as well as rod function. In the mouse, GTF2IRD1 is expressed in cell-fate determined photoreceptors at postnatal day 10. GTF2IRD1 binds to enhancer and promoter regions in the mouse rhodopsin, M- and S-opsin genes, but regulates their expression differentially. Through interaction with the transcription factors CRX and thyroid hormone receptor β 2, it enhances M-opsin expression, whereas it suppresses S-opsin expression; and with CRX and NRL, it enhances rhodopsin expression. In an apparent paradox, although GTF2IRD1 is widely expressed in multiple cell types across the retina, knock-out of GTF2IRD1 alters the retinal expression of only a limited number of annotated genes. Interestingly, however, the null mutation leads to altered topology of cone opsin expression in the retina, with aberrant S-opsin overexpression and M-opsin underexpression in M cones. Gtf2ird1-null mice also demonstrate abnormal M cone and rod electrophysiological responses. These findings suggest an important role for GTF2IRD1 in regulating the level and topology of rod and cone gene expression, and in maintaining normal retinal function.
Collapse
|
8
|
Canales CP, Wong ACY, Gunning PW, Housley GD, Hardeman EC, Palmer SJ. The role of GTF2IRD1 in the auditory pathology of Williams-Beuren Syndrome. Eur J Hum Genet 2014; 23:774-80. [PMID: 25248400 DOI: 10.1038/ejhg.2014.188] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 08/11/2014] [Accepted: 08/15/2014] [Indexed: 12/15/2022] Open
Abstract
Williams-Beuren Syndrome (WBS) is a rare genetic condition caused by a hemizygous deletion involving up to 28 genes within chromosome 7q11.23. Among the spectrum of physical and neurological defects in WBS, it is common to find a distinctive response to sound stimuli that includes extreme adverse reactions to loud, or sudden sounds and a fascination with certain sounds that may manifest as strengths in musical ability. However, hearing tests indicate that sensorineural hearing loss (SNHL) is frequently found in WBS patients. The functional and genetic basis of this unusual auditory phenotype is currently unknown. Here, we investigated the potential involvement of GTF2IRD1, a transcription factor encoded by a gene located within the WBS deletion that has been implicated as a contributor to the WBS assorted neurocognitive profile and craniofacial abnormalities. Using Gtf2ird1 knockout mice, we have analysed the expression of the gene in the inner ear and examined hearing capacity by evaluating the auditory brainstem response (ABR) and the distortion product of otoacoustic emissions (DPOAE). Our results show that Gtf2ird1 is expressed in a number of cell types within the cochlea, and Gtf2ird1 null mice showed higher auditory thresholds (hypoacusis) in both ABR and DPOAE hearing assessments. These data indicate that the principal hearing deficit in the mice can be traced to impairments in the amplification process mediated by the outer hair cells and suggests that similar mechanisms may underpin the SNHL experienced by WBS patients.
Collapse
Affiliation(s)
- Cesar P Canales
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, Australia
| | - Ann C Y Wong
- Translational Neuroscience Facility, Department of Physiology, School of Medical Sciences, UNSW Australia, Sydney, NWS, Australia
| | - Peter W Gunning
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, Australia
| | - Gary D Housley
- Translational Neuroscience Facility, Department of Physiology, School of Medical Sciences, UNSW Australia, Sydney, NWS, Australia
| | - Edna C Hardeman
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, Australia
| | - Stephen J Palmer
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, Australia
| |
Collapse
|
9
|
Fan AX, Papadopoulos GL, Hossain MA, Lin IJ, Hu J, Tang TM, Kilberg MS, Renne R, Strouboulis J, Bungert J. Genomic and proteomic analysis of transcription factor TFII-I reveals insight into the response to cellular stress. Nucleic Acids Res 2014; 42:7625-41. [PMID: 24875474 PMCID: PMC4081084 DOI: 10.1093/nar/gku467] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The ubiquitously expressed transcription factor TFII-I exerts both positive and negative effects on transcription. Using biotinylation tagging technology and high-throughput sequencing, we determined sites of chromatin interactions for TFII-I in the human erythroleukemia cell line K562. This analysis revealed that TFII-I binds upstream of the transcription start site of expressed genes, both upstream and downstream of the transcription start site of repressed genes, and downstream of RNA polymerase II peaks at the ATF3 and other stress responsive genes. At the ATF3 gene, TFII-I binds immediately downstream of a Pol II peak located 5 kb upstream of exon 1. Induction of ATF3 expression increases transcription throughout the ATF3 gene locus which requires TFII-I and correlates with increased association of Pol II and Elongin A. Pull-down assays demonstrated that TFII-I interacts with Elongin A. Partial depletion of TFII-I expression caused a reduction in the association of Elongin A with and transcription of the DNMT1 and EFR3A genes without a decrease in Pol II recruitment. The data reveal different interaction patterns of TFII-I at active, repressed, or inducible genes, identify novel TFII-I interacting proteins, implicate TFII-I in the regulation of transcription elongation and provide insight into the role of TFII-I during the response to cellular stress.
Collapse
Affiliation(s)
- Alex Xiucheng Fan
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, Gainesville, Florida, USA
| | - Giorgio L Papadopoulos
- Departmentof Biology, University of Crete, GR1409 Heraklion, Greece Divisionof Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Vari GR 16672, Greece
| | - Mir A Hossain
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, Gainesville, Florida, USA
| | - I-Ju Lin
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, Gainesville, Florida, USA
| | - Jianhong Hu
- Departmentof Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, Florida, 32610, USA
| | - Tommy Ming Tang
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, Gainesville, Florida, USA
| | - Michael S Kilberg
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, Gainesville, Florida, USA
| | - Rolf Renne
- Divisionof Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Vari GR 16672, Greece
| | - John Strouboulis
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, Gainesville, Florida, USA Departmentof Biology, University of Crete, GR1409 Heraklion, Greece Divisionof Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Vari GR 16672, Greece Departmentof Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, Florida, 32610, USA
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, Gainesville, Florida, USA
| |
Collapse
|
10
|
Segura-Puimedon M, Borralleras C, Pérez-Jurado LA, Campuzano V. TFII-I regulates target genes in the PI-3K and TGF-β signaling pathways through a novel DNA binding motif. Gene 2013; 527:529-36. [DOI: 10.1016/j.gene.2013.06.050] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 06/10/2013] [Accepted: 06/21/2013] [Indexed: 11/17/2022]
|
11
|
Bayarsaihan D, Makeyev AV, Enkhmandakh B. Epigenetic modulation by TFII-I during embryonic stem cell differentiation. J Cell Biochem 2013; 113:3056-60. [PMID: 22628223 DOI: 10.1002/jcb.24202] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
TFII-I transcription factors play an essential role during early vertebrate embryogenesis. Genome-wide mapping studies by ChIP-seq and ChIP-chip revealed that TFII-I primes multiple genomic loci in mouse embryonic stem cells and embryonic tissues. Moreover, many TFII-I-bound regions co-localize with H3K4me3/K27me3 bivalent chromatin within the promoters of lineage-specific genes. This minireview provides a summary of current knowledge regarding the function of TFII-I in epigenetic control of stem cell differentiation.
Collapse
Affiliation(s)
- Dashzeveg Bayarsaihan
- Center for Regenerative Medicine and Skeletal Development, Department of Reconstructive Sciences, School of Dentistry, University of Connecticut, Farmington, CT 06030, USA.
| | | | | |
Collapse
|
12
|
Makeyev AV, Bayarsaihan D. ChIP-Chip Identifies SEC23A, CFDP1, and NSD1 as TFII-I Target Genes in Human Neural Crest Progenitor Cells. Cleft Palate Craniofac J 2012; 50:347-50. [PMID: 23145914 DOI: 10.1597/12-069] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Objectives : GTF2I and GTF2IRD1 genes located in Williams-Beuren syndrome (WBS) critical region encode TFII-I family transcription factors. The aim of this study was to map genomic sites bound by these proteins across promoter regions of developmental regulators associated with craniofacial development. Design : Chromatin was isolated from human neural crest progenitor cells and the DNA-binding profile was generated using the human RefSeq tiling promoter ChIP-chip arrays. Results : TFII-I transcription factors are recruited to the promoters of SEC23A, CFDP1, and NSD1 previously defined as TFII-I target genes. Moreover, our analysis revealed additional binding elements that contain E-boxes and initiator-like motifs. Conclusions : Genome-wide promoter binding studies revealed SEC23A, CFDP1, and NSD1 linked to craniofacial or dental development as direct TFII-I targets. Developmental regulation of these genes by TFII-I factors could contribute to the WBS-specific facial dysmorphism.
Collapse
|
13
|
Makeyev AV, Enkhmandakh B, Hong SH, Joshi P, Shin DG, Bayarsaihan D. Diversity and complexity in chromatin recognition by TFII-I transcription factors in pluripotent embryonic stem cells and embryonic tissues. PLoS One 2012; 7:e44443. [PMID: 22970219 PMCID: PMC3438194 DOI: 10.1371/journal.pone.0044443] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 08/02/2012] [Indexed: 11/18/2022] Open
Abstract
GTF2I and GTF2IRD1 encode a family of closely related transcription factors TFII-I and BEN critical in embryonic development. Both genes are deleted in Williams-Beuren syndrome, a complex genetic disorder associated with neurocognitive, craniofacial, dental and skeletal abnormalities. Although genome-wide promoter analysis has revealed the existence of multiple TFII-I binding sites in embryonic stem cells (ESCs), there was no correlation between TFII-I occupancy and gene expression. Surprisingly, TFII-I recognizes the promoter sequences enriched for H3K4me3/K27me3 bivalent domain, an epigenetic signature of developmentally important genes. Moreover, we discovered significant differences in the association between TFII-I and BEN with the cis-regulatory elements in ESCs and embryonic craniofacial tissues. Our data indicate that in embryonic tissues BEN, but not the highly homologous TFII-I, is primarily recruited to target gene promoters. We propose a “feed-forward model” of gene regulation to explain the specificity of promoter recognition by TFII-I factors in eukaryotic cells.
Collapse
Affiliation(s)
- Aleksandr V. Makeyev
- Department of Reconstructive Sciences, Center for Regenerative Medicine and Skeletal Development, School of Dentistry, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Badam Enkhmandakh
- Department of Reconstructive Sciences, Center for Regenerative Medicine and Skeletal Development, School of Dentistry, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Seung-Hyun Hong
- Computer Science and Engineering, School of Engineering, University of Connecticut, Storrs, Connecticut, United States of America
| | - Pujan Joshi
- Computer Science and Engineering, School of Engineering, University of Connecticut, Storrs, Connecticut, United States of America
| | - Dong-Guk Shin
- Computer Science and Engineering, School of Engineering, University of Connecticut, Storrs, Connecticut, United States of America
| | - Dashzeveg Bayarsaihan
- Department of Reconstructive Sciences, Center for Regenerative Medicine and Skeletal Development, School of Dentistry, University of Connecticut Health Center, Farmington, Connecticut, United States of America
- * E-mail:
| |
Collapse
|
14
|
Palmer SJ, Taylor KM, Santucci N, Widagdo J, Chan YKA, Yeo JL, Adams M, Gunning PW, Hardeman EC. GTF2IRD2 from the Williams-Beuren critical region encodes a mobile-element-derived fusion protein that antagonizes the action of its related family members. J Cell Sci 2012; 125:5040-50. [PMID: 22899722 DOI: 10.1242/jcs.102798] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
GTF2IRD2 belongs to a family of transcriptional regulators (including TFII-I and GTF2IRD1) that are responsible for many of the key features of Williams-Beuren syndrome (WBS). Sequence evidence suggests that GTF2IRD2 arose in eutherian mammals by duplication and divergence from the gene encoding TFII-I. However, in GTF2IRD2, most of the C-terminal domain has been lost and replaced by the domesticated remnant of an in-frame hAT-transposon mobile element. In this first experimental analysis of function, we show that transgenic expression of each of the three family members in skeletal muscle causes significant fiber type shifts, but the GTF2IRD2 protein causes an extreme shift in the opposite direction to the two other family members. Mating of GTF2IRD1 and GTF2IRD2 mice restores the fiber type balance, indicating an antagonistic relationship between these two paralogs. In cells, GTF2IRD2 localizes to cytoplasmic microtubules and discrete speckles in the nuclear periphery. We show that it can interact directly with TFII-Iβ and GTF2IRD1, and upon co-transfection changes the normal distribution of these two proteins into a punctate nuclear pattern typical of GTF2IRD2. These data suggest that GTF2IRD2 has evolved as a regulator of GTF2IRD1 and TFII-I; inhibiting their function by direct interaction and sequestration into inactive nuclear zones.
Collapse
Affiliation(s)
- Stephen J Palmer
- Neuromuscular and Regenerative Medicine Unit, School of Medical Sciences, The University of New South Wales, Sydney 2052, Australia.
| | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Roy AL. Biochemistry and biology of the inducible multifunctional transcription factor TFII-I: 10 years later. Gene 2011; 492:32-41. [PMID: 22037610 DOI: 10.1016/j.gene.2011.10.030] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 10/08/2011] [Accepted: 10/11/2011] [Indexed: 12/12/2022]
Abstract
Exactly twenty years ago TFII-I was discovered as a biochemical entity that was able to bind to and function via a core promoter element called the Initiator (Inr). Since then several different properties of this signal-induced multifunctional factor were discovered. Here I update these ever expanding functions of TFII-I--focusing primarily on the last ten years since the first review appeared in this journal.
Collapse
Affiliation(s)
- Ananda L Roy
- Department of Pathology, Sackler School of Biomedical Sciences, Tufts University School of Medicine, 150 Harrison Avenue, Boston, MA 02111, USA.
| |
Collapse
|
16
|
Roy AL, Sen R, Roeder RG. Enhancer-promoter communication and transcriptional regulation of Igh. Trends Immunol 2011; 32:532-9. [PMID: 21855411 DOI: 10.1016/j.it.2011.06.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 06/23/2011] [Accepted: 06/23/2011] [Indexed: 12/18/2022]
Abstract
Transcriptional regulation of eukaryotic protein-coding genes requires the participation of site-specific transcription factors that bind distal regulatory elements, as well as factors that, together with RNA polymerase II, form the basal transcription machinery at the core promoter. Gene regulation requires proper communication between promoters and enhancers, often over great distances. Therefore, it is important to understand the potentially inter-related transcription factor interactions at both of these elements. How this is achieved on tissue-specific genes, such as the immunoglobulin heavy chain (IgH) in B cells remains unclear. Here, we review known interactions at the Igh variable region (V(H)) promoters and present our perspective on promoter-enhancer interactions that are likely important for Ig gene regulation in B cells.
Collapse
Affiliation(s)
- Ananda L Roy
- Program in Immunology, Department of Pathology, Tufts University School of Medicine, Boston, MA, USA.
| | | | | |
Collapse
|
17
|
Ren X, Siegel R, Kim U, Roeder RG. Direct interactions of OCA-B and TFII-I regulate immunoglobulin heavy-chain gene transcription by facilitating enhancer-promoter communication. Mol Cell 2011; 42:342-55. [PMID: 21549311 DOI: 10.1016/j.molcel.2011.04.011] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 02/16/2011] [Accepted: 04/16/2011] [Indexed: 02/07/2023]
Abstract
B cell-specific coactivator OCA-B, together with Oct-1/2, binds to octamer sites in promoters and enhancers to activate transcription of immunoglobulin (Ig) genes, although the mechanisms underlying their roles in enhancer-promoter communication are unknown. Here, we demonstrate a direct interaction of OCA-B with transcription factor TFII-I, which binds to DICE elements in Igh promoters, that affects transcription at two levels. First, OCA-B relieves HDAC3-mediated Igh promoter repression by competing with HDAC3 for binding to promoter-bound TFII-I. Second, and most importantly, Igh 3' enhancer-bound OCA-B and promoter-bound TFII-I mediate promoter-enhancer interactions, in both cis and trans, that are important for Igh transcription. These and other results reveal an important function for OCA-B in Igh 3' enhancer function in vivo and strongly favor an enhancer mechanism involving looping and facilitated factor recruitment rather than a tracking mechanism.
Collapse
Affiliation(s)
- Xiaodi Ren
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | | | | | | |
Collapse
|
18
|
Statnikov A, McVoy L, Lytkin N, Aliferis CF. Improving development of the molecular signature for diagnosis of acute respiratory viral infections. Cell Host Microbe 2010; 7:100-1; author reply 102. [PMID: 20159615 DOI: 10.1016/j.chom.2010.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Revised: 12/28/2009] [Accepted: 01/12/2010] [Indexed: 01/15/2023]
|
19
|
Kang J, Gemberling M, Nakamura M, Whitby FG, Handa H, Fairbrother WG, Tantin D. A general mechanism for transcription regulation by Oct1 and Oct4 in response to genotoxic and oxidative stress. Genes Dev 2009; 23:208-22. [PMID: 19171782 DOI: 10.1101/gad.1750709] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Oct1 and Oct4 are homologous transcription factors with similar DNA-binding specificities. Here we show that Oct1 is dynamically phosphorylated in vivo following exposure of cells to oxidative and genotoxic stress. We further show that stress regulates the selectivity of both proteins for specific DNA sequences. Mutation of conserved phosphorylation target DNA-binding domain residues in Oct1, and Oct4 confirms their role in regulating binding selectivity. Using chromatin immunoprecipitation, we show that association of Oct4 and Oct1 with a distinct group of in vivo targets is inducible by stress, and that Oct1 is essential for a normal post-stress transcriptional response. Finally, using an unbiased Oct1 target screen we identify a large number of genes targeted by Oct1 specifically under conditions of stress, and show that several of these inducible Oct1 targets are also inducibly bound by Oct4 in embryonic stem cells following stress exposure.
Collapse
Affiliation(s)
- Jinsuk Kang
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | | | | | | | | | | | | |
Collapse
|
20
|
Fabre EE, Raynaud-Simon A, Golmard JL, Hebert M, Dulcire X, Succari M, Myara J, Durand D, Nivet-Antoine V. Gene polymorphisms of oxidative stress enzymes: prediction of elderly renutrition. Am J Clin Nutr 2008; 87:1504-12. [PMID: 18469277 DOI: 10.1093/ajcn/87.5.1504] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The free radical theory of aging suggests that damage caused by oxidative stress leads to impaired physiologic functions. This damage is stemmed by an adequate antioxidant status, which minimizes the occurrence of infection, thus potentially playing a role in improving nutritional status. The role played by genetic factors remains unknown. OBJECTIVE The aim of this study was to investigate whether a single nucleotide polymorphism (SNP) of a gene coding for endogenous antioxidant enzymes could influence either nutritional status or renutrition process in an elderly population. DESIGN Nutritional and inflammatory status were studied in 77 elderly outpatients and in 99 malnourished elderly inpatients over 6 wk of health care treatment. Renutrition efficiency was evaluated with use of the ratio between initial transthyretinemia and 6-wk variation. A genetic study was performed on superoxide dismutase (Ala-9Val), glutathione peroxidase (Pro197Leu), and catalase (from promoter to the first intron). RESULTS Among the SNPs studied, the G-844A, A-89T, and C-20T catalase SNPs could each be markers predicting renutrition efficiency. These catalase mutant alleles were associated with a lower efficiency of renutrition in malnourished elderly subjects, regardless of initial nutritional and inflammatory status. Genotyping one of these catalase SNPs could make it possible to identify a high-risk subpopulation of mutant allele carriers within the elderly polypathological population. CONCLUSION In a malnutrition setting, this subpopulation should be given personalized health care, including a strengthened refeeding program. Thus, catalase genotyping could enable earlier recovery of satisfactory nutritional status and thus avoid the consequences of malnutrition, which are especially deleterious in the elderly.
Collapse
Affiliation(s)
- Emmanuelle E Fabre
- Biochemistry Department, Charles Foix Hospital, AP-HP, Ivry sur Seine, France
| | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Lazebnik MB, Tussie-Luna MI, Roy AL. Determination and functional analysis of the consensus binding site for TFII-I family member BEN, implicated in Williams-Beuren syndrome. J Biol Chem 2008; 283:11078-82. [PMID: 18326499 PMCID: PMC2431064 DOI: 10.1074/jbc.c800049200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 03/06/2008] [Indexed: 12/23/2022] Open
Abstract
The ubiquitously expressed TFII-I family of multifunctional transcription factors is involved in gene regulation as well as signaling. Despite the fact that they share significant sequence homology, these factors exhibit varied and distinct functions. The lack of knowledge about its binding sites and physiological target genes makes it more difficult to assign a definitive function for the TFII-I-related protein, BEN. We set out to determine its optimal binding site with the notion of predicting its physiological target genes. Here we report the identification of an optimal binding sequence for BEN by SELEX (systematic evolution of ligands by exponential enrichment) and confirm the relevance of this sequence by functional assays. We further performed a data base search to assign genes that have this consensus site(s) and validate several candidate genes by quantitative PCR upon stable silencing of BEN and by chromatin immunoprecipitation assay upon stable expression of BEN. Given that haploinsufficiency in BEN is causative to Williams-Beuren syndrome, these results may further lead to the identification of a set of physiologically relevant target genes for BEN and may help identify molecular determinants of Williams-Beuren syndrome.
Collapse
Affiliation(s)
- Maria B Lazebnik
- Programs in Genetics, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
| | | | | |
Collapse
|
22
|
Thompson PD, Webb M, Beckett W, Hinsley T, Jowitt T, Sharrocks AD, Tassabehji M. GTF2IRD1 regulates transcription by binding an evolutionarily conserved DNA motif ‘GUCE’. FEBS Lett 2007; 581:1233-42. [PMID: 17346708 DOI: 10.1016/j.febslet.2007.02.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Revised: 02/14/2007] [Accepted: 02/16/2007] [Indexed: 12/28/2022]
Abstract
GTF2IRD1 is a member of a family of transcription factors whose defining characteristic is varying numbers of a helix-loop-helix like motif, the I-repeat. Here, we present functional analysis of human GTF2IRD1 in regulation of three genes (HOXC8, GOOSECOID and TROPONIN I(SLOW)). We define a regulatory motif (GUCE-GTF2IRD1 Upstream Control Element) common to all three genes. GUCE is bound in vitro by domain I-4 of GTF2IRD1 and mediates transcriptional regulation by GTF2IRD1 in vivo. Definition of this site will assist in identification of other downstream targets of GTF2IRD1 and elucidation of its role in the human developmental disorder Williams-Beuren syndrome.
Collapse
Affiliation(s)
- P D Thompson
- Academic Unit of Medical Genetics, The University of Manchester, St Mary's Hospital, Hathersage Road, Manchester M13 0JH, UK
| | | | | | | | | | | | | |
Collapse
|
23
|
Chimge NO, Mungunsukh O, Ruddle F, Bayarsaihan D. Expression profiling of BEN regulated genes in mouse embryonic fibroblasts. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2007; 308:209-24. [PMID: 17041962 DOI: 10.1002/jez.b.21129] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BEN is a member of the TFII-I family of helix-loop-helix transcription factors. Both TFII-I and BEN are involved in gene regulation through interactions with tissue-specific transcription factors and chromatin remodeling complexes. Identification of the downstream target genes of TFII-I proteins is critical in delineating the regulatory effects of these proteins. In this study, we conducted a microarray analysis to determine gene expression alterations following the overexpression of BEN in primary mouse embryonic fibroblasts (MEFs). We found the BEN-dependent modulation in the expression of large groups of genes representing a wide variety of functional categories including genes important in the immune response, cell cycle, transcriptional regulation and cell signaling. A set of genes identified by the microarray analysis was validated by independent real-time PCR analysis. Among upregulated genes were Shrm, Tgfb2, Ube2l6, G1p2, Ccl7 while downregulated genes were Folr1, Tgfbr2, Csrp2, and Dlk1. These results support a versatile function of TFII-I proteins in vertebrate physiology and lead to an increased understanding of the BEN-dependent molecular events.
Collapse
Affiliation(s)
- Nyam-Osor Chimge
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | | | | | | |
Collapse
|
24
|
Chimge NO, Mungunsukh O, Ruddle F, Bayarsaihan D. Gene expression analysis of TFII-I modulated genes in mouse embryonic fibroblasts. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2007; 308:225-35. [PMID: 17094079 DOI: 10.1002/jez.b.21134] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
TFII-I is a founding member of a family of helix-loop-helix transcription factors involved in modulation of genes through interaction with various nuclear factors and chromatin remodeling complexes. Recent studies indicate that TFII-I performs important function in cell physiology and mouse embryogenesis. In order to understand its molecular role, TFII-I was overexpressed in primary mouse embryonic fibroblasts (MEFs) and alterations in gene expression were monitored with a mouse 16 K oligonucleotide microarray. These studies allowed us to identify genes that lie downstream of TFII-I-dependent pathways. Among the modulated candidates were genes involved in the immunity response, catalytic activity, signaling pathways and transcriptional regulation. Expression of several candidates including those for the interferon-stimulated protein (G1p2), small inducible cytokine A7 (Ccl7), ubiquitin-conjugating enzyme 8 (Ube2l6), cysteine-rich protein (Csrp2) and Drosophila delta-like 1 homolog (Dlk1) were confirmed by real-time PCR. The obtained results suggest that TFII-I participates in multiple signaling and regulatory pathways in MEFs.
Collapse
Affiliation(s)
- Nyam-Osor Chimge
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | | | | | | |
Collapse
|
25
|
Rajaiya J, Nixon JC, Ayers N, Desgranges ZP, Roy AL, Webb CF. Induction of immunoglobulin heavy-chain transcription through the transcription factor Bright requires TFII-I. Mol Cell Biol 2006; 26:4758-68. [PMID: 16738337 PMCID: PMC1489113 DOI: 10.1128/mcb.02009-05] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Revised: 11/30/2005] [Accepted: 04/01/2006] [Indexed: 02/04/2023] Open
Abstract
Bright/ARID3a/Dril1, a member of the ARID family of transcription factors, is expressed in a highly regulated fashion in B lymphocytes, where it enhances immunoglobulin transcription three- to sixfold. Recent publications from our lab indicated that functional, but not kinase-inactive, Bruton's tyrosine kinase (Btk) is critical for Bright activity in an in vitro model system, yet Bright itself is not appreciably tyrosine phosphorylated. These data suggested that a third protein, and Btk substrate, must contribute to Bright-enhanced immunoglobulin transcription. The ubiquitously expressed transcription factor TFII-I was identified as a substrate for Btk several years ago. In this work, we show that TFII-I directly interacts with human Bright through amino acids in Bright's protein interaction domain and that specific tyrosine residues of TFII-I are essential for Bright-induced activity of an immunoglobulin reporter gene. Moreover, inhibition of TFII-I function in a B-cell line resulted in decreased heavy-chain transcript levels. These data suggest that Bright functions as a three-component protein complex in the immunoglobulin locus and tie together previous data indicating important roles for Btk and TFII-I in B lymphocytes.
Collapse
Affiliation(s)
- Jaya Rajaiya
- Oklahoma Medical Research Foundation, Immunobiology and Cancer Research Program, 825 N. E. 13th Street, Oklahoma City, OK 73104, USA
| | | | | | | | | | | |
Collapse
|
26
|
Johnston CM, Wood AL, Bolland DJ, Corcoran AE. Complete Sequence Assembly and Characterization of the C57BL/6 Mouse Ig Heavy Chain V Region. THE JOURNAL OF IMMUNOLOGY 2006; 176:4221-34. [PMID: 16547259 DOI: 10.4049/jimmunol.176.7.4221] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The mechanisms that regulate variable (V) gene selection during the development of the mouse IgH repertoire are not fully understood, due in part to the absence of the complete locus sequence. To better understand these processes, we have assembled the entire 2.5-Mb mouse IgH (Igh) V region sequence of the C57BL/6 strain from public sequences and present the first complete annotated map of the region, including V genes, pseudogenes, repeats, and nonrepetitive intergenic sequences. In so doing, we have discovered a new V gene family, VH16. We have identified clusters of conserved region-specific intergenic sequences and have verified our assembly by genic and intergenic Southern blotting. We have observed that V pseudogenes are not evenly spread throughout the V region, but rather cluster together. The largest J558 family, which spans more than half of the locus, has two strikingly different domains, which suggest points of evolutionary divergence or duplication. The 5' end contains widely spaced J558 genes interspersed with 3609 genes and is pseudogene poor. The 3' end contains closely spaced J558 genes, no 3609 genes, and is pseudogene rich. Each occupies a different branch of the phylogenetic tree. Detailed analysis of 500-bp upstream of all functional genes has revealed several conserved binding sites, general and B cell-specific, as well as key differences between families. This complete and definitive assembly of the mouse Igh V region will facilitate detailed study of promoter function and large-scale mechanisms associated with V(D)J recombination including locus contraction and antisense intergenic transcription.
Collapse
Affiliation(s)
- Colette M Johnston
- Laboratory of Chromatin and Gene Expression, Babraham Institute, Cambridge, UK
| | | | | | | |
Collapse
|
27
|
Tantin D, Schild-Poulter C, Wang V, Haché RJG, Sharp PA. The octamer binding transcription factor Oct-1 is a stress sensor. Cancer Res 2006; 65:10750-8. [PMID: 16322220 DOI: 10.1158/0008-5472.can-05-2399] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The POU-domain transcription factor Oct-1 is widely expressed in adult tissues and has been proposed to regulate a large group of target genes. Microarray expression profiling was used to evaluate gene expression changes in Oct-1-deficient mouse fibroblasts. A number of genes associated with cellular stress exhibited altered expression. Consistent with this finding, Oct-1-deficient fibroblasts were hypersensitive to gamma radiation, doxorubicin, and hydrogen peroxide and harbored elevated reactive oxygen species. Expression profiling identified a second group of genes dysregulated in Oct-1-deficient fibroblasts following irradiation, including many associated with oxidative and metabolic stress. A number of these genes contain octamer sequences in their immediate 5' regulatory regions, some of which are conserved in human. These results indicate that Oct-1 modulates the activity of genes important for the cellular response to stress.
Collapse
Affiliation(s)
- Dean Tantin
- Center for Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
| | | | | | | | | |
Collapse
|
28
|
Lin YY, Hung CF, Wu TC. Functional Studies of Lymphocytes Using RNAi Technology. Transfus Med Hemother 2006. [DOI: 10.1159/000090204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
|
29
|
Tassabehji M, Hammond P, Karmiloff-Smith A, Thompson P, Thorgeirsson SS, Durkin ME, Popescu NC, Hutton T, Metcalfe K, Rucka A, Stewart H, Read AP, Maconochie M, Donnai D. GTF2IRD1 in craniofacial development of humans and mice. Science 2005; 310:1184-7. [PMID: 16293761 DOI: 10.1126/science.1116142] [Citation(s) in RCA: 145] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Craniofacial abnormalities account for about one-third of all human congenital defects, but our understanding of the genetic mechanisms governing craniofacial development is incomplete. We show that GTF2IRD1 is a genetic determinant of mammalian craniofacial and cognitive development, and we implicate another member of the TFII-I transcription factor family, GTF2I, in both aspects. Gtf2ird1-null mice exhibit phenotypic abnormalities reminiscent of the human microdeletion disorder Williams-Beuren syndrome (WBS); craniofacial imaging reveals abnormalities in both skull and jaws that may arise through misregulation of goosecoid, a downstream target of Gtf2ird1. In humans, a rare WBS individual with an atypical deletion, including GTF2IRD1, shows facial dysmorphism and cognitive deficits that differ from those of classic WBS cases. We propose a mechanism of cumulative dosage effects of duplicated and diverged genes applicable to other human chromosomal disorders.
Collapse
Affiliation(s)
- May Tassabehji
- Academic Unit of Medical Genetics, University of Manchester, St. Mary's Hospital, Manchester M13 9PL, UK.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Sadowski I, Mitchell DA. TFII-I and USF (RBF-2) regulate Ras/MAPK-responsive HIV-1 transcription in T cells. Eur J Cancer 2005; 41:2528-36. [PMID: 16223582 DOI: 10.1016/j.ejca.2005.08.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The HIV-1 long terminal repeat (LTR) is stringently controlled by T cell activation signals, and binds a variety of transcription factors whose activities are regulated downstream of the T cell receptor. One of the most highly conserved cis-elements on the LTR, designated RBEIII, binds the factor RBF-2 which is comprised of a USF-1/USF-2 heterodimer and a co-factor TFII-I. RBF-2 is necessary for transcription from the LTR in response to RAS-MAPK activation through T cell receptor engagement, but is also required for repression of viral expression in unstimulated cells. Considering the defined activities of USF and TFII-I, RBF-2 may be responsible for regulating promoter context by controlling chromatin organisation, thereby coordinating opportunity for transcriptional activation by additional factors bound to the enhancer region.
Collapse
Affiliation(s)
- Ivan Sadowski
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2146 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3.
| | | |
Collapse
|
31
|
Ku M, Sokol SY, Wu J, Tussie-Luna MI, Roy AL, Hata A. Positive and negative regulation of the transforming growth factor beta/activin target gene goosecoid by the TFII-I family of transcription factors. Mol Cell Biol 2005; 25:7144-57. [PMID: 16055724 PMCID: PMC1190264 DOI: 10.1128/mcb.25.16.7144-7157.2005] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Goosecoid (Gsc) is a homeodomain-containing transcription factor present in a wide variety of vertebrate species and known to regulate formation and patterning of embryos. Here we show that in embryonic carcinoma P19 cells, the transcription factor TFII-I forms a complex with Smad2 upon transforming growth factor beta (TGFbeta)/activin stimulation, is recruited to the distal element (DE) of the Gsc promoter, and activates Gsc transcription. Downregulation of endogenous TFII-I by small inhibitory RNA in P19 cells abolishes the TGFbeta-mediated induction of Gsc. Similarly, Xenopus embryos with endogenous TFII-I expression downregulated by injection of TFII-I-specific antisense oligonucleotides exhibit decreased Gsc expression. Unlike TFII-I, the related factor BEN (binding factor for early enhancer) is constitutively recruited to the distal element in the absence of TGFbeta/activin signaling and is replaced by the TFII-I/Smad2 complex upon TGFbeta/activin stimulation. Overexpression of BEN in P19 cells represses the TGFbeta-mediated transcriptional activation of Gsc. These results suggest a model in which TFII-I family proteins have opposing effects in the regulation of the Gsc gene in response to a TGFbeta/activin signal.
Collapse
MESH Headings
- Activins/metabolism
- Animals
- Blotting, Northern
- COS Cells
- Cell Line, Tumor
- Chromatin Immunoprecipitation
- DNA-Binding Proteins/metabolism
- Down-Regulation
- Female
- Gene Expression Regulation
- Gene Expression Regulation, Developmental
- Glutathione Transferase/metabolism
- Goosecoid Protein
- Green Fluorescent Proteins/metabolism
- Homeodomain Proteins/metabolism
- Humans
- Immunoblotting
- Immunoprecipitation
- Luciferases/metabolism
- Mice
- Microscopy, Fluorescence
- Models, Biological
- Nodal Protein
- Oligonucleotides, Antisense/pharmacology
- Plasmids/metabolism
- Promoter Regions, Genetic
- Protein Binding
- Protein Biosynthesis
- Protein Structure, Tertiary
- RNA/metabolism
- Repressor Proteins/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Signal Transduction
- Smad2 Protein
- Time Factors
- Trans-Activators/metabolism
- Transcription Factors/metabolism
- Transcription Factors, TFII/metabolism
- Transcription, Genetic
- Transcriptional Activation
- Transforming Growth Factor beta/metabolism
- Up-Regulation
- Xenopus
- Xenopus Proteins
- Xenopus laevis
Collapse
Affiliation(s)
- Manching Ku
- Molecular Cardiology Research Institute, Tufts-New England Medical Center, Boston, MA 02111, USA
| | | | | | | | | | | |
Collapse
|
32
|
Vullhorst D, Buonanno A. Multiple GTF2I-like repeats of general transcription factor 3 exhibit DNA binding properties. Evidence for a common origin as a sequence-specific DNA interaction module. J Biol Chem 2005; 280:31722-31. [PMID: 15987678 DOI: 10.1074/jbc.m500593200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A hallmark of general transcription factor 3 (GTF3) is the presence of multiple GTF2I-like repeats that were suggested to mediate protein-protein interactions. However, we have recently demonstrated that repeat 4 is necessary and sufficient for binding of GTF3 to the bicoid-like motif of the Troponin I slow enhancer. Given the sequence similarity between different GTF2I-like repeats we hypothesized that DNA binding might be a common property of this domain type. We subjected five repeats of GTF3 to random oligonucleotide selection (SELEX) to assess their DNA binding potentials. We delineated the consensus sequence G(TC)G(A)GATTA(G)BG(A) for repeat 4 and showed that binding sites for GTF3 in enhancers for Troponin I and homeobox c8 (HOXc8) are in very good agreement with this motif. SELEX selections for repeats 5 and 2 enriched for oligonucleotides that were also bound by R4, suggesting that they share common sequence preferences, whereas repeat 3 exhibited relaxed sequence requirements for DNA binding. No binding was observed for repeat 1. We also show that GTF2I-like repeats 4 and 6 of transcription factor II-I (TFII-I) exhibit modest DNA binding properties. Lastly, we identified several amino acids of GTF3 repeat 4 required for high affinity protein-DNA interaction. Based on the ability of many repeats to bind DNA in vitro, we suggest that GTF2I-like domains evolved by duplication and diversification of a prototypic DNA-binding ancestor.
Collapse
Affiliation(s)
- Detlef Vullhorst
- Section on Molecular Neurobiology, NICHD, National Institutes of Health, Bethesda, Maryland 20892, USA.
| | | |
Collapse
|
33
|
Jackson TA, Taylor HE, Sharma D, Desiderio S, Danoff SK. Vascular endothelial growth factor receptor-2: counter-regulation by the transcription factors, TFII-I and TFII-IRD1. J Biol Chem 2005; 280:29856-63. [PMID: 15941713 DOI: 10.1074/jbc.m500335200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The vascular endothelial growth factor receptor-2 (VEGFR-2/KDR/flk-1) functions as the primary mediator of vascular endothelial growth factor activation in endothelial cells. Regulation of VEGFR-2 expression appears critical in mitogenesis, differentiation, and angiogenesis. Transcriptional regulation of the VEGFR-2 is complex and may involve multiple putative upstream regulatory elements including E boxes. Transcript initiation is dependent on an initiator (Inr) element flanking the transcriptional start site. The transcription factor, TFII-I, enhances VEGFR-2 transcription in an Inr-dependent fashion. TFII-I is unusual both structurally and functionally. The TFII-I transcription factor family members contain multiple putative DNA binding domains. Functionally, TFII-I acts at both the basal, Inr element as well as at several distinct upstream regulatory sites. It has been postulated that the structure of TFII-I might allow simultaneous interaction with both basal and regulatory sites in a given promoter. As TFII-I is known to act at regulatory sites including E boxes as well as at the basal Inr element, we evaluated the possibility of Inr-independent TFII-I activation of the VEGFR-2 promoter. We found that an Inr-mutated VEGFR-2 reporter construct retains TFII-I-stimulated activity. We demonstrated that TFII-I binds to both the Inr and to three regulatory E boxes in the human VEGFR-2 promoter. In addition, reduction in TFII-I expression by siRNA results in decreased VEGFR-2 expression. We also describe counter-regulation of the VEGFR-2 promoter by TFII-IRD1. We found that TFII-I is capable of acting at both basal and regulatory sites in one promoter and that the human VEGFR-2 promoter is functionally counter-regulated by TFII-I and TFII-IRD1.
Collapse
Affiliation(s)
- Tanisha A Jackson
- Department of Medicine, The John Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | | | | | | |
Collapse
|
34
|
Hinsley TA, Cunliffe P, Tipney HJ, Brass A, Tassabehji M. Comparison of TFII-I gene family members deleted in Williams-Beuren syndrome. Protein Sci 2004; 13:2588-99. [PMID: 15388857 PMCID: PMC2286546 DOI: 10.1110/ps.04747604] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2004] [Revised: 06/30/2004] [Accepted: 07/02/2004] [Indexed: 12/21/2022]
Abstract
Williams-Beuren syndrome (WBS) is a neurological disorder resulting from a microdeletion, typically 1.5 megabases in size, at 7q11.23. Atypical patients implicate genes at the telomeric end of this multigene deletion as the main candidates for the pathology of WBS in particular the unequal cognitive profile associated with the condition. We recently identified a gene (GTF2IRD2) that shares homology with other members of a unique family of transcription factors (TFII-I family), which reside in the critical telomeric region. Using bioinformatics tools this study focuses on the detailed assessment of this gene family, concentrating on their characteristic structural components such as the leucine zipper (LZ) and I-repeat elements, in an attempt to identify features that could aid functional predictions. Phylogenetic analysis identified distinct I-repeat clades shared between family members. Linking functional data to one such clade has implicated them in DNA binding. The identification of PEST, synergy control motifs, and sumoylation sites common to all family members suggest a shared mechanism regulating the stability and transcriptional activity of these factors. In addition, the identification/isolation of short truncated isoforms for each TFII-I family member implies a mode of self-regulation. The exceptionally high identity shared between GTF2I and GTF2IRD2, suggests that heterodimers as well as homodimers are possible, and indicates overlapping functions between their respective short isoforms. Such cross-reactivity between GTF2I and GTF2IRD2 short isoforms might have been the evolutionary driving force for the 7q11.23 chromosomal rearrangement not present in the syntenic region in mice.
Collapse
Affiliation(s)
- Timothy A Hinsley
- Academic Department of Medical Genetics, St. Mary's Hospital, Hathersage Road, Manchester, M13 0JH, UK
| | | | | | | | | |
Collapse
|