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Amor-Salamanca A, Santana Rodríguez A, Rasoul H, Rodríguez-Palomares JF, Moldovan O, Hey TM, Delgado MG, Cuenca DL, de Castro Campos D, Basurte-Elorz MT, Macías-Ruiz R, Fuentes Cañamero ME, Galvin J, Bilbao Quesada R, de la Higuera Romero L, Trujillo-Quintero JP, García-Cruz LM, Cárdenas-Reyes I, Jiménez-Jáimez J, García-Hernández S, Valverde-Gómez M, Gómez-Díaz I, Limeres Freire J, García-Pinilla JM, Gimeno-Blanes JR, Savattis K, García-Pavía P, Ochoa JP. Role of TBX20 Truncating Variants in Dilated Cardiomyopathy and Left Ventricular Noncompaction. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2024; 17:e004404. [PMID: 38353104 PMCID: PMC11019988 DOI: 10.1161/circgen.123.004404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 01/07/2024] [Indexed: 04/18/2024]
Abstract
BACKGROUND Less than 40% of patients with dilated cardiomyopathy (DCM) have a pathogenic/likely pathogenic genetic variant identified. TBX20 has been linked to congenital heart defects; although an association with left ventricular noncompaction (LVNC) and DCM has been proposed, it is still considered a gene with limited evidence for these phenotypes. This study sought to investigate the association between the TBX20 truncating variant (TBX20tv) and DCM/LVNC. METHODS TBX20 was sequenced by next-generation sequencing in 7463 unrelated probands with a diagnosis of DCM or LVNC, 22 773 probands of an internal comparison group (hypertrophic cardiomyopathy, channelopathies, or aortic diseases), and 124 098 external controls (individuals from the gnomAD database). Enrichment of TBX20tv in DCM/LVNC was calculated, cosegregation was determined in selected families, and clinical characteristics and outcomes were analyzed in carriers. RESULTS TBX20tv was enriched in DCM/LVNC (24/7463; 0.32%) compared with internal (1/22 773; 0.004%) and external comparison groups (4/124 098; 0.003%), with odds ratios of 73.23 (95% CI, 9.90-541.45; P<0.0001) and 99.76 (95% CI, 34.60-287.62; P<0.0001), respectively. TBX20tv was cosegregated with DCM/LVNC phenotype in 21 families for a combined logarythm of the odds score of 4.53 (strong linkage). Among 57 individuals with TBX20tv (49.1% men; mean age, 35.9±20.8 years), 41 (71.9%) exhibited DCM/LVNC, of whom 14 (34.1%) had also congenital heart defects. After a median follow-up of 6.9 (95% CI, 25-75:3.6-14.5) years, 9.7% of patients with DCM/LVNC had end-stage heart failure events and 4.8% experienced malignant ventricular arrhythmias. CONCLUSIONS TBX20tv is associated with DCM/LVNC; congenital heart defect is also present in around one-third of cases. TBX20tv-associated DCM/LVNC is characterized by a nonaggressive phenotype, with a low incidence of major cardiovascular events. TBX20 should be considered a definitive gene for DCM and LVNC and routinely included in genetic testing panels for these phenotypes.
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Affiliation(s)
- Almudena Amor-Salamanca
- Cardiology Department, Health in Code SL, A Coruña, Spain (A.A.-S., L.d.l.H.R., I.C.-R., S.G.-H., M.V.-G., I.G.-D., J.P.O.)
| | - Alfredo Santana Rodríguez
- Clinical Genetics Unit, Complejo Hospitalario Universitario Insular Materno Infantil, Las Palmas de Gran Canaria, Spain (A.S.R., L.M.G.-C.)
- Research Institute of Biomedical and Health Sciences, University of Las Palmas de Gran Canaria, Spain (A.S.R., L.M.G.-C.)
| | - Hazhee Rasoul
- Inherited Cardiovascular Diseases Unit, St. Bartholomew’s Hospital, Barts Health NHS Trust, London, United Kingdom (H.R., K.S.)
| | - José F. Rodríguez-Palomares
- Cardiovascular Imaging Unit and Inherited Cardiac Diseases Unit, Cardiology Department, Vall d′Hebron University Hospital, Barcelona, Spain (J.F.R.-P., J.L.F.)
- Vall d′Hebron Rsrch Unit, Barcelona, Spain (J.F.R.-P.)
- Universitat Autònoma Barcelona, Spain (J.F.R.-P., J.P.T.-Q.)
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain (J.F.R.-P., M.G.D., J.M.G.-P., J.R.G.-B., P.G.-P.)
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart, ERN GUARD-Heart, Amsterdam, The Netherlands (J.F.R.-P., J.L.F., J.R.G.-B., P.G.-P.)
| | - Oana Moldovan
- Serviço de Genética Médica, Department de Pediatria, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Portugal (O.M.)
| | - Thomas Morris Hey
- Department of Cardiology, The Clinic of Inherited Cardiovascular Diseases, Odense University Hospital, Denmark (T.M.H.)
| | - María Gallego Delgado
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain (J.F.R.-P., M.G.D., J.M.G.-P., J.R.G.-B., P.G.-P.)
- Cardiology Department, Hospital Universitario de Salamanca, Spain (M.G.D.)
- Biomedical Research Institute of Salamanca, Gerencia Regional de Salud de Castilla y León, Spain (M.G.D.)
| | - David López Cuenca
- Department of Cardiology, Inherited Cardiac Diseases Unit, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain (D.L.C., J.R.G.-B.)
| | - Daniel de Castro Campos
- Department of Cardiology, Heart Failure and Inherited Cardiac Diseases Unit, Hospital Universitario Puerta de Hierro, IDIPHISA, Madrid, Spain (D.d.C.C., P.G.-P., J.P.O.)
| | | | - Rosa Macías-Ruiz
- Cardiology Department, Hospital Universitario Virgen de las Nieves, Granada, Spain (R.M.-R., J.J.-J.)
- Instituto de Investigación Biosanitaria Instituto de Investigación Biosanitaria de Granada (IBS-GRANADA), Spain (R.M.-R., J.J.-J.)
| | | | - Joseph Galvin
- Department of Cardiology, University College Dublin School of Medicine, Mater Misericordiae University Hospital, Ireland (J.G.)
| | | | - Luis de la Higuera Romero
- Cardiology Department, Health in Code SL, A Coruña, Spain (A.A.-S., L.d.l.H.R., I.C.-R., S.G.-H., M.V.-G., I.G.-D., J.P.O.)
| | - Juan Pablo Trujillo-Quintero
- Universitat Autònoma Barcelona, Spain (J.F.R.-P., J.P.T.-Q.)
- Center for Genomic Medicine, Parc Taulí Hospital Universitari, Sabadell, Spain (J.P.T.-Q.)
- Institut d’Investigació i Innovació Parc Taulí, Sabadell, Spain (J.P.T.-Q.)
| | - Loida María García-Cruz
- Clinical Genetics Unit, Complejo Hospitalario Universitario Insular Materno Infantil, Las Palmas de Gran Canaria, Spain (A.S.R., L.M.G.-C.)
- Research Institute of Biomedical and Health Sciences, University of Las Palmas de Gran Canaria, Spain (A.S.R., L.M.G.-C.)
| | - Ivonne Cárdenas-Reyes
- Cardiology Department, Health in Code SL, A Coruña, Spain (A.A.-S., L.d.l.H.R., I.C.-R., S.G.-H., M.V.-G., I.G.-D., J.P.O.)
| | - Juan Jiménez-Jáimez
- Cardiology Department, Hospital Universitario Virgen de las Nieves, Granada, Spain (R.M.-R., J.J.-J.)
- Instituto de Investigación Biosanitaria Instituto de Investigación Biosanitaria de Granada (IBS-GRANADA), Spain (R.M.-R., J.J.-J.)
| | - Soledad García-Hernández
- Cardiology Department, Health in Code SL, A Coruña, Spain (A.A.-S., L.d.l.H.R., I.C.-R., S.G.-H., M.V.-G., I.G.-D., J.P.O.)
- Inherited Cardiac Diseases Unit, Hospital Universitario San Cecilio, Granada, Spain (S.G.-H.)
| | - María Valverde-Gómez
- Cardiology Department, Health in Code SL, A Coruña, Spain (A.A.-S., L.d.l.H.R., I.C.-R., S.G.-H., M.V.-G., I.G.-D., J.P.O.)
- Cardiology Department, Hospital Universitario 12 de Octubre, Madrid, Spain (M.V.-G.)
| | - Iria Gómez-Díaz
- Cardiology Department, Health in Code SL, A Coruña, Spain (A.A.-S., L.d.l.H.R., I.C.-R., S.G.-H., M.V.-G., I.G.-D., J.P.O.)
| | - Javier Limeres Freire
- Cardiovascular Imaging Unit and Inherited Cardiac Diseases Unit, Cardiology Department, Vall d′Hebron University Hospital, Barcelona, Spain (J.F.R.-P., J.L.F.)
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart, ERN GUARD-Heart, Amsterdam, The Netherlands (J.F.R.-P., J.L.F., J.R.G.-B., P.G.-P.)
| | - José M. García-Pinilla
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain (J.F.R.-P., M.G.D., J.M.G.-P., J.R.G.-B., P.G.-P.)
- Department of Cardiology, Heart Failure and Inherited Cardiac Diseases Unit, Hospital Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain (J.M.G.-P.)
- Department of Medicine and Dermatology, Universidad de Málaga, Spain (J.M.G.-P.)
| | - Juan R. Gimeno-Blanes
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain (J.F.R.-P., M.G.D., J.M.G.-P., J.R.G.-B., P.G.-P.)
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart, ERN GUARD-Heart, Amsterdam, The Netherlands (J.F.R.-P., J.L.F., J.R.G.-B., P.G.-P.)
- Department of Cardiology, Inherited Cardiac Diseases Unit, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain (D.L.C., J.R.G.-B.)
| | - Konstantinos Savattis
- Inherited Cardiovascular Diseases Unit, St. Bartholomew’s Hospital, Barts Health NHS Trust, London, United Kingdom (H.R., K.S.)
- Institute for Cardiovascular Science, University College London, United Kingdom (K.S.)
- Biomedical Research Center, National Institute for Health and Care Research (NIHR) University College London Hospitals, United Kingdom (K.S.)
- William Harvey Research Institute, Queen Mary University of London, United Kingdom (K.S.)
| | - Pablo García-Pavía
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain (J.F.R.-P., M.G.D., J.M.G.-P., J.R.G.-B., P.G.-P.)
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart, ERN GUARD-Heart, Amsterdam, The Netherlands (J.F.R.-P., J.L.F., J.R.G.-B., P.G.-P.)
- Department of Cardiology, Heart Failure and Inherited Cardiac Diseases Unit, Hospital Universitario Puerta de Hierro, IDIPHISA, Madrid, Spain (D.d.C.C., P.G.-P., J.P.O.)
- Universidad Francisco de Vitoria, Pozuelo de Alarcón, Spain (P.G.-P.)
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (P.G.-P., J.P.O.)
| | - Juan Pablo Ochoa
- Cardiology Department, Health in Code SL, A Coruña, Spain (A.A.-S., L.d.l.H.R., I.C.-R., S.G.-H., M.V.-G., I.G.-D., J.P.O.)
- Department of Cardiology, Heart Failure and Inherited Cardiac Diseases Unit, Hospital Universitario Puerta de Hierro, IDIPHISA, Madrid, Spain (D.d.C.C., P.G.-P., J.P.O.)
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (P.G.-P., J.P.O.)
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Chen S, Hu J, Xu Y, Yan J, Li S, Chen L, Zhang J. Transcriptome analysis of human hypertrophic cardiomyopathy reveals inhibited cardiac development pathways in children. iScience 2024; 27:108642. [PMID: 38205249 PMCID: PMC10777066 DOI: 10.1016/j.isci.2023.108642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 10/22/2023] [Accepted: 12/01/2023] [Indexed: 01/12/2024] Open
Abstract
The epidemiological, etiological, and clinical characteristics vary greatly between pediatric (P-HCM) and adult (A-HCM) hypertrophic cardiomyopathy (HCM) patients, and the understanding of the heterogeneous pathogenesis mechanisms is insufficient to date. In this study, we aimed to comprehensively assess the respective transcriptome signatures and uncover the essential differences in gene expression patterns among A-HCM and P-HCM. The transcriptome data of adults were collected from public data (GSE89714), and novel pediatric data were first obtained by RNA sequencing from 14 P-HCM and 9 infantile donor heart samples. Our study demonstrates the common signatures of myofilament or protein synthesis and calcium ion regulation pathways in HCM. Mitochondrial function is specifically dysregulated in A-HCM, whereas the inhibition of cardiac developing networks typifies P-HCM. These findings not only distinguish the transcriptome characteristics in children and adults with HCM but also reveal the potential mechanism of the higher incidence of septal defects in P-HCM patients.
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Affiliation(s)
- Shi Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jingjing Hu
- Key Laboratory of Public Health Safety, Ministry of Education, Fudan University; Shanghai, China
- Shanghai Pinnacles Medical Technology Co., Ltd, Shanghai 200126, China
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Yidan Xu
- Department of Cardiac Surgery, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, Shenzhen, China
| | - Jun Yan
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shoujun Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liang Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Cardiac Surgery, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, Shenzhen, China
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3
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Edwards W, Bussey OK, Conlon FL. The Tbx20-TLE interaction is essential for the maintenance of the second heart field. Development 2023; 150:dev201677. [PMID: 37756602 PMCID: PMC10629681 DOI: 10.1242/dev.201677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023]
Abstract
T-box transcription factor 20 (Tbx20) plays a multifaceted role in cardiac morphogenesis and controls a broad gene regulatory network. However, the mechanism by which Tbx20 activates and represses target genes in a tissue-specific and temporal manner remains unclear. Studies show that Tbx20 directly interacts with the Transducin-like Enhancer of Split (TLE) family of proteins to mediate transcriptional repression. However, a function for the Tbx20-TLE transcriptional repression complex during heart development has yet to be established. We created a mouse model with a two amino acid substitution in the Tbx20 EH1 domain, thereby disrupting the Tbx20-TLE interaction. Disruption of this interaction impaired crucial morphogenic events, including cardiac looping and chamber formation. Transcriptional profiling of Tbx20EH1Mut hearts and analysis of putative direct targets revealed misexpression of the retinoic acid pathway and cardiac progenitor genes. Further, we show that altered cardiac progenitor development and function contribute to the severe cardiac defects in our model. Our studies indicate that TLE-mediated repression is a primary mechanism by which Tbx20 controls gene expression.
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Affiliation(s)
- Whitney Edwards
- Department of Biology and Genetics, McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Integrative Program for Biological & Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Olivia K. Bussey
- Department of Biology and Genetics, McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Integrative Program for Biological & Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Frank L. Conlon
- Department of Biology and Genetics, McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Integrative Program for Biological & Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Li N, Li YJ, Guo XJ, Wu SH, Jiang WF, Zhang DL, Wang KW, Li L, Sun YM, Xu YJ, Yang YQ, Qiu XB. Discovery of TBX20 as a Novel Gene Underlying Atrial Fibrillation. BIOLOGY 2023; 12:1186. [PMID: 37759586 PMCID: PMC10525918 DOI: 10.3390/biology12091186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Abstract
Atrial fibrillation (AF), the most prevalent type of sustained cardiac dysrhythmia globally, confers strikingly enhanced risks for cognitive dysfunction, stroke, chronic cardiac failure, and sudden cardiovascular demise. Aggregating studies underscore the crucial roles of inherited determinants in the occurrence and perpetuation of AF. However, due to conspicuous genetic heterogeneity, the inherited defects accounting for AF remain largely indefinite. Here, via whole-genome genotyping with genetic markers and a linkage assay in a family suffering from AF, a new AF-causative locus was located at human chromosome 7p14.2-p14.3, a ~4.89 cM (~4.43-Mb) interval between the markers D7S526 and D7S2250. An exome-wide sequencing assay unveiled that, at the defined locus, the mutation in the TBX20 gene, NM_001077653.2: c.695A>G; p.(His232Arg), was solely co-segregated with AF in the family. Additionally, a Sanger sequencing assay of TBX20 in another family suffering from AF uncovered a novel mutation, NM_001077653.2: c.862G>C; p.(Asp288His). Neither of the two mutations were observed in 600 unrelated control individuals. Functional investigations demonstrated that the two mutations both significantly reduced the transactivation of the target gene KCNH2 (a well-established AF-causing gene) and the ability to bind the promoter of KCNH2, while they had no effect on the nuclear distribution of TBX20. Conclusively, these findings reveal a new AF-causative locus at human chromosome 7p14.2-p14.3 and strongly indicate TBX20 as a novel AF-predisposing gene, shedding light on the mechanism underlying AF and suggesting clinical significance for the allele-specific treatment of AF patients.
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Affiliation(s)
- Ning Li
- Department of Cardiology, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200062, China;
| | - Yan-Jie Li
- Department of Cardiology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China; (Y.-J.L.); (S.-H.W.); (W.-F.J.)
| | - Xiao-Juan Guo
- Department of Cardiology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai 200240, China; (X.-J.G.); (Y.-J.X.)
- Center for Complex Cardiac Arrhythmias of Minhang District, Shanghai Fifth People′s Hospital, Fudan University, Shanghai 200240, China
| | - Shao-Hui Wu
- Department of Cardiology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China; (Y.-J.L.); (S.-H.W.); (W.-F.J.)
| | - Wei-Feng Jiang
- Department of Cardiology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China; (Y.-J.L.); (S.-H.W.); (W.-F.J.)
| | - Dao-Liang Zhang
- Cardiac Arrhythmia Center, Fuwai Hospital, Chinese Academy of Medical Sciences, Shenzhen 518057, China;
| | - Kun-Wei Wang
- Department of Cardiology, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China;
| | - Li Li
- Key Laboratory of Arrhythmias, Ministry of Education of China, Tongji University School of Medicine, Shanghai 200092, China;
| | - Yu-Min Sun
- Department of Cardiology, Shanghai Jing’an District Central Hospital, Fudan University, Shanghai 200040, China;
| | - Ying-Jia Xu
- Department of Cardiology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai 200240, China; (X.-J.G.); (Y.-J.X.)
- Center for Complex Cardiac Arrhythmias of Minhang District, Shanghai Fifth People′s Hospital, Fudan University, Shanghai 200240, China
| | - Yi-Qing Yang
- Department of Cardiology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai 200240, China; (X.-J.G.); (Y.-J.X.)
- Center for Complex Cardiac Arrhythmias of Minhang District, Shanghai Fifth People′s Hospital, Fudan University, Shanghai 200240, China
- Cardiovascular Research Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai 200240, China
- Central Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai 200240, China
| | - Xing-Biao Qiu
- Department of Cardiology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China; (Y.-J.L.); (S.-H.W.); (W.-F.J.)
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Kirkland NJ, Skalak SH, Whitehead AJ, Hocker JD, Beri P, Vogler G, Hum B, Wang M, Lakatta EG, Ren B, Bodmer R, Engler AJ. Age-dependent Lamin changes induce cardiac dysfunction via dysregulation of cardiac transcriptional programs. NATURE AGING 2023; 3:17-33. [PMID: 36845078 PMCID: PMC9956937 DOI: 10.1038/s43587-022-00323-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 10/31/2022] [Indexed: 12/24/2022]
Abstract
As we age, structural changes contribute to progressive decline in organ function, which in the heart act through poorly characterized mechanisms. Taking advantage of the short lifespan and conserved cardiac proteome of the fruit fly, we found that cardiomyocytes exhibit progressive loss of Lamin C (mammalian Lamin A/C homologue) with age, coincident with decreasing nuclear size and increasing nuclear stiffness. Premature genetic reduction of Lamin C phenocopies aging's effects on the nucleus, and subsequently decreases heart contractility and sarcomere organization. Surprisingly, Lamin C reduction downregulates myogenic transcription factors and cytoskeletal regulators, possibly via reduced chromatin accessibility. Subsequently, we find a role for cardiac transcription factors in regulating adult heart contractility and show that maintenance of Lamin C, and cardiac transcription factor expression, prevents age-dependent cardiac decline. Our findings are conserved in aged non-human primates and mice, demonstrating that age-dependent nuclear remodeling is a major mechanism contributing to cardiac dysfunction.
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Affiliation(s)
- Natalie J. Kirkland
- Department of Bioengineering, University California San Diego; La Jolla, CA, USA 92093
- Sanford Consortium for Regenerative Medicine; La Jolla, CA, USA 92037
| | - Scott H. Skalak
- Department of Bioengineering, University California San Diego; La Jolla, CA, USA 92093
- Sanford Consortium for Regenerative Medicine; La Jolla, CA, USA 92037
| | - Alexander J. Whitehead
- Department of Bioengineering, University California San Diego; La Jolla, CA, USA 92093
- Sanford Consortium for Regenerative Medicine; La Jolla, CA, USA 92037
| | - James D. Hocker
- Cell and Molecular Medicine, University California San Diego; La Jolla, CA, USA 92093
- Biomedical Sciences Program, University California San Diego; La Jolla, CA, USA 92093
| | - Pranjali Beri
- Department of Bioengineering, University California San Diego; La Jolla, CA, USA 92093
- Sanford Consortium for Regenerative Medicine; La Jolla, CA, USA 92037
| | - Geo Vogler
- Development, Aging and Regeneration Program, Sanford-Burnham-Prebys Medical Discovery Institute; La Jolla, CA, USA 92037
| | - Bill Hum
- Development, Aging and Regeneration Program, Sanford-Burnham-Prebys Medical Discovery Institute; La Jolla, CA, USA 92037
| | - Mingyi Wang
- Laboratory of Cardiovascular Science, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA 21224
| | - Edward G. Lakatta
- Laboratory of Cardiovascular Science, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA 21224
| | - Bing Ren
- Cell and Molecular Medicine, University California San Diego; La Jolla, CA, USA 92093
- Biomedical Sciences Program, University California San Diego; La Jolla, CA, USA 92093
- Ludwig Institute for Cancer Research; La Jolla, CA, USA 92037
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford-Burnham-Prebys Medical Discovery Institute; La Jolla, CA, USA 92037
| | - Adam J. Engler
- Department of Bioengineering, University California San Diego; La Jolla, CA, USA 92093
- Biomedical Sciences Program, University California San Diego; La Jolla, CA, USA 92093
- Sanford Consortium for Regenerative Medicine; La Jolla, CA, USA 92037
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6
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Wu T, Liang Z, Zhang Z, Liu C, Zhang L, Gu Y, Peterson KL, Evans SM, Fu XD, Chen J. PRDM16 Is a Compact Myocardium-Enriched Transcription Factor Required to Maintain Compact Myocardial Cardiomyocyte Identity in Left Ventricle. Circulation 2022; 145:586-602. [PMID: 34915728 PMCID: PMC8860879 DOI: 10.1161/circulationaha.121.056666] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/29/2021] [Indexed: 01/28/2023]
Abstract
BACKGROUND Left ventricular noncompaction cardiomyopathy (LVNC) was discovered half a century ago as a cardiomyopathy with excessive trabeculation and a thin ventricular wall. In the decades since, numerous studies have demonstrated that LVNC primarily has an effect on left ventricles (LVs) and is often associated with LV dilation and dysfunction. However, in part because of the lack of suitable mouse models that faithfully mirror the selective LV vulnerability in patients, mechanisms underlying the susceptibility of LVs to dilation and dysfunction in LVNC remain unknown. Genetic studies have revealed that deletions and mutations in PRDM16 (PR domain-containing 16) cause LVNC, but previous conditional Prdm16 knockout mouse models do not mirror the LVNC phenotype in patients, and the underlying molecular mechanisms by which PRDM16 deficiency causes LVNC are still unclear. METHODS Prdm16 cardiomyocyte-specific knockout (Prdm16cKO) mice were generated and analyzed for cardiac phenotypes. RNA sequencing and chromatin immunoprecipitation deep sequencing were performed to identify direct transcriptional targets of PRDM16 in cardiomyocytes. Single-cell RNA sequencing in combination with spatial transcriptomics was used to determine cardiomyocyte identity at the single-cell level. RESULTS Cardiomyocyte-specific ablation of Prdm16 in mice caused LV-specific dilation and dysfunction, as well as biventricular noncompaction, which fully recapitulated LVNC in patients. PRDM16 functioned mechanistically as a compact myocardium-enriched transcription factor that activated compact myocardial genes while repressing trabecular myocardial genes in LV compact myocardium. Consequently, Prdm16cKO LV compact myocardial cardiomyocytes shifted from their normal transcriptomic identity to a transcriptional signature resembling trabecular myocardial cardiomyocytes or neurons. Chamber-specific transcriptional regulation by PRDM16 was attributable in part to its cooperation with LV-enriched transcription factors Tbx5 and Hand1. CONCLUSIONS These results demonstrate that disruption of proper specification of compact cardiomyocytes may play a key role in the pathogenesis of LVNC. They also shed light on underlying mechanisms of the LV-restricted transcriptional program governing LV chamber growth and maturation, providing a tangible explanation for the susceptibility of LV in a subset of LVNC cardiomyopathies.
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Affiliation(s)
- Tongbin Wu
- Department of Medicine, University of California San Diego, La Jolla, CA
- These authors contributed equally
| | - Zhengyu Liang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
- These authors contributed equally
| | - Zengming Zhang
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Canzhao Liu
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Lunfeng Zhang
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
| | - Yusu Gu
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Kirk L. Peterson
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Sylvia M. Evans
- Department of Medicine, University of California San Diego, La Jolla, CA
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
- Institute of Genomic Medicine, University of California San Diego, La Jolla, CA
| | - Ju Chen
- Department of Medicine, University of California San Diego, La Jolla, CA
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7
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Bang ML, Bogomolovas J, Chen J. Understanding the molecular basis of cardiomyopathy. Am J Physiol Heart Circ Physiol 2022; 322:H181-H233. [PMID: 34797172 PMCID: PMC8759964 DOI: 10.1152/ajpheart.00562.2021] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 02/03/2023]
Abstract
Inherited cardiomyopathies are a major cause of mortality and morbidity worldwide and can be caused by mutations in a wide range of proteins located in different cellular compartments. The present review is based on Dr. Ju Chen's 2021 Robert M. Berne Distinguished Lectureship of the American Physiological Society Cardiovascular Section, in which he provided an overview of the current knowledge on the cardiomyopathy-associated proteins that have been studied in his laboratory. The review provides a general summary of the proteins in different compartments of cardiomyocytes associated with cardiomyopathies, with specific focus on the proteins that have been studied in Dr. Chen's laboratory.
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Affiliation(s)
- Marie-Louise Bang
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Milan Unit, Milan, Italy
- IRCCS Humanitas Research Hospital, Rozzano (Milan), Italy
| | - Julius Bogomolovas
- Division of Cardiovascular Medicine, Department of Medicine Cardiology, University of California, San Diego, La Jolla, California
| | - Ju Chen
- Division of Cardiovascular Medicine, Department of Medicine Cardiology, University of California, San Diego, La Jolla, California
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8
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Chen Y, Xiao D, Zhang L, Cai CL, Li BY, Liu Y. The Role of Tbx20 in Cardiovascular Development and Function. Front Cell Dev Biol 2021; 9:638542. [PMID: 33585493 PMCID: PMC7876368 DOI: 10.3389/fcell.2021.638542] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/08/2021] [Indexed: 01/05/2023] Open
Abstract
Tbx20 is a member of the Tbx1 subfamily of T-box-containing genes and is known to play a variety of fundamental roles in cardiovascular development and homeostasis as well as cardiac remodeling in response to pathophysiological stresses. Mutations in TBX20 are widely associated with the complex spectrum of congenital heart defects (CHDs) in humans, which includes defects in chamber septation, chamber growth, and valvulogenesis. In addition, genetic variants of TBX20 have been found to be associated with dilated cardiomyopathy and heart arrhythmia. This broad spectrum of cardiac morphogenetic and functional defects is likely due to its broad expression pattern in multiple cardiogenic cell lineages and its critical regulation of transcriptional networks during cardiac development. In this review, we summarize recent findings in our general understanding of the role of Tbx20 in regulating several important aspects of cardiac development and homeostasis and heart function.
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Affiliation(s)
- Yuwen Chen
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, China.,Cardiovascular Developmental Biology Program, Herman B Wells Center for Pediatric Research, Indianapolis, IN, United States
| | - Deyong Xiao
- Cardiovascular Developmental Biology Program, Herman B Wells Center for Pediatric Research, Indianapolis, IN, United States
| | - Lu Zhang
- Cardiovascular Developmental Biology Program, Herman B Wells Center for Pediatric Research, Indianapolis, IN, United States
| | - Chen-Leng Cai
- Cardiovascular Developmental Biology Program, Herman B Wells Center for Pediatric Research, Indianapolis, IN, United States
| | - Bai-Yan Li
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Ying Liu
- Cardiovascular Developmental Biology Program, Herman B Wells Center for Pediatric Research, Indianapolis, IN, United States
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9
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Li J, Fan Z, Shen F, Pendleton AL, Song Y, Xing J, Yue B, Kidd JM, Li J. Genomic Copy Number Variation Study of Nine Macaca Species Provides New Insights into Their Genetic Divergence, Adaptation, and Biomedical Application. Genome Biol Evol 2020; 12:2211-2230. [PMID: 32970804 PMCID: PMC7846157 DOI: 10.1093/gbe/evaa200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2020] [Indexed: 02/06/2023] Open
Abstract
Copy number variation (CNV) can promote phenotypic diversification and adaptive evolution. However, the genomic architecture of CNVs among Macaca species remains scarcely reported, and the roles of CNVs in adaptation and evolution of macaques have not been well addressed. Here, we identified and characterized 1,479 genome-wide hetero-specific CNVs across nine Macaca species with bioinformatic methods, along with 26 CNV-dense regions and dozens of lineage-specific CNVs. The genes intersecting CNVs were overrepresented in nutritional metabolism, xenobiotics/drug metabolism, and immune-related pathways. Population-level transcriptome data showed that nearly 46% of CNV genes were differentially expressed across populations and also mainly consisted of metabolic and immune-related genes, which implied the role of CNVs in environmental adaptation of Macaca. Several CNVs overlapping drug metabolism genes were verified with genomic quantitative polymerase chain reaction, suggesting that these macaques may have different drug metabolism features. The CNV-dense regions, including 15 first reported here, represent unstable genomic segments in macaques where biological innovation may evolve. Twelve gains and 40 losses specific to the Barbary macaque contain genes with essential roles in energy homeostasis and immunity defense, inferring the genetic basis of its unique distribution in North Africa. Our study not only elucidated the genetic diversity across Macaca species from the perspective of structural variation but also provided suggestive evidence for the role of CNVs in adaptation and genome evolution. Additionally, our findings provide new insights into the application of diverse macaques to drug study.
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Affiliation(s)
- Jing Li
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhenxin Fan
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Feichen Shen
- Department of Human Genetics, Medical School, University of Michigan
| | | | - Yang Song
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jinchuan Xing
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway
| | - Bisong Yue
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jeffrey M Kidd
- Department of Human Genetics, Medical School, University of Michigan
| | - Jing Li
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
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10
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Nuclear receptor corepressors in intellectual disability and autism. Mol Psychiatry 2020; 25:2220-2236. [PMID: 32034290 PMCID: PMC7842082 DOI: 10.1038/s41380-020-0667-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 12/24/2019] [Accepted: 01/28/2020] [Indexed: 02/06/2023]
Abstract
Autism spectrum disorder (ASD) is characterized by neurocognitive dysfunctions, such as impaired social interaction and language learning. Gene-environment interactions have a pivotal role in ASD pathogenesis. Nuclear receptor corepressors (NCORs) are transcription co-regulators physically associated with histone deacetylases (HDACs) and many known players in ASD etiology such as transducin β-like 1 X-linked receptor 1 and methyl-CpG binding protein 2. The epigenome-modifying NCOR complex is sensitive to many ASD risk factors, including HDAC inhibitor valproic acid and a variety of endocrine factors, xenobiotic chemicals, or metabolites that can directly bind to multiple nuclear receptors. Here, we review recent studies of NCORs in neurocognition using animal models and human genetics approaches. We discuss functional interplays between NCORs and other known players in ASD etiology. It is conceivable that the NCOR complex may bridge the in utero environmental risk factors of ASD with epigenetic remodeling and can serve as a converging point for many gene-environment interactions in the pathogenesis of ASD and intellectual disability.
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11
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Fang Y, Lai KS, She P, Sun J, Tao W, Zhong TP. Tbx20 Induction Promotes Zebrafish Heart Regeneration by Inducing Cardiomyocyte Dedifferentiation and Endocardial Expansion. Front Cell Dev Biol 2020; 8:738. [PMID: 32850848 PMCID: PMC7417483 DOI: 10.3389/fcell.2020.00738] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/16/2020] [Indexed: 12/17/2022] Open
Abstract
Heart regeneration requires replenishment of lost cardiomyocytes (CMs) and cells of the endocardial lining. However, the signaling regulation and transcriptional control of myocardial dedifferentiation and endocardial activation are incompletely understood during cardiac regeneration. Here, we report that T-Box Transcription Factor 20 (Tbx20) is induced rapidly in the myocardial wound edge in response to various sources of cardiac damages in zebrafish. Inducing Tbx20 specifically in the adult myocardium promotes injury-induced CM proliferation through CM dedifferentiation, leading to loss of CM cellular contacts and re-expression of cardiac embryonic or fetal gene programs. Unexpectedly, we identify that myocardial Tbx20 induction activates the endocardium at the injury site with enhanced endocardial cell extension and proliferation, where it induces the endocardial Bone morphogenetic protein 6 (Bmp6) signaling. Pharmacologically inactivating endocardial Bmp6 signaling reduces expression of its targets, Id1 and Id2b, attenuating the increased endocardial regeneration in tbx20-overexpressing hearts. Altogether, our study demonstrates that Tbx20 induction promotes adult heart regeneration by inducing cardiomyocyte dedifferentiation as well as non-cell-autonomously enhancing endocardial cell regeneration.
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Affiliation(s)
- Yabo Fang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, School of Life Sciences, East China Normal University, Shanghai, China
| | - Kaa Seng Lai
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, School of Life Sciences, East China Normal University, Shanghai, China
| | - Peilu She
- Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, School of Life Sciences, East China Normal University, Shanghai, China
| | - Jianjian Sun
- Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, School of Life Sciences, East China Normal University, Shanghai, China
| | - Wufan Tao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Tao P Zhong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, School of Life Sciences, East China Normal University, Shanghai, China
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12
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Richter F, Morton SU, Kim SW, Kitaygorodsky A, Wasson LK, Chen KM, Zhou J, Qi H, Patel N, DePalma SR, Parfenov M, Homsy J, Gorham JM, Manheimer KB, Velinder M, Farrell A, Marth G, Schadt EE, Kaltman JR, Newburger JW, Giardini A, Goldmuntz E, Brueckner M, Kim R, Porter GA, Bernstein D, Chung WK, Srivastava D, Tristani-Firouzi M, Troyanskaya OG, Dickel DE, Shen Y, Seidman JG, Seidman CE, Gelb BD. Genomic analyses implicate noncoding de novo variants in congenital heart disease. Nat Genet 2020; 52:769-777. [PMID: 32601476 PMCID: PMC7415662 DOI: 10.1038/s41588-020-0652-z] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 05/22/2020] [Indexed: 02/07/2023]
Abstract
A genetic etiology is identified for one-third of patients with congenital heart disease (CHD), with 8% of cases attributable to coding de novo variants (DNVs). To assess the contribution of noncoding DNVs to CHD, we compared genome sequences from 749 CHD probands and their parents with those from 1,611 unaffected trios. Neural network prediction of noncoding DNV transcriptional impact identified a burden of DNVs in individuals with CHD (n = 2,238 DNVs) compared to controls (n = 4,177; P = 8.7 × 10-4). Independent analyses of enhancers showed an excess of DNVs in associated genes (27 genes versus 3.7 expected, P = 1 × 10-5). We observed significant overlap between these transcription-based approaches (odds ratio (OR) = 2.5, 95% confidence interval (CI) 1.1-5.0, P = 5.4 × 10-3). CHD DNVs altered transcription levels in 5 of 31 enhancers assayed. Finally, we observed a DNV burden in RNA-binding-protein regulatory sites (OR = 1.13, 95% CI 1.1-1.2, P = 8.8 × 10-5). Our findings demonstrate an enrichment of potentially disruptive regulatory noncoding DNVs in a fraction of CHD at least as high as that observed for damaging coding DNVs.
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Affiliation(s)
- Felix Richter
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah U Morton
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Seong Won Kim
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Alexander Kitaygorodsky
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY, USA
| | - Lauren K Wasson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Jian Zhou
- Flatiron Institute, Simons Foundation, New York, NY, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hongjian Qi
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY, USA
| | - Nihir Patel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Jason Homsy
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Center for External Innovation, Takeda Pharmaceuticals USA, Cambridge, MA, USA
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Kathryn B Manheimer
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Matthew Velinder
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Andrew Farrell
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Gabor Marth
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonathan R Kaltman
- Heart Development and Structural Diseases Branch, Division of Cardiovascular Sciences, NHLBI/NIH, Bethesda, MD, USA
| | | | | | - Elizabeth Goldmuntz
- Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Martina Brueckner
- Departments of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Richard Kim
- Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - George A Porter
- Department of Pediatrics, University of Rochester, Rochester, NY, USA
| | - Daniel Bernstein
- Department of Pediatrics, Stanford University, Palo Alto, CA, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY, USA
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease and University of California San Francisco, San Francisco, CA, USA
| | - Martin Tristani-Firouzi
- Division of Pediatric Cardiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Olga G Troyanskaya
- Flatiron Institute, Simons Foundation, New York, NY, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Yufeng Shen
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY, USA
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Cardiology, Brigham and Women's Hospital, Boston, MA, USA
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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13
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Paraiso KD, Blitz IL, Coley M, Cheung J, Sudou N, Taira M, Cho KWY. Endodermal Maternal Transcription Factors Establish Super-Enhancers during Zygotic Genome Activation. Cell Rep 2020; 27:2962-2977.e5. [PMID: 31167141 PMCID: PMC6610736 DOI: 10.1016/j.celrep.2019.05.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/30/2019] [Accepted: 05/01/2019] [Indexed: 01/06/2023] Open
Abstract
Elucidation of the sequence of events underlying the dynamic interaction
between transcription factors and chromatin states is essential. Maternal
transcription factors function at the top of the regulatory hierarchy to specify
the primary germ layers at the onset of zygotic genome activation (ZGA). We
focus on the formation of endoderm progenitor cells and examine the interactions
between maternal transcription factors and chromatin state changes underlying
the cell specification process. Endoderm-specific factors Otx1 and Vegt together
with Foxh1 orchestrate endoderm formation by coordinated binding to select
regulatory regions. These interactions occur before the deposition of enhancer
histone marks around the regulatory regions, and these TFs recruit RNA
polymerase II, regulate enhancer activity, and establish super-enhancers
associated with important endodermal genes. Therefore, maternal transcription
factors Otx1, Vegt, and Foxh1 combinatorially regulate the activity of
super-enhancers, which in turn activate key lineage-specifying genes during
ZGA. How do maternal transcription factors interact with chromatin regions to
coordinate the endodermal gene regulatory program? Paraiso et al. demonstrate
that combinatorial binding of maternal Otx1, Vegt, and Foxh1 to select enhancers
and super-enhancers in the genome controls endodermal cell fate specification
during zygotic gene activation.
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Affiliation(s)
- Kitt D Paraiso
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Ira L Blitz
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Masani Coley
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Jessica Cheung
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Norihiro Sudou
- Department of Anatomy, Tokyo Women's Medical University, Tokyo, Japan
| | - Masanori Taira
- Department of Biological Sciences, Chuo University, Tokyo, Japan
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA.
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14
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He Q, Cai H, Bai M, Zhang M, Chen F, Huang Y, Priyadarshani SVGN, Chai M, Liu L, Liu Y, Chen H, Qin Y. A Soybean bZIP Transcription Factor GmbZIP19 Confers Multiple Biotic and Abiotic Stress Responses in Plant. Int J Mol Sci 2020; 21:E4701. [PMID: 32630201 PMCID: PMC7369738 DOI: 10.3390/ijms21134701] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/22/2020] [Accepted: 06/29/2020] [Indexed: 01/29/2023] Open
Abstract
The basic leucine zipper (bZIP) is a plant-specific transcription factor family that plays crucial roles in response to biotic and abiotic stresses. However, little is known about the function of bZIP genes in soybean. In this study, we isolated a bZIP gene, GmbZIP19, from soybean. A subcellular localization study of GmbZIP19 revealed its nucleus localization. We showed that GmbZIP19 expression was significantly induced by ABA (abscisic acid), JA (jasmonic acid) and SA (salicylic acid), but reduced under salt and drought stress conditions. Further, GmbZIP19 overexpression Arabidopsis lines showed increased resistance to S. sclerotiorum and Pseudomonas syringae associated with upregulated ABA-, JA-, ETH- (ethephon-)and SA-induced marker genes expression, but exhibited sensitivity to salt and drought stresses in association with destroyed stomatal closure and downregulated the salt and drought stresses marker genes' expression. We generated a soybean transient GmbZIP19 overexpression line, performed a Chromatin immunoprecipitation assay and found that GmbZIP19 bound to promoters of ABA-, JA-, ETH-, and SA-induced marker genes in soybean. The yeast one-hybrid verified the combination. The current study suggested that GmbZIP19 is a positive regulator of pathogen resistance and a negative regulator of salt and drought stress tolerance.
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Affiliation(s)
- Qing He
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.H.); (H.C.); (M.Z.); (F.C.); (Y.H.); (S.V.G.N.P.); (M.C.); (H.C.)
| | - Hanyang Cai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.H.); (H.C.); (M.Z.); (F.C.); (Y.H.); (S.V.G.N.P.); (M.C.); (H.C.)
| | - Mengyan Bai
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.B.); (L.L.); (Y.L.)
| | - Man Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.H.); (H.C.); (M.Z.); (F.C.); (Y.H.); (S.V.G.N.P.); (M.C.); (H.C.)
| | - Fangqian Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.H.); (H.C.); (M.Z.); (F.C.); (Y.H.); (S.V.G.N.P.); (M.C.); (H.C.)
| | - Youmei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.H.); (H.C.); (M.Z.); (F.C.); (Y.H.); (S.V.G.N.P.); (M.C.); (H.C.)
| | - S. V. G. N. Priyadarshani
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.H.); (H.C.); (M.Z.); (F.C.); (Y.H.); (S.V.G.N.P.); (M.C.); (H.C.)
| | - Mengnan Chai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.H.); (H.C.); (M.Z.); (F.C.); (Y.H.); (S.V.G.N.P.); (M.C.); (H.C.)
| | - Liping Liu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.B.); (L.L.); (Y.L.)
| | - Yanhui Liu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.B.); (L.L.); (Y.L.)
| | - Huihuang Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.H.); (H.C.); (M.Z.); (F.C.); (Y.H.); (S.V.G.N.P.); (M.C.); (H.C.)
| | - Yuan Qin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.H.); (H.C.); (M.Z.); (F.C.); (Y.H.); (S.V.G.N.P.); (M.C.); (H.C.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
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15
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Svendsen PC, Phillips LA, Deshwar AR, Ryu JR, Najand N, Brook WJ. The selector genes midline and H15 control ventral leg pattern by both inhibiting Dpp signaling and specifying ventral fate. Dev Biol 2019; 455:19-31. [PMID: 31299230 DOI: 10.1016/j.ydbio.2019.05.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 04/27/2019] [Accepted: 05/28/2019] [Indexed: 01/13/2023]
Abstract
mid and H15 encode Tbx20 transcription factors that specify ventral pattern in the Drosophila leg. We find that there are at least two pathways for mid and H15 specification of ventral fate. In the first pathway, mid and H15 negatively regulate Dpp, the dorsal signal in leg development. mid and H15 block the dorsalizing effects of Dpp signaling in the ventral leg. In loss- and gain-of-function experiments in imaginal discs, we show that mid and H15 block the accumulation of phospho-Mad, the activated form of the Drosophila pSmad1/5 homolog. In a second pathway, we find mid and H15 must also directly promote ventral fate because simultaneously blocking Dpp signaling in mid H15 mutants does not rescue the ventral to dorsal transformation in most ventral leg structures. We show that mid and H15 act as transcriptional repressors in ventral leg development. The two genes repress the Dpp target gene Dad, the laterally expressed gene Upd, and the mid VLE enhancer. This repression depends on the eh1 domain, a binding site for the Groucho co-repressor, and is likely direct because Mid localizes to target gene enhancers in PCR-ChIP assays. A mid allele mutant for the repressing domain (eh1), mideh1, was found to be compromised in gain-of-function assays and in rescue of mid H15 loss-of-function. We propose that mid and H15 specify ventral fate through inhibition of Dpp signaling and through coordinating the repression of genes in the ventral leg.
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Affiliation(s)
- Pia C Svendsen
- Alberta Children's Hospital Research Institute, Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N4N1, Canada
| | - Lindsay A Phillips
- Alberta Children's Hospital Research Institute, Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N4N1, Canada
| | - Ashish R Deshwar
- Alberta Children's Hospital Research Institute, Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N4N1, Canada
| | - Jae-Ryeon Ryu
- Alberta Children's Hospital Research Institute, Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N4N1, Canada
| | - Nima Najand
- Alberta Children's Hospital Research Institute, Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N4N1, Canada
| | - William J Brook
- Alberta Children's Hospital Research Institute, Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N4N1, Canada.
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16
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Boogerd CJ, Zhu X, Aneas I, Sakabe N, Zhang L, Sobreira DR, Montefiori L, Bogomolovas J, Joslin AC, Zhou B, Chen J, Nobrega MA, Evans SM. Tbx20 Is Required in Mid-Gestation Cardiomyocytes and Plays a Central Role in Atrial Development. Circ Res 2019; 123:428-442. [PMID: 29903739 PMCID: PMC6092109 DOI: 10.1161/circresaha.118.311339] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Supplemental Digital Content is available in the text. Rationale: Mutations in the transcription factor TBX20 (T-box 20) are associated with congenital heart disease. Germline ablation of Tbx20 results in abnormal heart development and embryonic lethality by embryonic day 9.5. Because Tbx20 is expressed in multiple cell lineages required for myocardial development, including pharyngeal endoderm, cardiogenic mesoderm, endocardium, and myocardium, the cell type–specific requirement for TBX20 in early myocardial development remains to be explored. Objective: Here, we investigated roles of TBX20 in midgestation cardiomyocytes for heart development. Methods and Results: Ablation of Tbx20 from developing cardiomyocytes using a doxycycline inducible cTnTCre transgene led to embryonic lethality. The circumference of developing ventricular and atrial chambers, and in particular that of prospective left atrium, was significantly reduced in Tbx20 conditional knockout mutants. Cell cycle analysis demonstrated reduced proliferation of Tbx20 mutant cardiomyocytes and their arrest at the G1-S phase transition. Genome-wide transcriptome analysis of mutant cardiomyocytes revealed differential expression of multiple genes critical for cell cycle regulation. Moreover, atrial and ventricular gene programs seemed to be aberrantly regulated. Putative direct TBX20 targets were identified using TBX20 ChIP-Seq (chromatin immunoprecipitation with high throughput sequencing) from embryonic heart and included key cell cycle genes and atrial and ventricular specific genes. Notably, TBX20 bound a conserved enhancer for a gene key to atrial development and identity, COUP-TFII/Nr2f2 (chicken ovalbumin upstream promoter transcription factor 2/nuclear receptor subfamily 2, group F, member 2). This enhancer interacted with the NR2F2 promoter in human cardiomyocytes and conferred atrial specific gene expression in a transgenic mouse in a TBX20-dependent manner. Conclusions: Myocardial TBX20 directly regulates a subset of genes required for fetal cardiomyocyte proliferation, including those required for the G1-S transition. TBX20 also directly downregulates progenitor-specific genes and, in addition to regulating genes that specify chamber versus nonchamber myocardium, directly activates genes required for establishment or maintenance of atrial and ventricular identity. TBX20 plays a previously unappreciated key role in atrial development through direct regulation of an evolutionarily conserved COUPT-FII enhancer.
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Affiliation(s)
- Cornelis J. Boogerd
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences (C.J.B., X.Z., L.Z., S.M.E.)
| | - Xiaoming Zhu
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences (C.J.B., X.Z., L.Z., S.M.E.)
| | - Ivy Aneas
- University of California, San Diego, La Jolla; Department of Human Genetics, University of Chicago, IL (I.A., N.S., D.R.S., L.M., A.C.J., M.A.N.)
| | - Noboru Sakabe
- University of California, San Diego, La Jolla; Department of Human Genetics, University of Chicago, IL (I.A., N.S., D.R.S., L.M., A.C.J., M.A.N.)
| | - Lunfeng Zhang
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences (C.J.B., X.Z., L.Z., S.M.E.)
| | - Debora R. Sobreira
- University of California, San Diego, La Jolla; Department of Human Genetics, University of Chicago, IL (I.A., N.S., D.R.S., L.M., A.C.J., M.A.N.)
| | - Lindsey Montefiori
- University of California, San Diego, La Jolla; Department of Human Genetics, University of Chicago, IL (I.A., N.S., D.R.S., L.M., A.C.J., M.A.N.)
| | - Julius Bogomolovas
- Department of Medicine (J.B., J.C., S.M.E.)
- Department of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany (J.B.)
| | - Amelia C. Joslin
- University of California, San Diego, La Jolla; Department of Human Genetics, University of Chicago, IL (I.A., N.S., D.R.S., L.M., A.C.J., M.A.N.)
| | - Bin Zhou
- Department of Genetics, Medicine and Pediatrics, Albert Einstein College of Medicine of Yeshiva University, New York, NY (B.Z.)
| | - Ju Chen
- Department of Medicine (J.B., J.C., S.M.E.)
| | - Marcelo A. Nobrega
- University of California, San Diego, La Jolla; Department of Human Genetics, University of Chicago, IL (I.A., N.S., D.R.S., L.M., A.C.J., M.A.N.)
| | - Sylvia M. Evans
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences (C.J.B., X.Z., L.Z., S.M.E.)
- Department of Medicine (J.B., J.C., S.M.E.)
- Department of Pharmacology (S.M.E.)
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17
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Mollazadeh S, Fazly Bazzaz BS, Neshati V, de Vries AAF, Naderi-Meshkin H, Mojarad M, Neshati Z, Kerachian MA. T- Box20 inhibits osteogenic differentiation in adipose-derived human mesenchymal stem cells: the role of T- Box20 on osteogenesis. ACTA ACUST UNITED AC 2019; 26:8. [PMID: 31548928 PMCID: PMC6751895 DOI: 10.1186/s40709-019-0099-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 08/29/2019] [Indexed: 12/12/2022]
Abstract
Background Skeletal development and its cellular function are regulated by various transcription factors. The T-box (Tbx) family of transcription factors have critical roles in cellular differentiation as well as heart and limbs organogenesis. These factors possess activator and/or repressor domains to modify the expression of target genes. Despite the obvious effects of Tbx20 on heart development, its impact on bone development is still unknown. Methods To investigate the consequence by forced Tbx20 expression in the osteogenic differentiation of human mesenchymal stem cells derived from adipose tissue (Ad-MSCs), these cells were transduced with a bicistronic lentiviral vector encoding Tbx20 and an enhanced green fluorescent protein. Results Tbx20 gene delivery system suppressed the osteogenic differentiation of Ad-MSCs, as indicated by reduction in alkaline phosphatase activity and Alizarin Red S staining. Consistently, reverse transcription-polymerase chain reaction analyses showed that Tbx20 gain-of-function reduced the expression levels of osteoblast marker genes in osteo-inductive Ad-MSCs cultures. Accordingly, Tbx20 negatively affected osteogenesis through modulating expression of key factors involved in this process. Conclusion The present study suggests that Tbx20 could inhibit osteogenic differentiation in adipose-derived human mesenchymal stem cells.
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Affiliation(s)
- Samaneh Mollazadeh
- 1Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran.,2Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Bibi Sedigheh Fazly Bazzaz
- 2Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,3Department of Food and Drug Control, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.,4School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Vajiheh Neshati
- 2Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Antoine A F de Vries
- 5Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hojjat Naderi-Meshkin
- 6Stem Cell and Regenerative Medicine Research Group, Academic Center for Education, Culture Research (ACECR), Khorasan Razavi Branch, Mashhad, Iran
| | - Majid Mojarad
- 7Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,8Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zeinab Neshati
- 9Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Amin Kerachian
- 7Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,8Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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18
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Transcriptomic Signatures of Postnatal and Adult Intrinsically Photosensitive Ganglion Cells. eNeuro 2019; 6:ENEURO.0022-19.2019. [PMID: 31387875 PMCID: PMC6712207 DOI: 10.1523/eneuro.0022-19.2019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 07/19/2019] [Accepted: 07/23/2019] [Indexed: 11/21/2022] Open
Abstract
Intrinsically photosensitive retinal ganglion cells (ipRGCs) are rare mammalian photoreceptors essential for non-image-forming vision functions, such as circadian photoentrainment and the pupillary light reflex. They comprise multiple subtypes distinguishable by morphology, physiology, projections, and levels of expression of melanopsin (Opn4), their photopigment. The molecular programs that distinguish ipRGCs from other ganglion cells and ipRGC subtypes from one another remain elusive. Here, we present comprehensive gene expression profiles of early postnatal and adult mouse ipRGCs purified from two lines of reporter mice that mark different sets of ipRGC subtypes. We find dozens of novel genes highly enriched in ipRGCs. We reveal that Rasgrp1 and Tbx20 are selectively expressed in subsets of ipRGCs, though these molecularly defined groups imperfectly match established ipRGC subtypes. We demonstrate that the ipRGCs regulating circadian photoentrainment are diverse at the molecular level. Our findings reveal unexpected complexity in gene expression patterns across mammalian ipRGC subtypes.
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19
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Pawlak M, Kedzierska KZ, Migdal M, Karim AN, Ramilowski JA, Bugajski L, Hashimoto K, Marconi A, Piwocka K, Carninci P, Winata CL. Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development. Genome Res 2019; 29:506-519. [PMID: 30760547 PMCID: PMC6396412 DOI: 10.1101/gr.244491.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/09/2019] [Indexed: 12/19/2022]
Abstract
Organogenesis involves dynamic regulation of gene transcription and complex multipathway interactions. Despite our knowledge of key factors regulating various steps of heart morphogenesis, considerable challenges in understanding its mechanism still exist because little is known about their downstream targets and interactive regulatory network. To better understand transcriptional regulatory mechanism driving heart development and the consequences of its disruption in vivo, we performed time-series analyses of the transcriptome and genome-wide chromatin accessibility in isolated cardiomyocytes (CMs) from wild-type zebrafish embryos at developmental stages corresponding to heart tube morphogenesis, looping, and maturation. We identified genetic regulatory modules driving crucial events of heart development that contained key cardiac TFs and are associated with open chromatin regions enriched for DNA sequence motifs belonging to the family of the corresponding TFs. Loss of function of cardiac TFs Gata5, Tbx5a, and Hand2 affected the cardiac regulatory networks and caused global changes in chromatin accessibility profile, indicating their role in heart development. Among regions with differential chromatin accessibility in mutants were highly conserved noncoding elements that represent putative enhancers driving heart development. The most prominent gene expression changes, which correlated with chromatin accessibility modifications within their proximal promoter regions, occurred between heart tube morphogenesis and looping, and were associated with metabolic shift and hematopoietic/cardiac fate switch during CM maturation. Our results revealed the dynamic regulatory landscape throughout heart development and identified interactive molecular networks driving key events of heart morphogenesis.
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Affiliation(s)
- Michal Pawlak
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Zebrafish Developmental Genomics, 02-109 Warsaw, Poland
| | - Katarzyna Z Kedzierska
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Zebrafish Developmental Genomics, 02-109 Warsaw, Poland
| | - Maciej Migdal
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Zebrafish Developmental Genomics, 02-109 Warsaw, Poland
| | - Abu Nahia Karim
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Zebrafish Developmental Genomics, 02-109 Warsaw, Poland
| | | | - Lukasz Bugajski
- Nencki Institute of Experimental Biology, Laboratory of Cytometry, 02-093 Warsaw, Poland
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan
| | - Aleksandra Marconi
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Zebrafish Developmental Genomics, 02-109 Warsaw, Poland
| | - Katarzyna Piwocka
- Nencki Institute of Experimental Biology, Laboratory of Cytometry, 02-093 Warsaw, Poland
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan
| | - Cecilia L Winata
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Zebrafish Developmental Genomics, 02-109 Warsaw, Poland
- Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
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20
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Montefiori LE, Sobreira DR, Sakabe NJ, Aneas I, Joslin AC, Hansen GT, Bozek G, Moskowitz IP, McNally EM, Nóbrega MA. A promoter interaction map for cardiovascular disease genetics. eLife 2018; 7:e35788. [PMID: 29988018 PMCID: PMC6053306 DOI: 10.7554/elife.35788] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/21/2018] [Indexed: 12/17/2022] Open
Abstract
Over 500 genetic loci have been associated with risk of cardiovascular diseases (CVDs); however, most loci are located in gene-distal non-coding regions and their target genes are not known. Here, we generated high-resolution promoter capture Hi-C (PCHi-C) maps in human induced pluripotent stem cells (iPSCs) and iPSC-derived cardiomyocytes (CMs) to provide a resource for identifying and prioritizing the functional targets of CVD associations. We validate these maps by demonstrating that promoters preferentially contact distal sequences enriched for tissue-specific transcription factor motifs and are enriched for chromatin marks that correlate with dynamic changes in gene expression. Using the CM PCHi-C map, we linked 1999 CVD-associated SNPs to 347 target genes. Remarkably, more than 90% of SNP-target gene interactions did not involve the nearest gene, while 40% of SNPs interacted with at least two genes, demonstrating the importance of considering long-range chromatin interactions when interpreting functional targets of disease loci.
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Affiliation(s)
| | - Debora R Sobreira
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
| | - Noboru J Sakabe
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
| | - Ivy Aneas
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
| | - Amelia C Joslin
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
| | - Grace T Hansen
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
| | - Grazyna Bozek
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
| | - Ivan P Moskowitz
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
- Department of Pediatrics and PathologyThe University of ChicagoChicagoUnited States
| | - Elizabeth M McNally
- Center for Genetic MedicineNorthwestern University Feinberg School of MedicineChicagoUnited States
| | - Marcelo A Nóbrega
- Department of Human GeneticsThe University of ChicagoChicagoUnited States
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21
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Genome-wide use of high- and low-affinity Tbrain transcription factor binding sites during echinoderm development. Proc Natl Acad Sci U S A 2018; 114:5854-5861. [PMID: 28584099 DOI: 10.1073/pnas.1610611114] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sea stars and sea urchins are model systems for interrogating the types of deep evolutionary changes that have restructured developmental gene regulatory networks (GRNs). Although cis-regulatory DNA evolution is likely the predominant mechanism of change, it was recently shown that Tbrain, a Tbox transcription factor protein, has evolved a changed preference for a low-affinity, secondary binding motif. The primary, high-affinity motif is conserved. To date, however, no genome-wide comparisons have been performed to provide an unbiased assessment of the evolution of GRNs between these taxa, and no study has attempted to determine the interplay between transcription factor binding motif evolution and GRN topology. The study here measures genome-wide binding of Tbrain orthologs by using ChIP-sequencing and associates these orthologs with putative target genes to assess global function. Targets of both factors are enriched for other regulatory genes, although nonoverlapping sets of functional enrichments in the two datasets suggest a much diverged function. The number of low-affinity binding motifs is significantly depressed in sea urchins compared with sea star, but both motif types are associated with genes from a range of functional categories. Only a small fraction (∼10%) of genes are predicted to be orthologous targets. Collectively, these data indicate that Tbr has evolved significantly different developmental roles in these echinoderms and that the targets and the binding motifs in associated cis-regulatory sequences are dispersed throughout the hierarchy of the GRN, rather than being biased toward terminal process or discrete functional blocks, which suggests extensive evolutionary tinkering.
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22
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Kennedy L, Kaltenbrun E, Greco TM, Temple B, Herring LE, Cristea IM, Conlon FL. Formation of a TBX20-CASZ1 protein complex is protective against dilated cardiomyopathy and critical for cardiac homeostasis. PLoS Genet 2017; 13:e1007011. [PMID: 28945738 PMCID: PMC5629033 DOI: 10.1371/journal.pgen.1007011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 10/05/2017] [Accepted: 09/07/2017] [Indexed: 01/01/2023] Open
Abstract
By the age of 40, one in five adults without symptoms of cardiovascular disease are at risk for developing congestive heart failure. Within this population, dilated cardiomyopathy (DCM) remains one of the leading causes of disease and death, with nearly half of cases genetically determined. Though genetic and high throughput sequencing-based approaches have identified sporadic and inherited mutations in a multitude of genes implicated in cardiomyopathy, how combinations of asymptomatic mutations lead to cardiac failure remains a mystery. Since a number of studies have implicated mutations of the transcription factor TBX20 in congenital heart diseases, we investigated the underlying mechanisms, using an unbiased systems-based screen to identify novel, cardiac-specific binding partners. We demonstrated that TBX20 physically and genetically interacts with the essential transcription factor CASZ1. This interaction is required for survival, as mice heterozygous for both Tbx20 and Casz1 die post-natally as a result of DCM. A Tbx20 mutation associated with human familial DCM sterically interferes with the TBX20-CASZ1 interaction and provides a physical basis for how this human mutation disrupts normal cardiac function. Finally, we employed quantitative proteomic analyses to define the molecular pathways mis-regulated upon disruption of this novel complex. Collectively, our proteomic, biochemical, genetic, and structural studies suggest that the physical interaction between TBX20 and CASZ1 is required for cardiac homeostasis, and further, that reduction or loss of this critical interaction leads to DCM. This work provides strong evidence that DCM can be inherited through a digenic mechanism. A molecular understanding of cardiomyocyte development is an essential goal for improving clinical approaches to CHD. While TBX20 is an essential transcription factor for heart development and its disease relevance is well established, many fundamental questions remain about the mechanism of TBX20 function. Principle among these is how TBX20 mutations associated with adult dilated cardiomyopathy circumvent (DCM) the essential embryonic requirement for TBX20 in heart development. Here we report using an integrated approach that TBX20 complexes with the cardiac transcription factor CASZ1 in vivo. We confirmed TBX20 and CASZ1 interact biochemically and genetically, and show mice heterozygous for both Tbx20 and Casz1 die, beginning at 4 to 8 weeks post birth, exhibiting hallmarks of DCM. Interestingly, the human mutant TBX20F256I bypasses the early essential requirement for TBX20 but leads to DCM. We report here that TBX20F256I disrupts the TBX20-CASZ1 interaction, ascribing clinical relevance to this protein complex. Further, by using quantitative proteomics we have identified the molecular pathways altered in TBX20-CASZ1-mediated DCM. Together, these results identify a novel interaction between TBX20 and CASZ1 that is essential for maintaining cardiac homeostasis and imply that DCM can be inherited through a digenic mechanism.
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Affiliation(s)
- Leslie Kennedy
- University of North Carolina McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC, United States of America
- Integrative Program for Biological & Genome Sciences, UNC-Chapel Hill, Chapel Hill, NC, United States of America
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, NC, United States of America
| | - Erin Kaltenbrun
- University of North Carolina McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC, United States of America
- Integrative Program for Biological & Genome Sciences, UNC-Chapel Hill, Chapel Hill, NC, United States of America
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, NC, United States of America
| | - Todd M. Greco
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Brenda Temple
- R.L. Juliano Structural Bioinformatics Core, Department of Biochemistry and Biophysics, UNC-Chapel Hill, Chapel Hill, NC, United States of America
| | - Laura E. Herring
- UNC Proteomics Core Facility, UNC-Chapel Hill, Chapel Hill, NC, United States of America
- Department of Pharmacology, UNC-Chapel Hill, Chapel Hill, NC, United States of America
| | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Frank L. Conlon
- University of North Carolina McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC, United States of America
- Integrative Program for Biological & Genome Sciences, UNC-Chapel Hill, Chapel Hill, NC, United States of America
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, NC, United States of America
- Department of Biology, UNC-Chapel Hill, Chapel Hill, NC, United States of America
- * E-mail:
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23
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Chakraborty S, Panda AK, Bose S, Roy D, Kajal K, Guha D, Sa G. Transcriptional regulation of FOXP3 requires integrated activation of both promoter and CNS regions in tumor-induced CD8 + Treg cells. Sci Rep 2017; 7:1628. [PMID: 28487507 PMCID: PMC5431671 DOI: 10.1038/s41598-017-01788-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 04/06/2017] [Indexed: 02/06/2023] Open
Abstract
T-regulatory cells are an upsurge in the tumor microenvironment and induce immune-evasion. CD4+ Treg cells are well characterized whereas the role of CD8+ Tregs in cancer has recently started to crease attention. Here, we report an augmentation CD8+FOXP3+ Tregs in breast tumor microenvironment. FOXP3, the lineage-specific transcription factor, is a dominant regulator of Treg cell development and function. FOXP3 is induced preferentially by divergent signaling in CD4+ Treg cells. But how FOXP3 is induced and maintained in tumor-CD8+ Tregs is the Cinderella of the investigation. We observed that RUNX3, a CD8+ lineage-specific transcription factor, binds at the FOXP3-promoter to induce its transcription. In addition to promoter activation, involvement of cis-elements CNS1 and CNS2 in the transcriptional regulation of FOXP3 was also evident in these cells. SMAD3 binds to CNS1 region and acts as transcription inducer, whereas GATA3 plays a temporal role in the FOXP3 transcription by differential chromatin modification in CNS regions. In CNS1 region, GATA3 acts as a repressor for FOXP3 in naïve CD8+ T cells. Whereas in CD8+ Tregs, GATA3 binds directly at CNS2 region and persuaded the maintenance of FOXP3. Therefore, the intervention of these concerted transcriptional machinery may have a therapeutic potential in immunotherapy of cancer.
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Affiliation(s)
- Sreeparna Chakraborty
- Division of Molecular Medicine, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata, 700054, India
| | - Abir K Panda
- Division of Molecular Medicine, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata, 700054, India
| | - Sayantan Bose
- Division of Molecular Medicine, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata, 700054, India
| | - Dia Roy
- Division of Molecular Medicine, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata, 700054, India
| | - Kirti Kajal
- Division of Molecular Medicine, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata, 700054, India
| | - Deblina Guha
- Division of Molecular Medicine, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata, 700054, India
| | - Gaurisankar Sa
- Division of Molecular Medicine, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata, 700054, India.
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24
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Patel T, Hobert O. Coordinated control of terminal differentiation and restriction of cellular plasticity. eLife 2017; 6. [PMID: 28422646 PMCID: PMC5397285 DOI: 10.7554/elife.24100] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 03/23/2017] [Indexed: 01/17/2023] Open
Abstract
The acquisition of a specific cellular identity is usually paralleled by a restriction of cellular plasticity. Whether and how these two processes are coordinated is poorly understood. Transcription factors called terminal selectors activate identity-specific effector genes during neuronal differentiation to define the structural and functional properties of a neuron. To study restriction of plasticity, we ectopically expressed C. elegans CHE-1, a terminal selector of ASE sensory neuron identity. In undifferentiated cells, ectopic expression of CHE-1 results in activation of ASE neuron type-specific effector genes. Once cells differentiate, their plasticity is restricted and ectopic expression of CHE-1 no longer results in activation of ASE effector genes. In striking contrast, removal of the respective terminal selectors of other sensory, inter-, or motor neuron types now enables ectopically expressed CHE-1 to activate its ASE-specific effector genes, indicating that terminal selectors not only activate effector gene batteries but also control the restriction of cellular plasticity. Terminal selectors mediate this restriction at least partially by organizing chromatin. The chromatin structure of a CHE-1 target locus is less compact in neurons that lack their resident terminal selector and genetic epistasis studies with H3K9 methyltransferases suggest that this chromatin modification acts downstream of a terminal selector to restrict plasticity. Taken together, terminal selectors activate identity-specific genes and make non-identity-defining genes less accessible, thereby serving as a checkpoint to coordinate identity specification with restriction of cellular plasticity. DOI:http://dx.doi.org/10.7554/eLife.24100.001
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Affiliation(s)
- Tulsi Patel
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, United States
| | - Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, United States
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25
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Hang S, Gergen JP. Different modes of enhancer-specific regulation by Runt and Even-skipped during Drosophila segmentation. Mol Biol Cell 2017; 28:681-691. [PMID: 28077616 PMCID: PMC5328626 DOI: 10.1091/mbc.e16-09-0630] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 12/13/2016] [Accepted: 01/04/2017] [Indexed: 12/04/2022] Open
Abstract
Expression of the Drosophila slp1 gene depends on nonadditive interactions between two cis-regulatory enhancers. These enhancers are repressed by preventing either Pol II recruitment or release of promoter-proximal paused Pol II in a manner that is both enhancer and transcription factor specific and can account for their nonadditive interaction. The initial metameric expression of the Drosophila sloppy paired 1 (slp1) gene is controlled by two distinct cis-regulatory DNA elements that interact in a nonadditive manner to integrate inputs from transcription factors encoded by the pair-rule segmentation genes. We performed chromatin immunoprecipitation on reporter genes containing these elements in different embryonic genotypes to investigate the mechanism of their regulation. The distal early stripe element (DESE) mediates both activation and repression by Runt. We find that the differential response of DESE to Runt is due to an inhibitory effect of Fushi tarazu (Ftz) on P-TEFb recruitment and the regulation of RNA polymerase II (Pol II) pausing. The proximal early stripe element (PESE) is also repressed by Runt, but in this case, Runt prevents PESE-dependent Pol II recruitment and preinitiation complex (PIC) assembly. PESE is also repressed by Even-skipped (Eve), but, of interest, this repression involves regulation of P-TEFb recruitment and promoter-proximal Pol II pausing. These results demonstrate that the mode of slp1 repression by Runt is enhancer specific, whereas the mode of repression of the slp1 PESE enhancer is transcription factor specific. We propose a model based on these differential regulatory interactions that accounts for the nonadditive interactions between the PESE and DESE enhancers during Drosophila segmentation.
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Affiliation(s)
- Saiyu Hang
- Department of Biochemistry and Cell Biology and Center for Developmental Genetics and.,Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Stony Brook, NY 11794
| | - J Peter Gergen
- Department of Biochemistry and Cell Biology and Center for Developmental Genetics and
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26
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Abstract
Long QT syndrome (LQTS) exhibits great phenotype variability among family members carrying the same mutation, which can be partially attributed to genetic factors. We functionally analyzed the KCNH2 (encoding for Kv11.1 or hERG channels) and TBX20 (encoding for the transcription factor Tbx20) variants found by next-generation sequencing in two siblings with LQTS in a Spanish family of African ancestry. Affected relatives harbor a heterozygous mutation in KCNH2 that encodes for p.T152HfsX180 Kv11.1 (hERG). This peptide, by itself, failed to generate any current when transfected into Chinese hamster ovary (CHO) cells but, surprisingly, exerted "chaperone-like" effects over native hERG channels in both CHO cells and mouse atrial-derived HL-1 cells. Therefore, heterozygous transfection of native (WT) and p.T152HfsX180 hERG channels generated a current that was indistinguishable from that generated by WT channels alone. Some affected relatives also harbor the p.R311C mutation in Tbx20. In human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), Tbx20 enhanced human KCNH2 gene expression and hERG currents (IhERG) and shortened action-potential duration (APD). However, Tbx20 did not modify the expression or activity of any other channel involved in ventricular repolarization. Conversely, p.R311C Tbx20 did not increase KCNH2 expression in hiPSC-CMs, which led to decreased IhERG and increased APD. Our results suggest that Tbx20 controls the expression of hERG channels responsible for the rapid component of the delayed rectifier current. On the contrary, p.R311C Tbx20 specifically disables the Tbx20 protranscriptional activity over KCNH2 Therefore, TBX20 can be considered a KCNH2-modifying gene.
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27
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Abstract
TBX5 is a member of the T-box transcription factor family and is primarily known for its role in cardiac and forelimb development. Human patients with dominant mutations in TBX5 are characterized by Holt-Oram syndrome, and show defects of the cardiac septa, cardiac conduction system, and the anterior forelimb. The range of cardiac defects associated with TBX5 mutations in humans suggests multiple roles for the transcription factor in cardiac development and function. Animal models demonstrate similar defects and have provided a useful platform for investigating the roles of TBX5 during embryonic development. During early cardiac development, TBX5 appears to act primarily as a transcriptional activator of genes associated with cardiomyocyte maturation and upstream of morphological signals for septation. During later cardiac development, TBX5 is required for patterning of the cardiac conduction system and maintenance of mature cardiomyocyte function. A comprehensive understanding of the integral roles of TBX5 throughout cardiac development and adult life will be critical for understanding human cardiac morphology and function.
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Affiliation(s)
- J D Steimle
- University of Chicago, Chicago, IL, United States
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28
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Kodo K, Ong SG, Jahanbani F, Termglinchan V, Hirono K, InanlooRahatloo K, Ebert AD, Shukla P, Abilez OJ, Churko JM, Karakikes I, Jung G, Ichida F, Wu SM, Snyder MP, Bernstein D, Wu JC. iPSC-derived cardiomyocytes reveal abnormal TGF-β signalling in left ventricular non-compaction cardiomyopathy. Nat Cell Biol 2016; 18:1031-42. [PMID: 27642787 PMCID: PMC5042877 DOI: 10.1038/ncb3411] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 08/12/2016] [Indexed: 02/07/2023]
Abstract
Left ventricular non-compaction (LVNC) is the third most prevalent cardiomyopathy in children and its pathogenesis has been associated with the developmental defect of the embryonic myocardium. We show that patient-specific induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) generated from LVNC patients carrying a mutation in the cardiac transcription factor TBX20 recapitulate a key aspect of the pathological phenotype at the single-cell level and this was associated with perturbed transforming growth factor beta (TGF-β) signalling. LVNC iPSC-CMs have decreased proliferative capacity due to abnormal activation of TGF-β signalling. TBX20 regulates the expression of TGF-β signalling modifiers including one known to be a genetic cause of LVNC, PRDM16, and genome editing of PRDM16 caused proliferation defects in iPSC-CMs. Inhibition of TGF-β signalling and genome correction of the TBX20 mutation were sufficient to reverse the disease phenotype. Our study demonstrates that iPSC-CMs are a useful tool for the exploration of pathological mechanisms underlying poorly understood cardiomyopathies including LVNC.
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Affiliation(s)
- Kazuki Kodo
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Sang-Ging Ong
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Fereshteh Jahanbani
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Vittavat Termglinchan
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California 94305, USA.,Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Keiichi Hirono
- Department of Pediatrics, University of Toyama, Toyama-shi, Toyama 930-8555, Japan
| | - Kolsoum InanlooRahatloo
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Antje D Ebert
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California 94305, USA.,Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Praveen Shukla
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Oscar J Abilez
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jared M Churko
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California 94305, USA.,Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Ioannis Karakikes
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California 94305, USA.,Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Gwanghyun Jung
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Fukiko Ichida
- Department of Pediatrics, University of Toyama, Toyama-shi, Toyama 930-8555, Japan
| | - Sean M Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Daniel Bernstein
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California 94305, USA.,Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
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29
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Abstract
T-box (Tbx) genes encode an ancient group of transcription factors that play important roles in patterning, specification, proliferation, and differentiation programs in vertebrate organogenesis. This is testified by severe organ malformation syndromes in mice homozygous for engineered null alleles of specific T-box genes and by the large number of human inherited organ-specific diseases that have been linked to mutations in these genes. One of the organ systems that has not been associated with loss of specific T-box gene function in human disease for long is the excretory system. However, this has changed with the finding that mutations in TBX18, a member of a vertebrate-specific subgroup within the Tbx1-subfamily of T-box transcription factor genes, cause congenital anomalies of the kidney and urinary tract, predominantly hydroureter and ureteropelvic junction obstruction. Gene expression analyses, loss-of-function studies, and lineage tracing in the mouse suggest a primary role for this transcription factor in specifying the ureteric mesenchyme in the common anlage of the kidney, the ureter, and the bladder. We review the function of Tbx18 in ureterogenesis and discuss the body of evidence that Tbx18 and other members of the T-box gene family, namely, Tbx1, Tbx2, Tbx3, and Tbx20, play additional roles in development and homeostasis of other components of the excretory system in vertebrates.
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30
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Boogerd CJ, Aneas I, Sakabe N, Dirschinger RJ, Cheng QJ, Zhou B, Chen J, Nobrega MA, Evans SM. Probing chromatin landscape reveals roles of endocardial TBX20 in septation. J Clin Invest 2016; 126:3023-35. [PMID: 27348591 DOI: 10.1172/jci85350] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 05/05/2016] [Indexed: 12/29/2022] Open
Abstract
Mutations in the T-box transcription factor TBX20 are associated with multiple forms of congenital heart defects, including cardiac septal abnormalities, but our understanding of the contributions of endocardial TBX20 to heart development remains incomplete. Here, we investigated how TBX20 interacts with endocardial gene networks to drive the mesenchymal and myocardial movements that are essential for outflow tract and atrioventricular septation. Selective ablation of Tbx20 in murine endocardial lineages reduced the expression of extracellular matrix and cell migration genes that are critical for septation. Using the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), we identified accessible chromatin within endocardial lineages and intersected these data with TBX20 ChIP-seq and chromatin loop maps to determine that TBX20 binds a conserved long-range enhancer to regulate versican (Vcan) expression. We also observed reduced Vcan expression in Tbx20-deficient mice, supporting a direct role for TBX20 in Vcan regulation. Further, we show that the Vcan enhancer drove reporter gene expression in endocardial lineages in a TBX20-binding site-dependent manner. This work illuminates gene networks that interact with TBX20 to orchestrate cardiac septation and provides insight into the chromatin landscape of endocardial lineages during septation.
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31
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Greulich F, Rudat C, Farin HF, Christoffels VM, Kispert A. Lack of Genetic Interaction between Tbx18 and Tbx2/Tbx20 in Mouse Epicardial Development. PLoS One 2016; 11:e0156787. [PMID: 27253890 PMCID: PMC4890940 DOI: 10.1371/journal.pone.0156787] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/19/2016] [Indexed: 11/18/2022] Open
Abstract
The epicardium, the outermost layer of the heart, is an essential source of cells and signals for the formation of the cardiac fibrous skeleton and the coronary vasculature, and for the maturation of the myocardium during embryonic development. The molecular factors that control epicardial mobilization and differentiation, and direct the epicardial-myocardial cross-talk are, however, insufficiently understood. The T-box transcription factor gene Tbx18 is specifically expressed in the epicardium of vertebrate embryos. Loss of Tbx18 is dispensable for epicardial development, but may influence coronary vessel maturation. In contrast, over-expression of an activator version of TBX18 severely impairs epicardial development by premature differentiation of epicardial cells into SMCs indicating a potential redundancy of Tbx18 with other repressors of the T-box gene family. Here, we show that Tbx2 and Tbx20 are co-expressed with Tbx18 at different stages of epicardial development. Using a conditional gene targeting approach we find that neither the epicardial loss of Tbx2 nor the combined loss of Tbx2 and Tbx18 affects epicardial development. Similarly, we observed that the heterozygous loss of Tbx20 with and without additional loss of Tbx18 does not impact on epicardial integrity and mobilization in mouse embryos. Thus, Tbx18 does not function redundantly with Tbx2 or Tbx20 in epicardial development.
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Affiliation(s)
- Franziska Greulich
- Institut für Molekularbiologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Carsten Rudat
- Institut für Molekularbiologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Henner F. Farin
- Institut für Molekularbiologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Vincent M. Christoffels
- Department of Anatomy, Embryology and Physiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Andreas Kispert
- Institut für Molekularbiologie, Medizinische Hochschule Hannover, Hannover, Germany
- * E-mail:
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32
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Furtado MB, Wilmanns JC, Chandran A, Tonta M, Biben C, Eichenlaub M, Coleman HA, Berger S, Bouveret R, Singh R, Harvey RP, Ramialison M, Pearson JT, Parkington HC, Rosenthal NA, Costa MW. A novel conditional mouse model for Nkx2-5 reveals transcriptional regulation of cardiac ion channels. Differentiation 2016; 91:29-41. [PMID: 26897459 DOI: 10.1016/j.diff.2015.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 12/08/2015] [Accepted: 12/09/2015] [Indexed: 01/30/2023]
Abstract
Nkx2-5 is one of the master regulators of cardiac development, homeostasis and disease. This transcription factor has been previously associated with a suite of cardiac congenital malformations and impairment of electrical activity. When disease causative mutations in transcription factors are considered, NKX2-5 gene dysfunction is the most common abnormality found in patients. Here we describe a novel mouse model and subsequent implications of Nkx2-5 loss for aspects of myocardial electrical activity. In this work we have engineered a new Nkx2-5 conditional knockout mouse in which flox sites flank the entire Nkx2-5 locus, and validated this line for the study of heart development, differentiation and disease using a full deletion strategy. While our homozygous knockout mice show typical embryonic malformations previously described for the lack of the Nkx2-5 gene, hearts of heterozygous adult mice show moderate morphological and functional abnormalities that are sufficient to sustain blood supply demands under homeostatic conditions. This study further reveals intriguing aspects of Nkx2-5 function in the control of cardiac electrical activity. Using a combination of mouse genetics, biochemistry, molecular and cell biology, we demonstrate that Nkx2-5 regulates the gene encoding Kcnh2 channel and others, shedding light on potential mechanisms generating electrical abnormalities observed in patients bearing NKX2-5 dysfunction and opening opportunities to the study of novel therapeutic targets for anti-arrhythmogenic therapies.
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Affiliation(s)
- Milena B Furtado
- Australian Regenerative Medicine Institute, Monash University, Clayton, Vic 3800, Australia; The Jackson Laboratory, ME 04609, United States
| | - Julia C Wilmanns
- Australian Regenerative Medicine Institute, Monash University, Clayton, Vic 3800, Australia; Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Anjana Chandran
- Australian Regenerative Medicine Institute, Monash University, Clayton, Vic 3800, Australia
| | - Mary Tonta
- Department of Physiology, Monash University, Clayton, Vic 3800, Australia
| | - Christine Biben
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Vic 3052, Australia
| | - Michael Eichenlaub
- Australian Regenerative Medicine Institute, Monash University, Clayton, Vic 3800, Australia
| | - Harold A Coleman
- Department of Physiology, Monash University, Clayton, Vic 3800, Australia
| | - Silke Berger
- Australian Regenerative Medicine Institute, Monash University, Clayton, Vic 3800, Australia
| | - Romaric Bouveret
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Reena Singh
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Richard P Harvey
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute, Monash University, Clayton, Vic 3800, Australia
| | - James T Pearson
- Department of Physiology, Monash University, Clayton, Vic 3800, Australia; Monash Biomedical Imaging, Monash University, Clayton, Vic 3800, Australia
| | | | - Nadia A Rosenthal
- Australian Regenerative Medicine Institute, Monash University, Clayton, Vic 3800, Australia; National Heart and Lung Institute, Imperial College London, SW3 6LY England, UK; The Jackson Laboratory, ME 04609, United States
| | - Mauro W Costa
- Australian Regenerative Medicine Institute, Monash University, Clayton, Vic 3800, Australia; The Jackson Laboratory, ME 04609, United States.
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33
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Luna-Zurita L, Stirnimann CU, Glatt S, Kaynak BL, Thomas S, Baudin F, Samee MAH, He D, Small EM, Mileikovsky M, Nagy A, Holloway AK, Pollard KS, Müller CW, Bruneau BG. Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis. Cell 2016; 164:999-1014. [PMID: 26875865 DOI: 10.1016/j.cell.2016.01.004] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 11/21/2015] [Accepted: 12/22/2015] [Indexed: 12/26/2022]
Abstract
Transcription factors (TFs) are thought to function with partners to achieve specificity and precise quantitative outputs. In the developing heart, heterotypic TF interactions, such as between the T-box TF TBX5 and the homeodomain TF NKX2-5, have been proposed as a mechanism for human congenital heart defects. We report extensive and complex interdependent genomic occupancy of TBX5, NKX2-5, and the zinc finger TF GATA4 coordinately controlling cardiac gene expression, differentiation, and morphogenesis. Interdependent binding serves not only to co-regulate gene expression but also to prevent TFs from distributing to ectopic loci and activate lineage-inappropriate genes. We define preferential motif arrangements for TBX5 and NKX2-5 cooperative binding sites, supported at the atomic level by their co-crystal structure bound to DNA, revealing a direct interaction between the two factors and induced DNA bending. Complex interdependent binding mechanisms reveal tightly regulated TF genomic distribution and define a combinatorial logic for heterotypic TF regulation of differentiation.
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Affiliation(s)
- Luis Luna-Zurita
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Christian U Stirnimann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Sebastian Glatt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Bogac L Kaynak
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Sean Thomas
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Florence Baudin
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; UJF-EMBL-CNRS UMI 3265, Unit of Virus Host-Cell Interactions, 38042 Grenoble Cedex 9, France
| | | | - Daniel He
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Eric M Small
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Maria Mileikovsky
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Andras Nagy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Obstetrics and Gynaecology and Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Alisha K Holloway
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Katherine S Pollard
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA.
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34
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Xiang FL, Guo M, Yutzey KE. Overexpression of Tbx20 in Adult Cardiomyocytes Promotes Proliferation and Improves Cardiac Function After Myocardial Infarction. Circulation 2016; 133:1081-92. [PMID: 26841808 DOI: 10.1161/circulationaha.115.019357] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 01/28/2016] [Indexed: 02/05/2023]
Abstract
BACKGROUND Adult mammalian cardiomyocytes (CMs) have the potential to proliferate, but this is not sufficient to generate adequate CMs after myocardial infarction (MI). The transcription factor Tbx20 is required for CM proliferation during development and adult CM homeostasis. The ability of Tbx20 overexpression (Tbx20(OE)) to promote adult CM proliferation and to improve cardiac function after MI was examined. METHODS AND RESULTS Tbx20(OE) was induced specifically in adult mouse differentiated CMs. Increased CM proliferation and fetal-like characteristics were found in Tbx20(OE) hearts compared with controls without causing pathology 4 weeks after Tbx20(OE) at baseline. Moreover, Tbx20(OE) in adult CM after MI significantly improved survival, cardiac function, and infarct size 4 weeks after MI. Improved cardiac repair, as indicated by increased CM proliferation and capillary density, was observed in the MI border zone of Tbx20(OE) hearts compared with controls. Expression of proliferation activator (cyclin D1, E1, and IGF1) and fetal contractile protein (ssTNI, βMHC) mRNA was increased whereas negative cell-cycle regulators (p21, Meis1) were decreased in Tbx20(OE) hearts compared with controls under both baseline and MI conditions. Tbx20(OE) in adult hearts activates multiple proproliferation pathways, including Akt, YAP and BMP. Interestingly, p21, Meis1, and a novel cell-cycle inhibitory gene, Btg2, are directly bound and repressed by Tbx20 with induction of proliferation in neonatal CM. CONCLUSIONS Tbx20(OE), specifically in adult CM, activates multiple cardiac proliferative pathways, directly represses cell-cycle inhibitory genes p21, Meis1, and Btg2, promotes adult CM proliferation; and preserves cardiac performance after MI.
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Affiliation(s)
- Fu-Li Xiang
- From Heart Institute, Cincinnati Children's Medical Center, OH (F.-l.X., K.E.Y.); and Department of Electrical Engineering and Computing Systems, University of Cincinnati, OH (M.G.)
| | - Minzhe Guo
- From Heart Institute, Cincinnati Children's Medical Center, OH (F.-l.X., K.E.Y.); and Department of Electrical Engineering and Computing Systems, University of Cincinnati, OH (M.G.)
| | - Katherine E Yutzey
- From Heart Institute, Cincinnati Children's Medical Center, OH (F.-l.X., K.E.Y.); and Department of Electrical Engineering and Computing Systems, University of Cincinnati, OH (M.G.).
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Hong SE, Nho KJ, Song HK, Kim DH. Deep sequencing-generated modules demonstrate coherent expression patterns for various cardiac diseases. Gene 2015; 574:53-60. [PMID: 26232333 DOI: 10.1016/j.gene.2015.07.080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 06/19/2015] [Accepted: 07/24/2015] [Indexed: 11/30/2022]
Abstract
As sequencing technology rapidly develops, gene annotations have also become increasingly sophisticated with incorporation of information regarding the temporal-spatial context of alternative splicing patterns, developmental stages, and tissue specificity. The present study aimed to identify the heart-enriched genes based on next-generation sequencing data and to investigate the gene modules demonstrating coherent expression patterns for various cardiac disease-related perturbations. Seven gene modules, including 382 heart-enriched genes, were identified. At least two modules containing differentially expressed genes were experimentally confirmed to be highly sensitive to various cardiac diseases. Transcription factors regulating the gene modules were then analyzed based on knowledgebase information; the expression of eight transcription factors changed significantly during pressure-overload cardiac hypertrophy, suggesting possible regulation of the modules by the identified transcription factors. Collectively, our results contribute to the classification of heart-enriched genes and their modules and would aid in identification of the transcription factors involved in cardiac pathogenesis in the future.
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Affiliation(s)
- Seong-Eui Hong
- College of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea.
| | - Kyoung Jin Nho
- College of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea.
| | - Hong Ki Song
- College of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea.
| | - Do Han Kim
- College of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea.
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36
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Dupays L, Shang C, Wilson R, Kotecha S, Wood S, Towers N, Mohun T. Sequential Binding of MEIS1 and NKX2-5 on the Popdc2 Gene: A Mechanism for Spatiotemporal Regulation of Enhancers during Cardiogenesis. Cell Rep 2015; 13:183-195. [PMID: 26411676 PMCID: PMC4597108 DOI: 10.1016/j.celrep.2015.08.065] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 06/17/2015] [Accepted: 08/21/2015] [Indexed: 12/22/2022] Open
Abstract
The homeobox transcription factors NKX2-5 and MEIS1 are essential for vertebrate heart development and normal physiology of the adult heart. We show that, during cardiac differentiation, the two transcription factors have partially overlapping expression patterns, with the result that as cardiac progenitors from the anterior heart field differentiate and migrate into the cardiac outflow tract, they sequentially experience high levels of MEIS1 and then increasing levels of NKX2-5. Using the Popdc2 gene as an example, we also show that a significant proportion of target genes for NKX2-5 contain a binding motif recognized by NKX2-5, which overlaps with a binding site for MEIS1. Binding of the two factors to such overlapping sites is mutually exclusive, and this provides a simple regulatory mechanism for spatial and temporal synchronization of a common pool of targets between NKX2-5 and MEIS1. NKX2-5 shares a DNA-binding site with MEIS1 MEIS1 and NKX2-5 successively bind a Popdc2 enhancer Successive binding by MEIS1 and NKX2-5 is a general mechanism of regulation NKX2-5 represses fast troponin isoforms in the atria
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Affiliation(s)
- Laurent Dupays
- The Francis Crick Institute, Mill Hill Laboratory, the Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Catherine Shang
- The Francis Crick Institute, Mill Hill Laboratory, the Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Robert Wilson
- The Francis Crick Institute, Mill Hill Laboratory, the Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Surendra Kotecha
- The Francis Crick Institute, Mill Hill Laboratory, the Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Sophie Wood
- Procedural Services Section, The Francis Crick Institute, Mill Hill Laboratory, the Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Norma Towers
- The Francis Crick Institute, Mill Hill Laboratory, the Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Timothy Mohun
- The Francis Crick Institute, Mill Hill Laboratory, the Ridgeway, Mill Hill, London NW7 1AA, UK.
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Liu S, Kracher B, Ziegler J, Birkenbihl RP, Somssich IE. Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100. eLife 2015. [PMID: 26076231 DOI: 10.7554/elife.07295.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
The Arabidopsis mutant wrky33 is highly susceptible to Botrytis cinerea. We identified >1680 Botrytis-induced WRKY33 binding sites associated with 1576 Arabidopsis genes. Transcriptional profiling defined 318 functional direct target genes at 14 hr post inoculation. Comparative analyses revealed that WRKY33 possesses dual functionality acting either as a repressor or as an activator in a promoter-context dependent manner. We confirmed known WRKY33 targets involved in hormone signaling and phytoalexin biosynthesis, but also uncovered a novel negative role of abscisic acid (ABA) in resistance towards B. cinerea 2100. The ABA biosynthesis genes NCED3 and NCED5 were identified as direct targets required for WRKY33-mediated resistance. Loss-of-WRKY33 function resulted in elevated ABA levels and genetic studies confirmed that WRKY33 acts upstream of NCED3/NCED5 to negatively regulate ABA biosynthesis. This study provides the first detailed view of the genome-wide contribution of a specific plant transcription factor in modulating the transcriptional network associated with plant immunity.
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Affiliation(s)
- Shouan Liu
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Barbara Kracher
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Jörg Ziegler
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Rainer P Birkenbihl
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Imre E Somssich
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
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38
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Liu S, Kracher B, Ziegler J, Birkenbihl RP, Somssich IE. Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100. eLife 2015. [PMID: 26076231 DOI: 10.7554/elife.07295.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Abstract
The Arabidopsis mutant wrky33 is highly susceptible to Botrytis cinerea. We identified >1680 Botrytis-induced WRKY33 binding sites associated with 1576 Arabidopsis genes. Transcriptional profiling defined 318 functional direct target genes at 14 hr post inoculation. Comparative analyses revealed that WRKY33 possesses dual functionality acting either as a repressor or as an activator in a promoter-context dependent manner. We confirmed known WRKY33 targets involved in hormone signaling and phytoalexin biosynthesis, but also uncovered a novel negative role of abscisic acid (ABA) in resistance towards B. cinerea 2100. The ABA biosynthesis genes NCED3 and NCED5 were identified as direct targets required for WRKY33-mediated resistance. Loss-of-WRKY33 function resulted in elevated ABA levels and genetic studies confirmed that WRKY33 acts upstream of NCED3/NCED5 to negatively regulate ABA biosynthesis. This study provides the first detailed view of the genome-wide contribution of a specific plant transcription factor in modulating the transcriptional network associated with plant immunity.
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Affiliation(s)
- Shouan Liu
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Barbara Kracher
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Jörg Ziegler
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Rainer P Birkenbihl
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Imre E Somssich
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
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39
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Liu S, Kracher B, Ziegler J, Birkenbihl RP, Somssich IE. Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100. eLife 2015; 4:e07295. [PMID: 26076231 PMCID: PMC4487144 DOI: 10.7554/elife.07295] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 06/13/2015] [Indexed: 02/07/2023] Open
Abstract
The Arabidopsis mutant wrky33 is highly susceptible to Botrytis cinerea. We identified >1680 Botrytis-induced WRKY33 binding sites associated with 1576 Arabidopsis genes. Transcriptional profiling defined 318 functional direct target genes at 14 hr post inoculation. Comparative analyses revealed that WRKY33 possesses dual functionality acting either as a repressor or as an activator in a promoter-context dependent manner. We confirmed known WRKY33 targets involved in hormone signaling and phytoalexin biosynthesis, but also uncovered a novel negative role of abscisic acid (ABA) in resistance towards B. cinerea 2100. The ABA biosynthesis genes NCED3 and NCED5 were identified as direct targets required for WRKY33-mediated resistance. Loss-of-WRKY33 function resulted in elevated ABA levels and genetic studies confirmed that WRKY33 acts upstream of NCED3/NCED5 to negatively regulate ABA biosynthesis. This study provides the first detailed view of the genome-wide contribution of a specific plant transcription factor in modulating the transcriptional network associated with plant immunity.
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Affiliation(s)
- Shouan Liu
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Barbara Kracher
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Jörg Ziegler
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Rainer P Birkenbihl
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Imre E Somssich
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
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40
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Nim HT, Furtado MB, Costa MW, Rosenthal NA, Kitano H, Boyd SE. VISIONET: intuitive visualisation of overlapping transcription factor networks, with applications in cardiogenic gene discovery. BMC Bioinformatics 2015; 16:141. [PMID: 25929466 PMCID: PMC4426166 DOI: 10.1186/s12859-015-0578-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/20/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Existing de novo software platforms have largely overlooked a valuable resource, the expertise of the intended biologist users. Typical data representations such as long gene lists, or highly dense and overlapping transcription factor networks often hinder biologists from relating these results to their expertise. RESULTS VISIONET, a streamlined visualisation tool built from experimental needs, enables biologists to transform large and dense overlapping transcription factor networks into sparse human-readable graphs via numerically filtering. The VISIONET interface allows users without a computing background to interactively explore and filter their data, and empowers them to apply their specialist knowledge on far more complex and substantial data sets than is currently possible. Applying VISIONET to the Tbx20-Gata4 transcription factor network led to the discovery and validation of Aldh1a2, an essential developmental gene associated with various important cardiac disorders, as a healthy adult cardiac fibroblast gene co-regulated by cardiogenic transcription factors Gata4 and Tbx20. CONCLUSIONS We demonstrate with experimental validations the utility of VISIONET for expertise-driven gene discovery that opens new experimental directions that would not otherwise have been identified.
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Affiliation(s)
- Hieu T Nim
- Systems Biology Institute (SBI) Australia, Monash University, Clayton, VIC, 3800, Australia.
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia.
| | - Milena B Furtado
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia.
| | - Mauro W Costa
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia.
| | - Nadia A Rosenthal
- Systems Biology Institute (SBI) Australia, Monash University, Clayton, VIC, 3800, Australia.
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia.
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK.
| | - Hiroaki Kitano
- Systems Biology Institute (SBI) Australia, Monash University, Clayton, VIC, 3800, Australia.
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia.
- Sony Computer Science Laboratories, Inc., Higashigotanda, Shinagawa, Tokyo, Japan.
- Okinawa Institute of Science and Technology, Onna, Onna-son, Kunigami, Okinawa, Japan.
| | - Sarah E Boyd
- Systems Biology Institute (SBI) Australia, Monash University, Clayton, VIC, 3800, Australia.
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia.
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Novel mutations in the transcriptional activator domain of the human TBX20 in patients with atrial septal defect. BIOMED RESEARCH INTERNATIONAL 2015; 2015:718786. [PMID: 25834824 PMCID: PMC4365367 DOI: 10.1155/2015/718786] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/20/2014] [Indexed: 12/20/2022]
Abstract
Background. The relevance of TBX20 gene in heart development has been demonstrated in many animal models, but there are few works that try to elucidate the effect of TBX20 mutations in human congenital heart diseases. In these studies, all missense mutations associated with atrial septal defect (ASD) were found in the DNA-binding T-box domain, none in the transcriptional activator domain. Methods. We search for TBX20 mutations in a group of patients with ASD or ventricular septal defect (VSD) using the High Resolution Melting (HRM) method and DNA sequencing. Results. We report three missense mutations (Y309D, T370O, and M395R) within the transcriptional activator domain of human TBX20 that were associated with ASD. Conclusions. This is the first association of TBX20 transcriptional activator domain missense mutations with ASD. These findings could have implications for diagnosis, genetic screening, and patient follow-up.
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42
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Di Salvo TG, Guo Y, Su YR, Clark T, Brittain E, Absi T, Maltais S, Hemnes A. Right ventricular long noncoding RNA expression in human heart failure. Pulm Circ 2015; 5:135-61. [PMID: 25992278 PMCID: PMC4405709 DOI: 10.1086/679721] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 08/13/2014] [Indexed: 12/11/2022] Open
Abstract
The expression of long noncoding RNAs (lncRNAs) in human heart failure (HF) has not been widely studied. Using RNA sequencing (RNA-Seq), we compared lncRNA expression in 22 explanted human HF hearts with lncRNA expression in 5 unused donor human hearts. We used Cufflinks to identify isoforms and DESeq to identify differentially expressed genes. We identified the noncoding RNAs by cross-reference to Ensembl release 73 (Genome Reference Consortium human genome build 37) and explored possible functional roles using a variety of online tools. In HF hearts, RNA-Seq identified 84,793 total messenger RNA coding and noncoding different transcripts, including 13,019 protein-coding genes, 2,085 total lncRNA genes, and 1,064 pseudogenes. By Ensembl noncoding RNA categories, there were 48 lncRNAs, 27 pseudogenes, and 30 antisense RNAs for a total of 105 differentially expressed lncRNAs in HF hearts. Compared with donor hearts, HF hearts exhibited differential expression of 7.7% of protein-coding genes, 3.7% of lncRNAs (including pseudogenes), and 2.5% of pseudogenes. There were not consistent correlations between antisense lncRNAs and parent genes and between pseudogenes and parent genes, implying differential regulation of expression. Exploratory in silico functional analyses using online tools suggested a variety of possible lncRNA regulatory roles. By providing a comprehensive profile of right ventricular polyadenylated messenger RNA transcriptome in HF, RNA-Seq provides an inventory of differentially expressed lncRNAs, including antisense transcripts and pseudogenes, for future mechanistic study.
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Affiliation(s)
- Thomas G. Di Salvo
- Division of Cardiovascular Medicine, Vanderbilt Heart and Vascular Institute, Nashville, Tennessee, USA
| | - Yan Guo
- Vanderbilt Medical Center VANTAGE Core Laboratory, Nashville, Tennessee, USA
| | - Yan Ru Su
- Division of Cardiovascular Medicine, Vanderbilt Heart and Vascular Institute, Nashville, Tennessee, USA
| | - Travis Clark
- Vanderbilt Medical Center VANTAGE Core Laboratory, Nashville, Tennessee, USA
| | - Evan Brittain
- Division of Cardiovascular Medicine, Vanderbilt Heart and Vascular Institute, Nashville, Tennessee, USA
| | - Tarek Absi
- Division of Cardiovascular Surgery, Vanderbilt Heart and Vascular Institute, Nashville, Tennessee, USA
| | - Simon Maltais
- Division of Cardiovascular Surgery, Vanderbilt Heart and Vascular Institute, Nashville, Tennessee, USA
| | - Anna Hemnes
- Pulmonary and Critical Care Medicine, Vanderbilt Department of Medicine, Nashville, Tennessee, USA
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di Salvo TG, Yang KC, Brittain E, Absi T, Maltais S, Hemnes A. Right ventricular myocardial biomarkers in human heart failure. J Card Fail 2015; 21:398-411. [PMID: 25725476 DOI: 10.1016/j.cardfail.2015.02.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 12/31/2014] [Accepted: 01/27/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND Right ventricular (RV) dysfunction contributes to mortality in chronic heart failure (HF). However, the molecular mechanisms of RV failure remain poorly understood, and RV myocardial biomarkers have yet to be developed. METHODS AND RESULTS We performed RNA sequencing (RNA-seq) on 22 explanted human HF RVs and 5 unused donor human heart RVs (DON RV) and compared results to those recently reported from 16 explanted human LVs We used Bowtie-Tophat for transcript alignment and transcriptome assembly, DESeq for identification of differentially expressed genes (DEGs) and Ingenuity for exploration of gene ontologies. In the HF RV, RNA-seq identified 130,790 total RNA transcripts including 13,272 protein coding genes, 10,831 long non-coding RNA genes and 8,605 pseudogenes. There were 800-1000 DEGs between DON and HF RV comparison groups with differences concentrated in cytoskeletal, basement membrane, extracellular matrix (ECM), inflammatory mediator, hemostasis, membrane transport and transcription factor genes, lncRNAs and pseudogenes. In an unbiased approach, the top 10 DEGs SERPINA3, SERPINA5, LCN6, LCN10, STEAP4, AKR1C1, STAC2, SPARCL1, VSIG4 and F8 exhibited no overlap in read counts between DON and HF RVs, high sensitivities, specificities, predictive values and areas under the receiver operating characteristic curves. STEAP4, SPARCL1 and VSIG4 were differentially expressed between RVs and LVs, supporting their roles as RV-specific myocardial biomarkers. CONCLUSIONS Unbiased, comprehensive profiling of the RV transcriptome by RNA-seq suggests structural changes and abnormalities in inflammatory processes and yields specific, novel HF RV vs HF LV myocardial biomarkers not previously identified by more limited transcriptome profiling approaches.
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Affiliation(s)
- Thomas G di Salvo
- Division of Cardiovascular Medicine, Vanderbilt Heart and Vascular Institute, Nashville, Tennessee.
| | - Kai-Chien Yang
- Department of Pharmacology, National Taiwan University, Taipei, Taiwan
| | - Evan Brittain
- Division of Cardiovascular Medicine, Vanderbilt Heart and Vascular Institute, Nashville, Tennessee
| | - Tarek Absi
- Division of Cardiovascular Surgery, Vanderbilt Heart and Vascular Institute, Nashville, Tennessee
| | - Simon Maltais
- Division of Cardiovascular Surgery, Vanderbilt Heart and Vascular Institute, Nashville, Tennessee
| | - Anna Hemnes
- Pulmonary and Critical Care Medicine, Vanderbilt Department of Medicine, Nashville, Tennessee
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Cheatle Jarvela AM, Brubaker L, Vedenko A, Gupta A, Armitage BA, Bulyk ML, Hinman VF. Modular evolution of DNA-binding preference of a Tbrain transcription factor provides a mechanism for modifying gene regulatory networks. Mol Biol Evol 2014; 31:2672-88. [PMID: 25016582 PMCID: PMC4166925 DOI: 10.1093/molbev/msu213] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Gene regulatory networks (GRNs) describe the progression of transcriptional states that take a single-celled zygote to a multicellular organism. It is well documented that GRNs can evolve extensively through mutations to cis-regulatory modules (CRMs). Transcription factor proteins that bind these CRMs may also evolve to produce novelty. Coding changes are considered to be rarer, however, because transcription factors are multifunctional and hence are more constrained to evolve in ways that will not produce widespread detrimental effects. Recent technological advances have unearthed a surprising variation in DNA-binding abilities, such that individual transcription factors may recognize both a preferred primary motif and an additional secondary motif. This provides a source of modularity in function. Here, we demonstrate that orthologous transcription factors can also evolve a changed preference for a secondary binding motif, thereby offering an unexplored mechanism for GRN evolution. Using protein-binding microarray, surface plasmon resonance, and in vivo reporter assays, we demonstrate an important difference in DNA-binding preference between Tbrain protein orthologs in two species of echinoderms, the sea star, Patiria miniata, and the sea urchin, Strongylocentrotus purpuratus. Although both orthologs recognize the same primary motif, only the sea star Tbr also has a secondary binding motif. Our in vivo assays demonstrate that this difference may allow for greater evolutionary change in timing of regulatory control. This uncovers a layer of transcription factor binding divergence that could exist for many pairs of orthologs. We hypothesize that this divergence provides modularity that allows orthologous transcription factors to evolve novel roles in GRNs through modification of binding to secondary sites.
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Affiliation(s)
| | - Lisa Brubaker
- Department of Biological Sciences, Carnegie Mellon University
| | - Anastasia Vedenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Anisha Gupta
- Department of Chemistry, Carnegie Mellon University
| | | | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
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Molina-Navarro MM, Triviño JC, Martínez-Dolz L, Lago F, González-Juanatey JR, Portolés M, Rivera M. Functional networks of nucleocytoplasmic transport-related genes differentiate ischemic and dilated cardiomyopathies. A new therapeutic opportunity. PLoS One 2014; 9:e104709. [PMID: 25137373 PMCID: PMC4138080 DOI: 10.1371/journal.pone.0104709] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 07/10/2014] [Indexed: 01/31/2023] Open
Abstract
Heart failure provokes alterations in the expression of nucleocytoplasmic transport-related genes. To elucidate the nucleocytoplasmic transport-linked functional network underlying the two major causes of heart failure, ischemic cardiomyopathy (ICM) and dilated cardiomyopathy (DCM), we examined global transcriptome profiles of left ventricular myocardium tissue samples from 31 patients (ICM, n = 10; DCM, n = 13) undergoing heart transplantation and control donors (CNT, n = 8) using RNA-Sequencing and GeneMANIA. Comparative profiling of ICM versus control and DCM versus control showed 1081 and 2440 differentially expressed genes, respectively (>1.29-fold; P<0.05). GeneMANIA revealed differentially regulated functional networks specific to ICM and DCM. In comparison with CNT, differential expression was seen in 9 and 12 nucleocytoplasmic transport-related genes in ICM and DCM groups, respectively. DDX3X, KPNA2, and PTK2B were related to ICM, while SMURF2, NUP153, IPO5, RANBP3, NOXA1, and RHOJ were involved in DCM pathogenesis. Furthermore, the two pathologies shared 6 altered genes: XPO1, ARL4, NFKB2, FHL3, RANBP2, and RHOU showing an identical trend in expression in both ICM and DCM. Notably, the core of the derived functional networks composed of nucleocytoplasmic transport-related genes (XPO1, RANBP2, NUP153, IPO5, KPNA2, and RANBP3) branched into several pathways with downregulated genes. Moreover, we identified genes whose expression levels correlated with left ventricular mass index and left ventricular function parameters in HF patients. Collectively, our study provides a clear distinction between the two pathologies at the transcriptome level and opens up new possibilities to search for appropriate therapeutic targets for ICM and DCM.
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Affiliation(s)
| | | | - Luis Martínez-Dolz
- Heart Failure and Transplantation Unit, Cardiology Department, La Fe University Hospital, Valencia, Spain
| | - Francisca Lago
- Cellular and Molecular Cardiology Research Unit, Department of Cardiology and Institute of Biomedical Research, University Clinical Hospital, Santiago de Compostela, Spain
| | - Jose Ramón González-Juanatey
- Cellular and Molecular Cardiology Research Unit, Department of Cardiology and Institute of Biomedical Research, University Clinical Hospital, Santiago de Compostela, Spain
| | - Manuel Portolés
- Cardiocirculatory Unit, Health Research Institute Hospital La Fe, Valencia, Spain
| | - Miguel Rivera
- Cardiocirculatory Unit, Health Research Institute Hospital La Fe, Valencia, Spain
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DeWoskin D, Geng W, Stinchcombe AR, Forger DB. It is not the parts, but how they interact that determines the behaviour of circadian rhythms across scales and organisms. Interface Focus 2014; 4:20130076. [PMID: 24904739 PMCID: PMC3996588 DOI: 10.1098/rsfs.2013.0076] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Biological rhythms, generated by feedback loops containing interacting genes, proteins and/or cells, time physiological processes in many organisms. While many of the components of the systems that generate biological rhythms have been identified, much less is known about the details of their interactions. Using examples from the circadian (daily) clock in three organisms, Neurospora, Drosophila and mouse, we show, with mathematical models of varying complexity, how interactions among (i) promoter sites, (ii) proteins forming complexes, and (iii) cells can have a drastic effect on timekeeping. Inspired by the identification of many transcription factors, for example as involved in the Neurospora circadian clock, that can both activate and repress, we show how these multiple actions can cause complex oscillatory patterns in a transcription–translation feedback loop (TTFL). Inspired by the timekeeping complex formed by the NMO–PER–TIM–SGG complex that regulates the negative TTFL in the Drosophila circadian clock, we show how the mechanism of complex formation can determine the prevalence of oscillations in a TTFL. Finally, we note that most mathematical models of intracellular clocks model a single cell, but compare with experimental data from collections of cells. We find that refitting the most detailed model of the mammalian circadian clock, so that the coupling between cells matches experimental data, yields different dynamics and makes an interesting prediction that also matches experimental data: individual cells are bistable, and network coupling removes this bistability and causes the network to be more robust to external perturbations. Taken together, we propose that the interactions between components in biological timekeeping systems are carefully tuned towards proper function. We also show how timekeeping can be controlled by novel mechanisms at different levels of organization.
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Affiliation(s)
- Daniel DeWoskin
- Department of Mathematics , University of Michigan , 2074 East Hall, 530 Church Street, Ann Arbor, MI 48109 , USA
| | - Weihua Geng
- Department of Mathematics , Southern Methodist University , 135 Clements Hall, Dallas, TX 75275 , USA
| | - Adam R Stinchcombe
- Department of Mathematics , University of Michigan , 2074 East Hall, 530 Church Street, Ann Arbor, MI 48109 , USA
| | - Daniel B Forger
- Department of Mathematics , University of Michigan , 2074 East Hall, 530 Church Street, Ann Arbor, MI 48109 , USA ; Center for Computational Medicine and Bioinformatics , University of Michigan , 2074 East Hall, 530 Church Street, Ann Arbor, MI 48109 , USA
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47
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van den Boogaard M, Smemo S, Burnicka-Turek O, Arnolds DE, van de Werken HJG, Klous P, McKean D, Muehlschlegel JD, Moosmann J, Toka O, Yang XH, Koopmann TT, Adriaens ME, Bezzina CR, de Laat W, Seidman C, Seidman JG, Christoffels VM, Nobrega MA, Barnett P, Moskowitz IP. A common genetic variant within SCN10A modulates cardiac SCN5A expression. J Clin Invest 2014; 124:1844-52. [PMID: 24642470 DOI: 10.1172/jci73140] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 01/09/2014] [Indexed: 12/19/2022] Open
Abstract
Variants in SCN10A, which encodes a voltage-gated sodium channel, are associated with alterations of cardiac conduction parameters and the cardiac rhythm disorder Brugada syndrome; however, it is unclear how SCN10A variants promote dysfunctional cardiac conduction. Here we showed by high-resolution 4C-seq analysis of the Scn10a-Scn5a locus in murine heart tissue that a cardiac enhancer located in Scn10a, encompassing SCN10A functional variant rs6801957, interacts with the promoter of Scn5a, a sodium channel-encoding gene that is critical for cardiac conduction. We observed that SCN5A transcript levels were several orders of magnitude higher than SCN10A transcript levels in both adult human and mouse heart tissue. Analysis of BAC transgenic mouse strains harboring an engineered deletion of the enhancer within Scn10a revealed that the enhancer was essential for Scn5a expression in cardiac tissue. Furthermore, the common SCN10A variant rs6801957 modulated Scn5a expression in the heart. In humans, the SCN10A variant rs6801957, which correlated with slowed conduction, was associated with reduced SCN5A expression. These observations establish a genomic mechanism for how a common genetic variation at SCN10A influences cardiac physiology and predisposes to arrhythmia.
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48
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Abstract
ChIP-seq has become the primary method for identifying in vivo protein-DNA interactions on a genome-wide scale, with nearly 800 publications involving the technique appearing in PubMed as of December 2012. Individually and in aggregate, these data are an important and information-rich resource. However, uncertainties about data quality confound their use by the wider research community. Recently, the Encyclopedia of DNA Elements (ENCODE) project developed and applied metrics to objectively measure ChIP-seq data quality. The ENCODE quality analysis was useful for flagging datasets for closer inspection, eliminating or replacing poor data, and for driving changes in experimental pipelines. There had been no similarly systematic quality analysis of the large and disparate body of published ChIP-seq profiles. Here, we report a uniform analysis of vertebrate transcription factor ChIP-seq datasets in the Gene Expression Omnibus (GEO) repository as of April 1, 2012. The majority (55%) of datasets scored as being highly successful, but a substantial minority (20%) were of apparently poor quality, and another ∼25% were of intermediate quality. We discuss how different uses of ChIP-seq data are affected by specific aspects of data quality, and we highlight exceptional instances for which the metric values should not be taken at face value. Unexpectedly, we discovered that a significant subset of control datasets (i.e., no immunoprecipitation and mock immunoprecipitation samples) display an enrichment structure similar to successful ChIP-seq data. This can, in turn, affect peak calling and data interpretation. Published datasets identified here as high-quality comprise a large group that users can draw on for large-scale integrated analysis. In the future, ChIP-seq quality assessment similar to that used here could guide experimentalists at early stages in a study, provide useful input in the publication process, and be used to stratify ChIP-seq data for different community-wide uses.
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49
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Sakabe NJ, Nobrega MA. Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130022. [PMID: 24218635 DOI: 10.1098/rstb.2013.0022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The complex expression patterns observed for many genes are often regulated by distal transcription enhancers. Changes in the nucleotide sequences of enhancers may therefore lead to changes in gene expression, representing a central mechanism by which organisms evolve. With the development of the experimental technique of chromatin immunoprecipitation (ChIP), in which discrete regions of the genome bound by specific proteins can be identified, it is now possible to identify transcription factor binding events (putative cis-regulatory elements) in entire genomes. Comparing protein-DNA binding maps allows us, for the first time, to attempt to identify regulatory differences and infer global patterns of change in gene expression across species. Here, we review studies that used genome-wide ChIP to study the evolution of enhancers. The trend is one of high divergence of cis-regulatory elements between species, possibly compensated by extensive creation and loss of regulatory elements and rewiring of their target genes. We speculate on the meaning of the differences observed and discuss that although ChIP experiments identify the biochemical event of protein-DNA interaction, it cannot determine whether the event results in a biological function, and therefore more studies are required to establish the effect of divergence of binding events on species-specific gene expression.
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Affiliation(s)
- Noboru Jo Sakabe
- Department of Human Genetics, University of Chicago, , Chicago, IL 60637, USA
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50
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Kaltenbrun E, Greco TM, Slagle CE, Kennedy LM, Li T, Cristea IM, Conlon FL. A Gro/TLE-NuRD corepressor complex facilitates Tbx20-dependent transcriptional repression. J Proteome Res 2013; 12:5395-409. [PMID: 24024827 DOI: 10.1021/pr400818c] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The cardiac transcription factor Tbx20 has a critical role in the proper morphogenetic development of the vertebrate heart, and its misregulation has been implicated in human congenital heart disease. Although it is established that Tbx20 exerts its function in the embryonic heart through positive and negative regulation of distinct gene programs, it is unclear how Tbx20 mediates proper transcriptional regulation of its target genes. Here, using a combinatorial proteomic and bioinformatic approach, we present the first characterization of Tbx20 transcriptional protein complexes. We have systematically investigated Tbx20 protein-protein interactions by immunoaffinity purification of tagged Tbx20 followed by proteomic analysis using GeLC-MS/MS, gene ontology classification, and functional network analysis. We demonstrate that Tbx20 is associated with a chromatin remodeling network composed of TLE/Groucho corepressors, members of the Nucleosome Remodeling and Deacetylase (NuRD) complex, the chromatin remodeling ATPases RUVBL1/RUVBL2, and the T-box repressor Tbx18. We determined that the interaction with TLE corepressors is mediated via an eh1 binding motif in Tbx20. Moreover, we demonstrated that ablation of this motif results in a failure to properly assemble the repression network and disrupts Tbx20 function in vivo. Importantly, we validated Tbx20-TLE interactions in the mouse embryonic heart, and identified developmental genes regulated by Tbx20-TLE binding, thereby confirming a primary role for a Tbx20-TLE repressor complex in embryonic heart development. Together, these studies suggest a model in which Tbx20 associates with a Gro/TLE-NuRD repressor complex to prevent inappropriate gene activation within the forming heart.
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Affiliation(s)
- Erin Kaltenbrun
- Departments of Biology and ‡Genetics, University of North Carolina , Chapel Hill, North Carolina 27599, United States
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