1
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Cornman RS. A genomic hotspot of diversifying selection and structural change in the hoary bat ( Lasiurus cinereus). PeerJ 2024; 12:e17482. [PMID: 38832043 PMCID: PMC11146322 DOI: 10.7717/peerj.17482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 05/07/2024] [Indexed: 06/05/2024] Open
Abstract
Background Previous work found that numerous genes positively selected within the hoary bat (Lasiurus cinereus) lineage are physically clustered in regions of conserved synteny. Here I further validate and expand on those finding utilizing an updated L. cinereus genome assembly and additional bat species as well as other tetrapod outgroups. Methods A chromosome-level assembly was generated by chromatin-contact mapping and made available by DNAZoo (www.dnazoo.org). The genomic organization of orthologous genes was extracted from annotation data for multiple additional bat species as well as other tetrapod clades for which chromosome-level assemblies were available from the National Center for Biotechnology Information (NCBI). Tests of branch-specific positive selection were performed for L. cinereus using PAML as well as with the HyPhy package for comparison. Results Twelve genes exhibiting significant diversifying selection in the L. cinereus lineage were clustered within a 12-Mb genomic window; one of these (Trpc4) also exhibited diversifying selection in bats generally. Ten of the 12 genes are landmarks of two distinct blocks of ancient synteny that are not linked in other tetrapod clades. Bats are further distinguished by frequent structural rearrangements within these synteny blocks, which are rarely observed in other Tetrapoda. Patterns of gene order and orientation among bat taxa are incompatible with phylogeny as presently understood, implying parallel evolution or subsequent reversals. Inferences of positive selection were found to be robust to alternative phylogenetic topologies as well as a strong shift in background nucleotide composition in some taxa. Discussion This study confirms and further localizes a genomic hotspot of protein-coding divergence in the hoary bat, one that also exhibits an increased tempo of structural change in bats compared with other mammals. Most genes in the two synteny blocks have elevated expression in brain tissue in humans and model organisms, and genetic studies implicate the selected genes in cranial and neurological development, among other functions.
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Affiliation(s)
- Robert S. Cornman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, United States
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2
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Alhazmi S, Alzahrani M, Farsi R, Alharbi M, Algothmi K, Alburae N, Ganash M, Azhari S, Basingab F, Almuhammadi A, Alqosaibi A, Alkhatabi H, Elaimi A, Jan M, Aldhalaan HM, Alrafiah A, Alrofaidi A. Multiple Recurrent Copy Number Variations (CNVs) in Chromosome 22 Including 22q11.2 Associated with Autism Spectrum Disorder. Pharmgenomics Pers Med 2022; 15:705-720. [PMID: 35898556 PMCID: PMC9309317 DOI: 10.2147/pgpm.s366826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/14/2022] [Indexed: 11/29/2022] Open
Abstract
Introduction Autism spectrum disorder (ASD) is a developmental disorder that can cause substantial social, communication, and behavioral challenges. Genetic factors play a significant role in ASD, where the risk of ASD has been increased for unclear reasons. Twin studies have shown important evidence of both genetic and environmental contributions in ASD, where the level of contribution of these factors has not been proven yet. It has been suggested that copy number variation (CNV) duplication and the deletion of many genes in chromosome 22 (Ch22) may have a strong association with ASD. This study screened the CNVs in Ch22 in autistic Saudi children and assessed the candidate gene in the CNVs region of Ch22 that is most associated with ASD. Methods This study included 15 autistic Saudi children as well as 4 healthy children as controls; DNA was extracted from samples and analyzed using array comparative genomic hybridization (aCGH) and DNA sequencing. Results The aCGH detected (in only 6 autistic samples) deletion and duplication in many regions of Ch22, including some critical genes. Moreover, DNA sequencing determined a genetic mutation in the TBX1 gene sequence in autistic samples. This study, carried out using aCGH, found that six autistic patients had CNVs in Ch22, and DNA sequencing revealed mutations in the TBX1 gene in autistic samples but none in the control. Conclusion CNV deletion and the duplication of the TBX1 gene could be related to ASD; therefore, this gene needs more analysis in terms of expression levels.
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Affiliation(s)
- Safiah Alhazmi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Maryam Alzahrani
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Reem Farsi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mona Alharbi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khloud Algothmi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Najla Alburae
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Magdah Ganash
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sheren Azhari
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fatemah Basingab
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asma Almuhammadi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amany Alqosaibi
- Department of Biology, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Heba Alkhatabi
- Centre of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Aisha Elaimi
- Centre of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed Jan
- College of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hesham M Aldhalaan
- Center for Autism Research at King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Aziza Alrafiah
- Department of Medical Laboratory Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Correspondence: Aziza Alrafiah, Department of Medical Laboratory Science, King Abdulaziz University, P.O Box 80200, Jeddah, 21589, Saudi Arabia, Tel +966 126401000 Ext. 23495, Fax +966 126401000 Ext. 21686, Email
| | - Aisha Alrofaidi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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3
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Lewis MA, Ingham NJ, Chen J, Pearson S, Di Domenico F, Rekhi S, Allen R, Drake M, Willaert A, Rook V, Pass J, Keane T, Adams DJ, Tucker AS, White JK, Steel KP. Identification and characterisation of spontaneous mutations causing deafness from a targeted knockout programme. BMC Biol 2022; 20:67. [PMID: 35296311 PMCID: PMC8928630 DOI: 10.1186/s12915-022-01257-8] [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: 08/27/2021] [Accepted: 02/17/2022] [Indexed: 11/30/2022] Open
Abstract
Background Mice carrying targeted mutations are important for investigating gene function and the role of genes in disease, but off-target mutagenic effects associated with the processes of generating targeted alleles, for instance using Crispr, and culturing embryonic stem cells, offer opportunities for spontaneous mutations to arise. Identifying spontaneous mutations relies on the detection of phenotypes segregating independently of targeted alleles, and having a broad estimate of the level of mutations generated by intensive breeding programmes is difficult given that many phenotypes are easy to miss if not specifically looked for. Here we present data from a large, targeted knockout programme in which mice were analysed through a phenotyping pipeline. Such spontaneous mutations segregating within mutant lines may confound phenotypic analyses, highlighting the importance of record-keeping and maintaining correct pedigrees. Results Twenty-five lines out of 1311 displayed different deafness phenotypes that did not segregate with the targeted allele. We observed a variety of phenotypes by Auditory Brainstem Response (ABR) and behavioural assessment and isolated eight lines showing early-onset severe progressive hearing loss, later-onset progressive hearing loss, low frequency hearing loss, or complete deafness, with vestibular dysfunction. The causative mutations identified include deletions, insertions, and point mutations, some of which involve new genes not previously associated with deafness while others are new alleles of genes known to underlie hearing loss. Two of the latter show a phenotype much reduced in severity compared to other mutant alleles of the same gene. We investigated the ES cells from which these lines were derived and determined that only one of the 8 mutations could have arisen in the ES cell, and in that case, only after targeting. Instead, most of the non-segregating mutations appear to have occurred during breeding of mutant mice. In one case, the mutation arose within the wildtype colony used for expanding mutant lines. Conclusions Our data show that spontaneous mutations with observable effects on phenotype are a common side effect of intensive breeding programmes, including those underlying targeted mutation programmes. Such spontaneous mutations segregating within mutant lines may confound phenotypic analyses, highlighting the importance of record-keeping and maintaining correct pedigrees. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01257-8.
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Affiliation(s)
- Morag A Lewis
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England. .,Wellcome Sanger Institute, Hinxton, CB10 1SA, England.
| | - Neil J Ingham
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - Jing Chen
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | | | - Francesca Di Domenico
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Sohinder Rekhi
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Rochelle Allen
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Matthew Drake
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Annelore Willaert
- Research Group of Experimental Oto-Rhino-Laryngology, Department of Neurosciences, KU Leuven - University of Leuven, Leuven, Belgium
| | - Victoria Rook
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Johanna Pass
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - Thomas Keane
- Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - David J Adams
- Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - Abigail S Tucker
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, England
| | | | - Karen P Steel
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
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4
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Lu S, Louphrasitthiphol P, Goradia N, Lambert JP, Schmidt J, Chauhan J, Rughani MG, Larue L, Wilmanns M, Goding CR. TBX2 controls a proproliferative gene expression program in melanoma. Genes Dev 2021; 35:1657-1677. [PMID: 34819350 PMCID: PMC8653791 DOI: 10.1101/gad.348746.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/22/2021] [Indexed: 12/20/2022]
Abstract
Senescence shapes embryonic development, plays a key role in aging, and is a critical barrier to cancer initiation, yet how senescence is regulated remains incompletely understood. TBX2 is an antisenescence T-box family transcription repressor implicated in embryonic development and cancer. However, the repertoire of TBX2 target genes, its cooperating partners, and how TBX2 promotes proliferation and senescence bypass are poorly understood. Here, using melanoma as a model, we show that TBX2 lies downstream from PI3K signaling and that TBX2 binds and is required for expression of E2F1, a key antisenescence cell cycle regulator. Remarkably, TBX2 binding in vivo is associated with CACGTG E-boxes, present in genes down-regulated by TBX2 depletion, more frequently than the consensus T-element DNA binding motif that is restricted to Tbx2 repressed genes. TBX2 is revealed to interact with a wide range of transcription factors and cofactors, including key components of the BCOR/PRC1.1 complex that are recruited by TBX2 to the E2F1 locus. Our results provide key insights into how PI3K signaling modulates TBX2 function in cancer to drive proliferation.
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Affiliation(s)
- Sizhu Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom.,Department of Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Nishit Goradia
- European Molecular Biology Laboratory, Hamburg Unit, 22607 Hamburg, Germany
| | - Jean-Philippe Lambert
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Medicine and Cancer Research Centre, Université Laval, Québec City, Québec G1R 3S3, Canada; CHU de Québec Research Center, Centre Hospitalier de l'Université Laval, Québec City, Québec G1V 4G2, Canada
| | - Johannes Schmidt
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Jagat Chauhan
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Milap G Rughani
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Lionel Larue
- Institut Curie, PSL Research University, U1021, Institut National de la Santé et de la Recherche Médicale, Normal and Pathological Development of Melanocytes, 91405 Orsay Cedex, France.,Université Paris-Sud, Université Paris-Saclay, UMR 3347 Centre National de la Recherche Scientifique, 91405 Orsay Cedex, France.,Equipe Labellisée Ligue Contre le Cancer, 91405 Orsay Cedex, France
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, 22607 Hamburg, Germany.,University Hamburg Clinical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
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5
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6
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Alghamdi M, Al Khalifah R, Al Homyani DK, Alkhamis WH, Arold ST, Ekhzaimy A, El-Wetidy M, Kashour T, Halwani R. A Novel TBX1 Variant Causing Hypoparathyroidism and Deafness. J Endocr Soc 2019; 4:bvz028. [PMID: 32110744 PMCID: PMC7041699 DOI: 10.1210/jendso/bvz028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 11/28/2019] [Indexed: 12/13/2022] Open
Abstract
Background The TBX1 gene encodes the T-box 1 protein that is a transcription factor involved in development. Haploinsufficiency of the TBX1 gene is reported to cause features similar to DiGeorge syndrome. The TBX1 gene is located within the DiGeorge syndrome region, and studies support that the TBX1gene is responsible for most of the features of the phenotype of hemizygous deletion of chromosome 22q11.2. In this study, we report a family of 4 (a father with 3 children) who presented with congenital hypoparathyroidism and hypocalcemia, facial asymmetry, deafness, normal intelligence, and no cardiac involvement. Methods We performed whole genome sequencing, computational structural analysis of the mutants, and gene expression studies for all affected family members. Results Whole genome sequencing revealed a paternal inherited novel heterozygous variant, c.1158_1159delinsT p.(Gly387Alafs*73), in the exon 9 isoform C TBX1 gene, causing a loss of nuclear localization sequence (NLS) and transactivation domain (TAD) with no change in gene expression and resulted in a DiGeorge-like phenotype. Conclusion A pathogenic variant in the TBX1 gene exon 9 C that predicted to cause a loss in the NLS region and most of TAD leads to variable features of hypoparathyroidism, distinctive facial features, deafness, and no cardiac involvement. In addition, our report and previous reports indicate the presence of a wide phenotypic spectrum of TBX1 genetic variants and the consistent absence of cardiac involvement in the case of pathogenic variants on exon 9 isoform C TBX1 gene.
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Affiliation(s)
- Malak Alghamdi
- Medical Genetic Division, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Reem Al Khalifah
- Pediatric Endocrinology Division, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Doua K Al Homyani
- Pediatric Endocrinology, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Waleed H Alkhamis
- Department of Obstetrics and Gynecology, King Saud University Medical City, Riyadh, Saudi Arabia
| | - Stefan T Arold
- Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Aishah Ekhzaimy
- Adult Endocrinology, Department of Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed El-Wetidy
- College of Medicine Research Center, King Saud University, Riyadh, Saudi Arabia
| | - Tarek Kashour
- Cardiology Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Rabih Halwani
- Sharjah Institute for Medical Research (SIMR), Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.,Immunology Research Laboratory, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
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7
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Fernandez Garcia M, Moore CD, Schulz KN, Alberto O, Donague G, Harrison MM, Zhu H, Zaret KS. Structural Features of Transcription Factors Associating with Nucleosome Binding. Mol Cell 2019; 75:921-932.e6. [PMID: 31303471 DOI: 10.1016/j.molcel.2019.06.009] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/01/2019] [Accepted: 06/07/2019] [Indexed: 10/26/2022]
Abstract
Fate-changing transcription factors (TFs) scan chromatin to initiate new genetic programs during cell differentiation and reprogramming. Yet the protein structure domains that allow TFs to target nucleosomal DNA remain unexplored. We screened diverse TFs for binding to nucleosomes containing motif-enriched sequences targeted by pioneer factors in vivo. FOXA1, OCT4, ASCL1/E12α, PU1, CEBPα, and ZELDA display a range of nucleosome binding affinities that correlate with their cell reprogramming potential. We further screened 593 full-length human TFs on protein microarrays against different nucleosome sequences, followed by confirmation in solution, to distinguish among factors that bound nucleosomes, such as the neuronal AP-2α/β/γ, versus factors that only bound free DNA. Structural comparisons of DNA binding domains revealed that efficient nucleosome binders use short anchoring α helices to bind DNA, whereas weak nucleosome binders use unstructured regions and/or β sheets. Thus, specific modes of DNA interaction allow nucleosome scanning that confers pioneer activity to transcription factors.
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Affiliation(s)
- Meilin Fernandez Garcia
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-5157, USA
| | - Cedric D Moore
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Katharine N Schulz
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin Madison, Madison, WI 53706, USA
| | - Oscar Alberto
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-5157, USA
| | - Greg Donague
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-5157, USA
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin Madison, Madison, WI 53706, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-5157, USA.
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8
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O'Donoghue SI, Baldi BF, Clark SJ, Darling AE, Hogan JM, Kaur S, Maier-Hein L, McCarthy DJ, Moore WJ, Stenau E, Swedlow JR, Vuong J, Procter JB. Visualization of Biomedical Data. Annu Rev Biomed Data Sci 2018. [DOI: 10.1146/annurev-biodatasci-080917-013424] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The rapid increase in volume and complexity of biomedical data requires changes in research, communication, and clinical practices. This includes learning how to effectively integrate automated analysis with high–data density visualizations that clearly express complex phenomena. In this review, we summarize key principles and resources from data visualization research that help address this difficult challenge. We then survey how visualization is being used in a selection of emerging biomedical research areas, including three-dimensional genomics, single-cell RNA sequencing (RNA-seq), the protein structure universe, phosphoproteomics, augmented reality–assisted surgery, and metagenomics. While specific research areas need highly tailored visualizations, there are common challenges that can be addressed with general methods and strategies. Also common, however, are poor visualization practices. We outline ongoing initiatives aimed at improving visualization practices in biomedical research via better tools, peer-to-peer learning, and interdisciplinary collaboration with computer scientists, science communicators, and graphic designers. These changes are revolutionizing how we see and think about our data.
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Affiliation(s)
- Seán I. O'Donoghue
- Data61, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Eveleigh NSW 2015, Australia
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW), Kensington NSW 2033, Australia
| | - Benedetta Frida Baldi
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia
| | - Susan J. Clark
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia
| | - Aaron E. Darling
- The ithree Institute, University of Technology Sydney, Ultimo NSW 2007, Australia
| | - James M. Hogan
- School of Electrical Engineering and Computer Science, Queensland University of Technology, Brisbane QLD, 4000, Australia
| | - Sandeep Kaur
- School of Computer Science and Engineering, University of New South Wales (UNSW), Kensington NSW 2033, Australia
| | - Lena Maier-Hein
- Division of Computer Assisted Medical Interventions (CAMI), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Davis J. McCarthy
- European Bioinformatics Institute (EBI), European Molecular Biology Laboratory (EMBL), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
- St. Vincent's Institute of Medical Research, Fitzroy VIC 3065, Australia
| | - William J. Moore
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Esther Stenau
- Division of Computer Assisted Medical Interventions (CAMI), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jason R. Swedlow
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Jenny Vuong
- Data61, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Eveleigh NSW 2015, Australia
| | - James B. Procter
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
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9
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Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites. Proc Natl Acad Sci U S A 2016; 113:E6572-E6581. [PMID: 27791029 DOI: 10.1073/pnas.1613914113] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The transcription factor T-bet (Tbox protein expressed in T cells) is one of the master regulators of both the innate and adaptive immune responses. It plays a central role in T-cell lineage commitment, where it controls the TH1 response, and in gene regulation in plasma B-cells and dendritic cells. T-bet is a member of the Tbox family of transcription factors; however, T-bet coordinately regulates the expression of many more genes than other Tbox proteins. A central unresolved question is how T-bet is able to simultaneously recognize distant Tbox binding sites, which may be located thousands of base pairs away. We have determined the crystal structure of the Tbox DNA binding domain (DBD) of T-bet in complex with a palindromic DNA. The structure shows a quaternary structure in which the T-bet dimer has its DNA binding regions splayed far apart, making it impossible for a single dimer to bind both sites of the DNA palindrome. In contrast to most other Tbox proteins, a single T-bet DBD dimer binds simultaneously to identical half-sites on two independent DNA. A fluorescence-based assay confirms that T-bet dimers are able to bring two independent DNA molecules into close juxtaposition. Furthermore, chromosome conformation capture assays confirm that T-bet functions in the direct formation of chromatin loops in vitro and in vivo. The data are consistent with a looping/synapsing model for transcriptional regulation by T-bet in which a single dimer of the transcription factor can recognize and coalesce distinct genetic elements, either a promoter plus a distant regulatory element, or promoters on two different genes.
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10
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Abstract
The nematode Caenorhabditis elegans is a simple metazoan animal that is widely used as a model to understand the genetic control of development. The completely sequenced C. elegans genome contains 22 T-box genes, and they encode factors that show remarkable diversity in sequence, DNA-binding specificity, and function. Only three of the C. elegans T-box factors can be grouped into the conserved subfamilies found in other organisms, while the remaining factors are significantly diverged and unlike those in most other animals. While some of the C. elegans factors can bind canonical T-box binding elements, others bind and regulate target gene expression through distinct sequences. The nine genetically characterized T-box factors have varied functions in development and morphogenesis of muscle, hypodermal tissues, and neurons, as well as in early blastomere fate specification, cell migration, apoptosis, and sex determination, but the functions of most of the C. elegans T-box factors have not yet been extensively characterized. Like T-box factors in other animals, interaction with a Groucho-family corepressor and posttranslational SUMOylation have been shown to affect C. elegans T-box factor activity, and it is likely that additional mechanisms affecting T-box factor activity will be discovered using the effective genetic approaches in this organism.
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11
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Abstract
Recent data have paved the way to mechanistic studies into the role of Tbx1 during development. Tbx1 is haploinsufficient and is involved in an important genetic disorder. The gene encodes a T-box transcription factor that is expressed from approximately E7.5 in mouse embryos and continues to be expressed in a highly dynamic manner. It is neither a strong transcriptional activator nor a strong repressor, but it regulates a large number of genes through epigenetic modifications. Here, we review recent literature concerning mechanisms of gene regulation by Tbx1 and its role in mammalian development, with a special focus on the cardiac, vascular, and central nervous systems.
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12
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Pradhan L, Gopal S, Li S, Ashur S, Suryanarayanan S, Kasahara H, Nam HJ. Intermolecular Interactions of Cardiac Transcription Factors NKX2.5 and TBX5. Biochemistry 2016; 55:1702-10. [DOI: 10.1021/acs.biochem.6b00171] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Lagnajeet Pradhan
- Department
of Bioengineering, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Sunil Gopal
- Department
of Bioengineering, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Shichang Li
- Department
of Bioengineering, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Shayan Ashur
- Department
of Bioengineering, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Saai Suryanarayanan
- Department
of Bioengineering, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Hideko Kasahara
- Department of Functional Genomics, University of Florida, Gainesville, Florida 32610, United States
| | - Hyun-Joo Nam
- Department
of Bioengineering, University of Texas at Dallas, Richardson, Texas 75080, United States
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13
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Vivante A, Kleppa MJ, Schulz J, Kohl S, Sharma A, Chen J, Shril S, Hwang DY, Weiss AC, Kaminski MM, Shukrun R, Kemper MJ, Lehnhardt A, Beetz R, Sanna-Cherchi S, Verbitsky M, Gharavi AG, Stuart HM, Feather SA, Goodship JA, Goodship THJ, Woolf AS, Westra SJ, Doody DP, Bauer SB, Lee RS, Adam RM, Lu W, Reutter HM, Kehinde EO, Mancini EJ, Lifton RP, Tasic V, Lienkamp SS, Jüppner H, Kispert A, Hildebrandt F. Mutations in TBX18 Cause Dominant Urinary Tract Malformations via Transcriptional Dysregulation of Ureter Development. Am J Hum Genet 2015; 97:291-301. [PMID: 26235987 DOI: 10.1016/j.ajhg.2015.07.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 07/07/2015] [Indexed: 12/22/2022] Open
Abstract
Congenital anomalies of the kidneys and urinary tract (CAKUT) are the most common cause of chronic kidney disease in the first three decades of life. Identification of single-gene mutations that cause CAKUT permits the first insights into related disease mechanisms. However, for most cases the underlying defect remains elusive. We identified a kindred with an autosomal-dominant form of CAKUT with predominant ureteropelvic junction obstruction. By whole exome sequencing, we identified a heterozygous truncating mutation (c.1010delG) of T-Box transcription factor 18 (TBX18) in seven affected members of the large kindred. A screen of additional families with CAKUT identified three families harboring two heterozygous TBX18 mutations (c.1570C>T and c.487A>G). TBX18 is essential for developmental specification of the ureteric mesenchyme and ureteric smooth muscle cells. We found that all three TBX18 altered proteins still dimerized with the wild-type protein but had prolonged protein half life and exhibited reduced transcriptional repression activity compared to wild-type TBX18. The p.Lys163Glu substitution altered an amino acid residue critical for TBX18-DNA interaction, resulting in impaired TBX18-DNA binding. These data indicate that dominant-negative TBX18 mutations cause human CAKUT by interference with TBX18 transcriptional repression, thus implicating ureter smooth muscle cell development in the pathogenesis of human CAKUT.
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Affiliation(s)
- Asaf Vivante
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Marc-Jens Kleppa
- Institut für Molekularbiologie, Medizinische Hochschule Hannover 30625, Germany
| | - Julian Schulz
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Stefan Kohl
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amita Sharma
- Pediatric Nephrology Unit and Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jing Chen
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Daw-Yang Hwang
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Nephrology, Department of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Anna-Carina Weiss
- Institut für Molekularbiologie, Medizinische Hochschule Hannover 30625, Germany
| | - Michael M Kaminski
- Department of Medicine, Renal Division, University of Freiburg Medical Center, 79106 Freiburg, Germany
| | - Rachel Shukrun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Markus J Kemper
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Anja Lehnhardt
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Rolf Beetz
- Center for Pediatric and Adolescent Medicine, University Medical Clinic, 55131 Mainz, Germany
| | | | - Miguel Verbitsky
- Department of Medicine, Columbia University, New York, NY 10023, USA
| | - Ali G Gharavi
- Department of Medicine, Columbia University, New York, NY 10023, USA
| | - Helen M Stuart
- Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre and the Royal Manchester Children's and St Mary's Hospitals, Manchester M13 9WL, UK
| | | | - Judith A Goodship
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Timothy H J Goodship
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Adrian S Woolf
- Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre and the Royal Manchester Children's and St Mary's Hospitals, Manchester M13 9WL, UK
| | - Sjirk J Westra
- Pediatric Radiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Daniel P Doody
- Department of Pediatric Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Stuart B Bauer
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Richard S Lee
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rosalyn M Adam
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Weining Lu
- Renal Section, Department of Medicine, Boston University Medical Center, Boston, MA 02118, USA
| | - Heiko M Reutter
- Department of Neonatology, Children's Hospital, University of Bonn, 53127 Bonn, Germany
| | - Elijah O Kehinde
- Division of Urology, Department of Surgery, Kuwait University, 13110 Safat, Kuwait
| | - Erika J Mancini
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK; School of Life Sciences, University of Sussex, Brighton BN1 9QD, UK
| | - Richard P Lifton
- Department of Human Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Howard Hughes Medical Institute
| | - Velibor Tasic
- Medical School Skopje, University Children's Hospital, 1000 Skopje, Macedonia
| | - Soeren S Lienkamp
- Department of Medicine, Renal Division, University of Freiburg Medical Center, 79106 Freiburg, Germany; Center for Biological Signaling Studies (BIOSS), 79104 Freiburg, Germany
| | - Harald Jüppner
- Pediatric Nephrology Unit and Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Andreas Kispert
- Institut für Molekularbiologie, Medizinische Hochschule Hannover 30625, Germany
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute.
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Papaioannou VE. The T-box gene family: emerging roles in development, stem cells and cancer. Development 2014; 141:3819-33. [PMID: 25294936 DOI: 10.1242/dev.104471] [Citation(s) in RCA: 205] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The T-box family of transcription factors exhibits widespread involvement throughout development in all metazoans. T-box proteins are characterized by a DNA-binding motif known as the T-domain that binds DNA in a sequence-specific manner. In humans, mutations in many of the genes within the T-box family result in developmental syndromes, and there is increasing evidence to support a role for these factors in certain cancers. In addition, although early studies focused on the role of T-box factors in early embryogenesis, recent studies in mice have uncovered additional roles in unsuspected places, for example in adult stem cell populations. Here, I provide an overview of the key features of T-box transcription factors and highlight their roles and mechanisms of action during various stages of development and in stem/progenitor cell populations.
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Affiliation(s)
- Virginia E Papaioannou
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
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15
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Xu YJ, Chen S, Zhang J, Fang SH, Guo QQ, Wang J, Fu QH, Li F, Xu R, Sun K. Novel TBX1 loss-of-function mutation causes isolated conotruncal heart defects in Chinese patients without 22q11.2 deletion. BMC MEDICAL GENETICS 2014; 15:78. [PMID: 24998776 PMCID: PMC4099205 DOI: 10.1186/1471-2350-15-78] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/24/2014] [Indexed: 12/18/2022]
Abstract
Background TBX1 and CRKL haploinsufficiency is thought to cause the cardiac phenotype of the 22q11.2 deletion syndrome. However, few unequivocal mutations of TBX1 and CRKL have been discovered in isolated conotrucal heart defects (CTDs) patients. The aim of the study was to screen the mutation of TBX1 and CRKL in isolated CTDs Chinese patients without 22q11.2 deletion and identify the pathomechanism of the missense mutations. Methods We enrolled 199 non-22q11.2 deletion patients with CTDs and 139 unrelated healthy controls. Gene sequencing were performed for all of them. The functional data of mutations were obtained by in vitro transfection and luciferase experiments and computer modelling. Results Screening of the TBX1 coding sequence identified a de novo missense mutation (c.385G → A; p.E129K) and a known polymorphism (c.928G → A; p.G310S). In vitro experiments demonstrate that the TBX1E129K variant almost lost transactivation activity. The TBX1G310S variant seems to affect the interaction of TBX1 with other factors. Computer molecular dynamics simulations showed the de novo missense mutation is likely to affect TBX1-DNA interaction. No mutation of CRKL gene was found. Conclusions These observations suggest that the TBX1 loss-of-function mutation may be involved in the pathogenesis of isolated CTDs. This is the first human missense mutation showing that TBX1 is a candidate causing isolated CTDs in Chinese patients without 22q11.2 deletion.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Rang Xu
- Department of Pediatric Cardiology, Xinhua hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai 200092, China.
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16
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Castellanos R, Xie Q, Zheng D, Cvekl A, Morrow BE. Mammalian TBX1 preferentially binds and regulates downstream targets via a tandem T-site repeat. PLoS One 2014; 9:e95151. [PMID: 24797903 PMCID: PMC4010391 DOI: 10.1371/journal.pone.0095151] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 03/24/2014] [Indexed: 11/20/2022] Open
Abstract
Haploinsufficiency or mutation of TBX1 is largely responsible for the etiology of physical malformations in individuals with velo-cardio-facial/DiGeorge syndrome (VCFS/DGS/22q11.2 deletion syndrome). TBX1 encodes a transcription factor protein that contains an evolutionarily conserved DNA binding domain termed the T-box that is shared with other family members. All T-box proteins, examined so far, bind to similar but not identical consensus DNA sequences, indicating that they have specific binding preferences. To identify the TBX1 specific consensus sequence, Systematic Evolution of Ligands by Exponential Enrichment (SELEX) was performed. In contrast to other TBX family members recognizing palindrome sequences, we found that TBX1 preferentially binds to a tandem repeat of 5′-AGGTGTGAAGGTGTGA-3′. We also identified a second consensus sequence comprised of a tandem repeat with a degenerated downstream site. We show that three known human disease-causing TBX1 missense mutations (F148Y, H194Q and G310S) do not alter nuclear localization, or disrupt binding to the tandem repeat consensus sequences, but they reduce transcriptional activity in cell culture reporter assays. To identify Tbx1-downstream genes, we performed an in silico genome wide analysis of potential cis-acting elements in DNA and found strong enrichment of genes required for developmental processes and transcriptional regulation. We found that TBX1 binds to 19 different loci in vitro, which may correspond to putative cis-acting binding sites. In situ hybridization coupled with luciferase gene reporter assays on three gene loci, Fgf8, Bmper, Otog-MyoD, show that these motifs are directly regulated by TBX1 in vitro. Collectively, the present studies establish new insights into molecular aspects of TBX1 binding to DNA. This work lays the groundwork for future in vivo studies, including chromatin immunoprecipitation followed by next generation sequencing (ChIP-Seq) to further elucidate the molecular pathogenesis of VCFS/DGS.
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Affiliation(s)
- Raquel Castellanos
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Qing Xie
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Ophthalmology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Ales Cvekl
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Ophthalmology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Bernice E. Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail:
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Wang W, Razy-Krajka F, Siu E, Ketcham A, Christiaen L. NK4 antagonizes Tbx1/10 to promote cardiac versus pharyngeal muscle fate in the ascidian second heart field. PLoS Biol 2013; 11:e1001725. [PMID: 24311985 PMCID: PMC3849182 DOI: 10.1371/journal.pbio.1001725] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 10/23/2013] [Indexed: 12/27/2022] Open
Abstract
Cross inhibition between NK4 and TBX1 transcription factors specifies heart versus pharyngeal muscle fates by promoting the activation of tissue-specific regulators in distinct precursors within the cardiopharyngeal lineage of the ascidian, Ciona intestinalis. The heart and head muscles share common developmental origins and genetic underpinnings in vertebrates, including humans. Parts of the heart and cranio-facial musculature derive from common mesodermal progenitors that express NKX2-5, ISL1, and TBX1. This ontogenetic kinship is dramatically reflected in the DiGeorge/Cardio-Velo-Facial syndrome (DGS/CVFS), where mutations of TBX1 cause malformations in the pharyngeal apparatus and cardiac outflow tract. Cardiac progenitors of the first heart field (FHF) do not require TBX1 and segregate precociously from common progenitors of the second heart field (SHF) and pharyngeal muscles. However, the cellular and molecular mechanisms that govern heart versus pharyngeal muscle specification within this lineage remain elusive. Here, we harness the simplicity of the ascidian larva to show that, following asymmetric cell division of common progenitors, NK4/NKX2-5 promotes GATAa/GATA4/5/6 expression and cardiac specification in the second heart precursors by antagonizing Tbx1/10-mediated inhibition of GATAa and activation of Collier/Olf/EBF (COE), the determinant of atrial siphon muscle (ASM) specification. Our results uncover essential regulatory connections between the conserved cardio-pharyngeal factor Tbx1/10 and muscle determinant COE, as well as a mutual antagonism between NK4 and Tbx1/10 activities upstream of GATAa and COE. The latter cross-antagonism underlies a fundamental heart versus pharyngeal muscle fate choice that occurs in a conserved lineage of cardio-pharyngeal progenitors. We propose that this basic ontogenetic motif underlies cardiac and pharyngeal muscle development and evolution in chordates. Mutations in the regulatory genes encoding the transcription factors NKX2-5 and TBX1, which govern heart and head muscle development, cause prevalent congenital defects. Recent studies using vertebrate models have shown that the heart and pharyngeal head muscle cells derive from common progenitors in the early embryo. To better understand the genetic mechanisms by which these progenitors select one of the two developmental trajectories, we studied the activity of these transcription factors in a simple invertebrate chordate model, the sea squirt Ciona intestinalis. We show that the sea squirt homolog of NKX2-5 promotes early heart specification by inhibiting the formation of pharyngeal muscles. Conversely, the TBX1 homolog determines pharyngeal muscle fate by inhibiting GATAa and thereby the heart program it instructs, as well as promoting the pharyngeal muscle program through activation of COE (Collier/Olf-1/EBF), a recently identified regulator of skeletal muscle differentiation. Finally, we show that the NKX2-5 homolog protein directly binds to the COE gene to repress its activity. Notably, these antagonistic interactions occur in heart and pharyngeal precursors immediately following the division of their pluripotent mother cells, thus contributing to their respective fate choice. These mechanistic insights into the process of early heart versus head muscle specification in this simple chordate provide the grounds for establishing the etiology of human congenital cardio-craniofacial defects.
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Affiliation(s)
- Wei Wang
- Department of Biology, New York University, New York, New York, United States of America
| | - Florian Razy-Krajka
- Department of Biology, New York University, New York, New York, United States of America
| | - Eric Siu
- Department of Biology, New York University, New York, New York, United States of America
| | - Alexandra Ketcham
- Department of Biology, New York University, New York, New York, United States of America
| | - Lionel Christiaen
- Department of Biology, New York University, New York, New York, United States of America
- * E-mail:
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18
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Takashima Y, Suzuki A. Regulation of organogenesis and stem cell properties by T-box transcription factors. Cell Mol Life Sci 2013; 70:3929-45. [PMID: 23479132 PMCID: PMC11113830 DOI: 10.1007/s00018-013-1305-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 02/07/2013] [Accepted: 02/18/2013] [Indexed: 12/28/2022]
Abstract
T-box transcription factors containing the common DNA-binding domain T-box contribute to the organization of multiple tissues in vertebrates and invertebrates. In mammals, 17 T-box genes are divided into five subfamilies depending on their amino acid homology. The proper distribution and expression of individual T-box transcription factors in different tissues enable regulation of the proliferation and differentiation of tissue-specific stem cells and progenitor cells in a suitable time schedule for tissue organization. Consequently, uncontrollable expressions of T-box genes induce abnormal tissue organization, and eventually cause various diseases with malformation and malfunction of tissues and organs. Furthermore, some T-box transcription factors are essential for maintaining embryonic stem cell pluripotency, improving the quality of induced pluripotent stem cells, and inducing cell-lineage conversion of differentiated cells. These lines of evidence indicate fundamental roles of T-box transcription factors in tissue organization and stem cell properties, and suggest that these transcription factors will be useful for developing therapeutic approaches in regenerative medicine.
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Affiliation(s)
- Yasuo Takashima
- Division of Organogenesis and Regeneration, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582 Japan
| | - Atsushi Suzuki
- Division of Organogenesis and Regeneration, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582 Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012 Japan
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19
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Function of the C. elegans T-box factor TBX-2 depends on SUMOylation. Cell Mol Life Sci 2013; 70:4157-68. [PMID: 23595631 PMCID: PMC3802552 DOI: 10.1007/s00018-013-1336-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 03/19/2013] [Accepted: 04/02/2013] [Indexed: 01/22/2023]
Abstract
T-box transcription factors are critical developmental regulators in all multi-cellular organisms, and altered T-box factor activity is associated with a variety of human congenital diseases and cancers. Despite the biological significance of T-box factors, their mechanism of action is not well understood. Here we examine whether SUMOylation affects the function of the C. elegans Tbx2 sub-family T-box factor TBX-2. We have previously shown that TBX-2 interacts with the E2 SUMO-conjugating enzyme UBC-9, and that loss of TBX-2 or UBC-9 produces identical defects in ABa-derived pharyngeal muscle development. We now show that TBX-2 is SUMOylated in mammalian cell assays, and that both UBC-9 interaction and SUMOylation depends on two SUMO consensus sites located in the T-box DNA binding domain and near the TBX-2 C-terminus, respectively. In co-transfection assays, a TBX-2:GAL4 fusion protein represses expression of a 5xGal4:tk:luciferase construct. However, this activity does not require SUMOylation, indicating SUMO is not generally required for TBX-2 repressor activity. In C. elegans, reducing SUMOylation enhances the phenotype of a temperature-sensitive tbx-2 mutant and results in ectopic expression of a gene normally repressed by TBX-2, demonstrating that SUMOylation is important for TBX-2 function in vivo. Finally, we show mammalian orthologs of TBX-2, Tbx2, and Tbx3, can also be SUMOylated, suggesting SUMOylation may be a conserved mechanism controlling T-box factor activity.
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