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Shepherdson JL, Friedman RZ, Zheng Y, Sun C, Oh IY, Granas DM, Cohen BA, Chen S, White MA. Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors. Genome Res 2024; 34:243-255. [PMID: 38355306 PMCID: PMC10984388 DOI: 10.1101/gr.278133.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
Dozens of variants in the gene for the homeodomain transcription factor (TF) cone-rod homeobox (CRX) are linked with human blinding diseases that vary in their severity and age of onset. How different variants in this single TF alter its function in ways that lead to a range of phenotypes is unclear. We characterized the effects of human disease-causing variants on CRX cis-regulatory function by deploying massively parallel reporter assays (MPRAs) in mouse retina explants carrying knock-ins of two variants, one in the DNA-binding domain (p.R90W) and the other in the transcriptional effector domain (p.E168d2). The degree of reporter gene dysregulation in these mutant Crx retinas corresponds with their phenotypic severity. The two variants affect similar sets of enhancers, and p.E168d2 has distinct effects on silencers. Cis-regulatory elements (CREs) near cone photoreceptor genes are enriched for silencers that are derepressed in the presence of p.E168d2. Chromatin environments of CRX-bound loci are partially predictive of episomal MPRA activity, and distal elements whose accessibility increases later in retinal development are enriched for CREs with silencer activity. We identified a set of potentially pleiotropic regulatory elements that convert from silencers to enhancers in retinas that lack a functional CRX effector domain. Our findings show that phenotypically distinct variants in different domains of CRX have partially overlapping effects on its cis-regulatory function, leading to misregulation of similar sets of enhancers while having a qualitatively different impact on silencers.
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Affiliation(s)
- James L Shepherdson
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Ryan Z Friedman
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Yiqiao Zheng
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Chi Sun
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Inez Y Oh
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - David M Granas
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Barak A Cohen
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA;
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Michael A White
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA;
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
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2
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Shepherdson JL, Friedman RZ, Zheng Y, Sun C, Oh IY, Granas DM, Cohen BA, Chen S, White MA. Pathogenic variants in Crx have distinct cis-regulatory effects on enhancers and silencers in photoreceptors. bioRxiv 2023:2023.05.27.542576. [PMID: 37292699 PMCID: PMC10245955 DOI: 10.1101/2023.05.27.542576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Dozens of variants in the photoreceptor-specific transcription factor (TF) CRX are linked with human blinding diseases that vary in their severity and age of onset. It is unclear how different variants in this single TF alter its function in ways that lead to a range of phenotypes. We examined the effects of human disease-causing variants on CRX cis-regulatory function by deploying massively parallel reporter assays (MPRAs) in live mouse retinas carrying knock-ins of two variants, one in the DNA binding domain (p.R90W) and the other in the transcriptional effector domain (p.E168d2). The degree of reporter gene dysregulation caused by the variants corresponds with their phenotypic severity. The two variants affect similar sets of enhancers, while p.E168d2 has stronger effects on silencers. Cis-regulatory elements (CREs) near cone photoreceptor genes are enriched for silencers that are de-repressed in the presence of p.E168d2. Chromatin environments of CRX-bound loci were partially predictive of episomal MPRA activity, and silencers were notably enriched among distal elements whose accessibility increases later in retinal development. We identified a set of potentially pleiotropic regulatory elements that convert from silencers to enhancers in retinas that lack a functional CRX effector domain. Our findings show that phenotypically distinct variants in different domains of CRX have partially overlapping effects on its cis-regulatory function, leading to misregulation of similar sets of enhancers, while having a qualitatively different impact on silencers.
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Affiliation(s)
- James L. Shepherdson
- Department of Genetics
- Edison Family Center for Genome Sciences & Systems Biology
| | - Ryan Z. Friedman
- Department of Genetics
- Edison Family Center for Genome Sciences & Systems Biology
| | | | - Chi Sun
- Department of Ophthalmology and Visual Sciences
| | - Inez Y. Oh
- Department of Ophthalmology and Visual Sciences
| | - David M. Granas
- Department of Genetics
- Edison Family Center for Genome Sciences & Systems Biology
| | - Barak A. Cohen
- Department of Genetics
- Edison Family Center for Genome Sciences & Systems Biology
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Michael A. White
- Department of Genetics
- Edison Family Center for Genome Sciences & Systems Biology
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3
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Drury F, Grover M, Hintze M, Saunders J, Fasseas MK, Constantinou C, Barkoulas M. A PAX6-regulated receptor tyrosine kinase pairs with a pseudokinase to activate immune defense upon oomycete recognition in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2023; 120:e2300587120. [PMID: 37725647 PMCID: PMC10523662 DOI: 10.1073/pnas.2300587120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 08/21/2023] [Indexed: 09/21/2023] Open
Abstract
Oomycetes were recently discovered as natural pathogens of Caenorhabditis elegans, and pathogen recognition alone was shown to be sufficient to activate a protective transcriptional program characterized by the expression of multiple chitinase-like (chil) genes. However, the molecular mechanisms underlying oomycete recognition in animals remain fully unknown. We performed here a forward genetic screen to uncover regulators of chil gene induction and found several independent loss-of-function alleles of old-1 and flor-1, which encode receptor tyrosine kinases belonging to the C. elegans-specific KIN-16 family. We report that OLD-1 and FLOR-1 are both necessary for mounting the immune response and act in the epidermis. FLOR-1 is a pseudokinase that acts downstream of the active kinase OLD-1 and regulates OLD-1 levels at the plasma membrane. Interestingly, the old-1 locus is adjacent to the chil genes in the C. elegans genome, thereby revealing a genetic cluster important for oomycete resistance. Furthermore, we demonstrate that old-1 expression at the anterior side of the epidermis is regulated by the VAB-3/PAX6 transcription factor, well known for its role in visual system development in other animals. Taken together, our study reveals both conserved and species-specific factors shaping the activation and spatial characteristics of the immune response to oomycete recognition.
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Affiliation(s)
- Florence Drury
- Department of Life Sciences, Imperial College, LondonSW7 2AZ, United Kingdom
| | - Manish Grover
- Department of Life Sciences, Imperial College, LondonSW7 2AZ, United Kingdom
| | - Mark Hintze
- Department of Life Sciences, Imperial College, LondonSW7 2AZ, United Kingdom
| | - Jonathan Saunders
- Department of Life Sciences, Imperial College, LondonSW7 2AZ, United Kingdom
| | - Michael K. Fasseas
- Department of Life Sciences, Imperial College, LondonSW7 2AZ, United Kingdom
| | - Charis Constantinou
- Department of Life Sciences, Imperial College, LondonSW7 2AZ, United Kingdom
| | - Michalis Barkoulas
- Department of Life Sciences, Imperial College, LondonSW7 2AZ, United Kingdom
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4
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Cain B, Webb J, Yuan Z, Cheung D, Lim HW, Kovall R, Weirauch MT, Gebelein B. Prediction of cooperative homeodomain DNA binding sites from high-throughput-SELEX data. Nucleic Acids Res 2023; 51:6055-6072. [PMID: 37114997 PMCID: PMC10325903 DOI: 10.1093/nar/gkad318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/12/2023] [Accepted: 04/25/2023] [Indexed: 04/29/2023] Open
Abstract
Homeodomain proteins constitute one of the largest families of metazoan transcription factors. Genetic studies have demonstrated that homeodomain proteins regulate many developmental processes. Yet, biochemical data reveal that most bind highly similar DNA sequences. Defining how homeodomain proteins achieve DNA binding specificity has therefore been a long-standing goal. Here, we developed a novel computational approach to predict cooperative dimeric binding of homeodomain proteins using High-Throughput (HT) SELEX data. Importantly, we found that 15 of 88 homeodomain factors form cooperative homodimer complexes on DNA sites with precise spacing requirements. Approximately one third of the paired-like homeodomain proteins cooperatively bind palindromic sequences spaced 3 bp apart, whereas other homeodomain proteins cooperatively bind sites with distinct orientation and spacing requirements. Combining structural models of a paired-like factor with our cooperativity predictions identified key amino acid differences that help differentiate between cooperative and non-cooperative factors. Finally, we confirmed predicted cooperative dimer sites in vivo using available genomic data for a subset of factors. These findings demonstrate how HT-SELEX data can be computationally mined to predict cooperativity. In addition, the binding site spacing requirements of select homeodomain proteins provide a mechanism by which seemingly similar AT-rich DNA sequences can preferentially recruit specific homeodomain factors.
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Affiliation(s)
- Brittany Cain
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH 45221, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA
| | - Jordan Webb
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Zhenyu Yuan
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - David Cheung
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Rhett A Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Matthew T Weirauch
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Divisions of Human Genetics, Biomedical Informatics and Developmental Biology, Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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5
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Bian F, Daghsni M, Lu F, Liu S, Gross JM, Aldiri I. Functional analysis of the Vsx2 super-enhancer uncovers distinct cis-regulatory circuits controlling Vsx2 expression during retinogenesis. Development 2022; 149:dev200642. [PMID: 35831950 PMCID: PMC9440754 DOI: 10.1242/dev.200642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/24/2022] [Indexed: 11/20/2022]
Abstract
Vsx2 is a transcription factor essential for retinal proliferation and bipolar cell differentiation, but the molecular mechanisms underlying its developmental roles are unclear. Here, we have profiled VSX2 genomic occupancy during mouse retinogenesis, revealing extensive retinal genetic programs associated with VSX2 during development. VSX2 binds and transactivates its enhancer in association with the transcription factor PAX6. Mice harboring deletions in the Vsx2 regulatory landscape exhibit specific abnormalities in retinal proliferation and in bipolar cell differentiation. In one of those deletions, a complete loss of bipolar cells is associated with a bias towards photoreceptor production. VSX2 occupies cis-regulatory elements nearby genes associated with photoreceptor differentiation and homeostasis in the adult mouse and human retina, including a conserved region nearby Prdm1, a factor implicated in the specification of rod photoreceptors and suppression of bipolar cell fate. VSX2 interacts with the transcription factor OTX2 and can act to suppress OTX2-dependent enhancer transactivation of the Prdm1 enhancer. Taken together, our analyses indicate that Vsx2 expression can be temporally and spatially uncoupled at the enhancer level, and they illuminate important mechanistic insights into how VSX2 is engaged with gene regulatory networks that are essential for retinal proliferation and cell fate acquisition.
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Affiliation(s)
- Fuyun Bian
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Marwa Daghsni
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Fangfang Lu
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Jeffrey M Gross
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Issam Aldiri
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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6
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Zhuo X, Knox BE. Interaction of human CRX and NRL in live HEK293T cells measured using fluorescence resonance energy transfer (FRET). Sci Rep 2022; 12:6937. [PMID: 35484285 DOI: 10.1038/s41598-022-10689-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/11/2022] [Indexed: 12/04/2022] Open
Abstract
CRX and NRL are retina-specific transcription factors that control rod photoreceptor differentiation and synergistically activate rod phototransduction gene expression. Previous experiments showed they interact in vitro and in yeast two-hybrid assays. Here, we examined CRX-NRL interaction in live HEK293T cells using two fluorescence resonance energy transfer (FRET) approaches: confocal microscopy and flow cytometry (FC-FRET). FC-FRET can provide measurements from many cells having wide donor–acceptor expression ranges. FRET efficiencies were calibrated with a series of donor (EGFP)-acceptor (mCherry) fusion proteins separated with linkers between 6–45 amino acids. CRX and NRL were fused at either terminus with EGFP or mCherry to create fluorescent proteins, and all combinations were tested in transiently transfected cells. FRET signals between CRX or NRL homo-pairs were highest with both fluorophores fused to the DNA binding domains (DBD), lower with both fused to the activation domains (AD), and not significant when fused on opposite termini. NRL had stronger FRET signals than CRX. A significant FRET signal between CRX and NRL hetero-pairs was detected when donor was fused to the CRX DNA binding domain and the acceptor fused to the NRL activation domain. FRET signals increased with CRX or NRL expression levels at a rate much higher than expected for collisional FRET alone. Together, our results show the formation of CRX-NRL complexes in live HEK293T cells that are close enough for FRET.
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7
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Fernandes G, Tran H, Andrieu M, Diaw Y, Perez Romero C, Fradin C, Coppey M, Walczak AM, Dostatni N. Synthetic reconstruction of the hunchback promoter specifies the role of Bicoid, Zelda and Hunchback in the dynamics of its transcription. eLife 2022; 11:74509. [PMID: 35363606 PMCID: PMC8975551 DOI: 10.7554/elife.74509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 03/10/2022] [Indexed: 11/23/2022] Open
Abstract
For over 40 years, the Bicoid-hunchback (Bcd-hb) system in the fruit fly embryo has been used as a model to study how positional information in morphogen concentration gradients is robustly translated into step-like responses. A body of quantitative comparisons between theory and experiment have since questioned the initial paradigm that the sharp hb transcription pattern emerges solely from diffusive biochemical interactions between the Bicoid transcription factor and the gene promoter region. Several alternative mechanisms have been proposed, such as additional sources of positional information, positive feedback from Hb proteins or out-of-equilibrium transcription activation. By using the MS2-MCP RNA-tagging system and analysing in real time, the transcription dynamics of synthetic reporters for Bicoid and/or its two partners Zelda and Hunchback, we show that all the early hb expression pattern features and temporal dynamics are compatible with an equilibrium model with a short decay length Bicoid activity gradient as a sole source of positional information. Meanwhile, Bicoid’s partners speed-up the process by different means: Zelda lowers the Bicoid concentration threshold required for transcriptional activation while Hunchback reduces burstiness and increases the polymerase firing rate.
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Affiliation(s)
- Gonçalo Fernandes
- Institut Curie, Université PSL, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France
| | - Huy Tran
- Institut Curie, Université PSL, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France.,Laboratoire de Physique de l'École Normale Supérieure, CNRS, Université PSL, Sorbonne Université and Université de Paris, Paris, France
| | - Maxime Andrieu
- Institut Curie, Université PSL, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France
| | - Youssoupha Diaw
- Institut Curie, Université PSL, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France
| | - Carmina Perez Romero
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Cécile Fradin
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.,Department of Physics and Astronomy, McMaster University, Hamilton, Canada
| | - Mathieu Coppey
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de Physique de l'École Normale Supérieure, CNRS, Université PSL, Sorbonne Université and Université de Paris, Paris, France
| | - Nathalie Dostatni
- Institut Curie, Université PSL, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France
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8
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Datta RR, Rister J. The power of the (imperfect) palindrome: Sequence-specific roles of palindromic motifs in gene regulation. Bioessays 2022; 44:e2100191. [PMID: 35195290 PMCID: PMC8957550 DOI: 10.1002/bies.202100191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 12/22/2022]
Abstract
In human languages, a palindrome reads the same forward as backward (e.g., 'madam'). In regulatory DNA, a palindrome is an inverted sequence repeat that allows a transcription factor to bind as a homodimer or as a heterodimer with another type of transcription factor. Regulatory palindromes are typically imperfect, that is, the repeated sequences differ in at least one base pair, but the functional significance of this asymmetry remains poorly understood. Here, we review the use of imperfect palindromes in Drosophila photoreceptor differentiation and mammalian steroid receptor signaling. Moreover, we discuss mechanistic explanations for the predominance of imperfect palindromes over perfect palindromes in these two gene regulatory contexts. Lastly, we propose to elucidate whether specific imperfectly palindromic variants have specific regulatory functions in steroid receptor signaling and whether such variants can help predict transcriptional outcomes as well as the response of individual patients to drug treatments.
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Affiliation(s)
- Rhea R Datta
- Department of Biology, Hamilton College, Clinton, New York, USA
| | - Jens Rister
- Department of Biology, University of Massachusetts Boston, Integrated Sciences Complex, Boston, Massachusetts, USA
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9
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Ettensohn CA, Guerrero-Santoro J, Khor JM. Lessons from a transcription factor: Alx1 provides insights into gene regulatory networks, cellular reprogramming, and cell type evolution. Curr Top Dev Biol 2022; 146:113-148. [PMID: 35152981 DOI: 10.1016/bs.ctdb.2021.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The skeleton-forming cells of sea urchins and other echinoderms have been studied by developmental biologists as models of cell specification and morphogenesis for many decades. The gene regulatory network (GRN) deployed in the embryonic skeletogenic cells of euechinoid sea urchins is one of the best understood in any developing animal. Recent comparative studies have leveraged the information contained in this GRN, bringing renewed attention to the diverse patterns of skeletogenesis within the phylum and the evolutionary basis for this diversity. The homeodomain-containing transcription factor, Alx1, was originally shown to be a core component of the skeletogenic GRN of the sea urchin embryo. Alx1 has since been found to be key regulator of skeletal cell identity throughout the phylum. As such, Alx1 is currently serving as a lens through which multiple developmental processes are being investigated. These include not only GRN organization and evolution, but also cell reprogramming, cell type evolution, and the gene regulatory control of morphogenesis. This review summarizes our current state of knowledge concerning Alx1 and highlights the insights it is yielding into these important developmental and evolutionary processes.
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Affiliation(s)
- Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States.
| | | | - Jian Ming Khor
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
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10
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Hosokawa K, Ishimaru H, Watanabe T, Fujimuro M. Pax5 mediates the transcriptional activation of the CD81 gene. Sci Rep 2021; 11:22919. [PMID: 34824296 PMCID: PMC8616915 DOI: 10.1038/s41598-021-02082-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 11/10/2021] [Indexed: 11/13/2022] Open
Abstract
CD81 is an integral membrane protein of the tetraspanin family and forms complexes with a variety of other cell surface membrane proteins. CD81 is involved in cell migration and B cell activation. However, the mechanism of the transcriptional regulation of the CD81 gene remains unclear. Here, we revealed that CD81 transcriptional activation was required for binding of the transcription factor Pax5 at the Pax5-binding sequence (-54)GCGGGAC(-48) located upstream of the transcriptional start site (TSS) of the CD81 gene. The reporter assay showed that the DNA sequence between - 130 and - 39 bp upstream of the TSS of the CD81 gene had promoter activity for CD81 transcription. The DNA sequence between - 130 and - 39 bp upstream of TSS of CD81 harbors two potential Pax5-binding sequences (-87)GCGTGAG(-81) and (-54)GCGGGAC(-48). Reporter, electrophoresis mobility shift, and chromatin immunoprecipitation (ChIP) assays disclosed that Pax5 bound to the (-54)GCGGGAC(-48) in the promoter region of the CD81 gene in order to activate CD81 transcription. Pax5 overexpression increased the expression level of CD81 protein, while the Pax5-knockdown by shRNA decreased CD81 expression. Moreover, we found that the expression level of CD81 was positively correlated with Pax5 expression in human tumor cell lines. Because CD81 was reported to be involved in cell migration, we evaluated the effects of Pax5 overexpression by wound healing and transwell assays. The data showed that overexpression of either Pax5 or CD81 promoted the epithelial cell migration. Thus, our findings provide insights into the transcriptional mechanism of the CD81 gene through transcription factor Pax5.
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Affiliation(s)
- Kohei Hosokawa
- grid.411212.50000 0000 9446 3559Department of Cell Biology, Kyoto Pharmaceutical University, Misasagi-Shichonocho 1, Yamashinaku, Kyoto-shi, Kyoto, 607-8412 Japan
| | - Hanako Ishimaru
- grid.411212.50000 0000 9446 3559Department of Cell Biology, Kyoto Pharmaceutical University, Misasagi-Shichonocho 1, Yamashinaku, Kyoto-shi, Kyoto, 607-8412 Japan
| | - Tadashi Watanabe
- grid.411212.50000 0000 9446 3559Department of Cell Biology, Kyoto Pharmaceutical University, Misasagi-Shichonocho 1, Yamashinaku, Kyoto-shi, Kyoto, 607-8412 Japan ,grid.267625.20000 0001 0685 5104Present Address: Department of Virology, Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215 Japan
| | - Masahiro Fujimuro
- Department of Cell Biology, Kyoto Pharmaceutical University, Misasagi-Shichonocho 1, Yamashinaku, Kyoto-shi, Kyoto, 607-8412, Japan.
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11
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Pelletier A, Mayran A, Gouhier A, Omichinski JG, Balsalobre A, Drouin J. Pax7 pioneer factor action requires both paired and homeo DNA binding domains. Nucleic Acids Res 2021; 49:7424-7436. [PMID: 34197620 PMCID: PMC8287922 DOI: 10.1093/nar/gkab561] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/02/2021] [Accepted: 06/15/2021] [Indexed: 12/20/2022] Open
Abstract
The pioneer transcription factor Pax7 contains two DNA binding domains (DBD), a paired and a homeo domain. Previous work on Pax7 and the related Pax3 showed that each DBD binds a cognate DNA sequence, thus defining two targets of binding and possibly modalities of action. Genomic targets of Pax7 pioneer action leading to chromatin opening are enriched for composite DNA target sites containing juxtaposed sites for both paired and homeo domains. The present work investigated the implication of the DBDs in pioneer action. We show that the composite sequence is a higher affinity binding site and that efficient binding to this site involves both DBDs of the same Pax7 molecule. This binding is not sensitive to cytosine methylation of the DNA sites consistent with pioneer action within nucleosomal heterochromatin. Introduction of single amino acid mutations in either paired or homeo domain that impair binding to cognate DNA sequences showed that both DBDs must be intact for pioneer action. In contrast, only the paired domain is required for low affinity binding of heterochromatin sites. Thus, Pax7 pioneer action on heterochromatin requires unique protein:DNA interactions that are more complex compared to its simpler DNA binding modalities at accessible enhancer target sites.
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Affiliation(s)
- Audrey Pelletier
- Laboratory of Molecular Genetics, Institut de recherches cliniques de Montréal (IRCM), Montréal QC H2W 1R7, Canada.,Department of Biochemistry, Faculté of Médecine, Université de Montréal, Montréal H3C 3J7, Canada
| | - Alexandre Mayran
- Laboratory of Molecular Genetics, Institut de recherches cliniques de Montréal (IRCM), Montréal QC H2W 1R7, Canada.,EPFL SV ISREC UPDUB, CH-1015 Lausanne, Switzerland
| | - Arthur Gouhier
- Laboratory of Molecular Genetics, Institut de recherches cliniques de Montréal (IRCM), Montréal QC H2W 1R7, Canada
| | - James G Omichinski
- Department of Biochemistry, Faculté of Médecine, Université de Montréal, Montréal H3C 3J7, Canada
| | - Aurelio Balsalobre
- Laboratory of Molecular Genetics, Institut de recherches cliniques de Montréal (IRCM), Montréal QC H2W 1R7, Canada
| | - Jacques Drouin
- Laboratory of Molecular Genetics, Institut de recherches cliniques de Montréal (IRCM), Montréal QC H2W 1R7, Canada.,Department of Biochemistry, Faculté of Médecine, Université de Montréal, Montréal H3C 3J7, Canada
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12
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Guerrero-Santoro J, Khor JM, Açıkbaş AH, Jaynes JB, Ettensohn CA. Analysis of the DNA-binding properties of Alx1, an evolutionarily conserved regulator of skeletogenesis in echinoderms. J Biol Chem 2021; 297:100901. [PMID: 34157281 PMCID: PMC8319359 DOI: 10.1016/j.jbc.2021.100901] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 06/09/2021] [Accepted: 06/18/2021] [Indexed: 11/24/2022] Open
Abstract
Alx1, a homeodomain-containing transcription factor, is a highly conserved regulator of skeletogenesis in echinoderms. In sea urchins, Alx1 plays a central role in the differentiation of embryonic primary mesenchyme cells (PMCs) and positively regulates the transcription of most biomineralization genes expressed by these cells. The alx1 gene arose via duplication and acquired a skeletogenic function distinct from its paralog (alx4) through the exonization of a 41–amino acid motif (the D2 domain). Alx1 and Alx4 contain glutamine-50 paired-type homeodomains, which interact preferentially with palindromic binding sites in vitro. Chromatin immunoprecipitation sequencing (ChIP-seq) studies have shown, however, that Alx1 binds both to palindromic and half sites in vivo. To address this apparent discrepancy and explore the function of the D2 domain, we used an endogenous cis-regulatory module associated with Sp-mtmmpb, a gene that encodes a PMC-specific metalloprotease, to analyze the DNA-binding properties of Alx1. We find that Alx1 forms dimeric complexes on TAAT-containing half sites by a mechanism distinct from the well-known mechanism of dimerization on palindromic sites. We used transgenic reporter assays to analyze the functional roles of half sites in vivo and demonstrate that two sites with partially redundant functions are essential for the PMC-specific activity of the Sp-mtmmpb cis-regulatory module. Finally, we show that the D2 domain influences the DNA-binding properties of Alx1 in vitro, suggesting that the exonization of this motif may have facilitated the acquisition of new transcriptional targets and consequently a novel developmental function.
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Affiliation(s)
| | - Jian Ming Khor
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Ayşe Haruka Açıkbaş
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - James B Jaynes
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
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13
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Liu F, Fu J, Wang L, Nie Q, Luo Z, Hou M, Yang Y, Gong X, Wang Y, Xiao Y, Xiang J, Hu X, Zhang L, Wu M, Chen W, Cheng B, Luo L, Zhang X, Liu X, Zheng D, Huang S, Liu Y, Li DW. Molecular signature for senile and complicated cataracts derived from analysis of sumoylation enzymes and their substrates in human cataract lenses. Aging Cell 2020; 19:e13222. [PMID: 32827359 PMCID: PMC7576240 DOI: 10.1111/acel.13222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 07/14/2020] [Accepted: 07/26/2020] [Indexed: 11/30/2022] Open
Abstract
Sumoylation is one of the key regulatory mechanisms in eukaryotes. Our previous studies reveal that sumoylation plays indispensable roles during lens differentiation (Yan et al. 2010. Proc Natl Acad Sci USA. 107:21034-21039; Gong et al. 2014. Proc Natl Acad Sci USA. 111:5574-5579). Whether sumoylation is implicated in cataractogenesis, a disease largely derived from aging, remains elusive. In the present study, we have examined the changing patterns of the sumoylation ligases and de-sumoylation enzymes (SENPs) and their substrates including Pax6 and other proteins in cataractous lenses of different age groups from 50 to 90 years old. It is found that compared with normal lenses, sumoylation ligases 1 and 3, de-sumoylation enzymes SENP3/7/8, and p46 Pax6 are clearly increased. In contrast, Ubc9 is significantly decreased. Among different cataract patients from 50s to 70s, male patients express more sumoylation enzymes and p46 Pax6. Ubc9 and SENP6 display age-dependent increase. The p46 Pax6 displays age-dependent decrease in normal lens, remains relatively stable in senile cataracts but becomes di-sumoylated in complicated cataracts. In contrast, sumoylation of p32 Pax6 is observed in senile cataracts and increases its stability. Treatment of rat lenses with oxidative stress increases Pax6 expression without sumoylation but promotes apoptosis. Thus, our results show that the changing patterns in Ubc9, SENP6, and Pax6 levels can act as molecular markers for senile cataract and the di-sumoylated p46 Pax6 for complicated cataract. Together, our results reveal the presence of molecular signature for both senile and complicated cataracts. Moreover, our study indicates that sumoylation is implicated in control of aging and cataractogenesis.
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Affiliation(s)
- Fang‐Yuan Liu
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Jia‐Ling Fu
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Ling Wang
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Qian Nie
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Zhongwen Luo
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Min Hou
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Yuan Yang
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Xiao‐Dong Gong
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Yan Wang
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Yuan Xiao
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Jiawen Xiang
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Xuebin Hu
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Lan Zhang
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Mingxing Wu
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Weirong Chen
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Bing Cheng
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Lixia Luo
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Xinyu Zhang
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Xialin Liu
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Danying Zheng
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Shengsong Huang
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
| | - David Wan‐Cheng Li
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat‐Sen University Guangzhou China
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14
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Somashekar PH, Upadhyai P, Narayanan DL, Kamath N, Bajaj S, Girisha KM, Shukla A. Phenotypic diversity and genetic complexity of PAX3-related Waardenburg syndrome. Am J Med Genet A 2020; 182:2951-2958. [PMID: 32990402 DOI: 10.1002/ajmg.a.61893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/11/2020] [Accepted: 09/12/2020] [Indexed: 11/09/2022]
Abstract
Waardenburg syndrome subtypes 1 and 3 are caused by pathogenic variants in PAX3. We investigated 12 individuals from four unrelated families clinically diagnosed with Waardenburg syndrome type 1/3. Novel pathogenic variants identified in PAX3 included single nucleotide variants (c.166C>T, c.829C>T), a 2-base pair deletion (c.366_367delAA) and a multi-exonic deletion. Two novel variants, c.166C>T and c.829C>T and a previously reported variant, c.256A>T in PAX3 were evaluated for their nuclear localization and ability to activate MITF promoter. The coexistence of two subtypes of Waardenburg syndrome with pathogenic variants in PAX3 and EDNRB was seen in one of the affected individuals. Multiple genetic diagnoses of Waardenburg syndrome type 3 and autosomal recessive deafness 1A was identified in an individual. We also review the phenotypic and genomic spectrum of individuals with PAX3-related Waardenburg syndrome reported in the literature.
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Affiliation(s)
- Puneeth H Somashekar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Priyanka Upadhyai
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Dhanya L Narayanan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Nutan Kamath
- Department of Pediatrics, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India
| | | | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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15
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Yamazaki A, Morino Y, Urata M, Yamaguchi M, Minokawa T, Furukawa R, Kondo M, Wada H. pmar1/ phb homeobox genes and the evolution of the double-negative gate for endomesoderm specification in echinoderms. Development 2020; 147:dev.182139. [PMID: 32001441 DOI: 10.1242/dev.182139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 01/20/2020] [Indexed: 12/18/2022]
Abstract
In several model animals, the earliest phases of embryogenesis are regulated by lineage-specific genes, such as Drosophila bicoid Sea urchin (echinoid) embryogenesis is initiated by zygotic expression of pmar1, a paired-class homeobox gene that has been considered to be present only in the lineage of modern urchins (euechinoids). In euechinoids, Pmar1 promotes endomesoderm specification by repressing the hairy and enhancer of split C (hesC) gene. Here, we have identified the basal echinoid (cidaroid) pmar1 gene, which also promotes endomesoderm specification but not by repressing hesC A further search for related genes demonstrated that other echinoderms have pmar1-related genes named phb Functional analyses of starfish Phb proteins indicated that, similar to cidaroid Pmar1, they promote activation of endomesoderm regulatory gene orthologs via an unknown repressor that is not HesC. Based on these results, we propose that Pmar1 may have recapitulated the regulatory function of Phb during the early diversification of echinoids and that the additional repressor HesC was placed under the control of Pmar1 in the euechinoid lineage. This case provides an exceptional model for understanding how early developmental processes diverge.
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Affiliation(s)
- Atsuko Yamazaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan
| | - Yoshiaki Morino
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan
| | - Makoto Urata
- Noto Marine Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Ogi, Noto-cho, Ishikawa 927-0553, Japan.,Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan
| | - Masaaki Yamaguchi
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan
| | - Takuya Minokawa
- Research Center for Marine Biology, Tohoku University, Sakamoto 9, Asamushi, Aomori 039-3501, Japan
| | - Ryohei Furukawa
- Department of Biology, Research and Education Center for Natural Sciences, Keio University, Hiyoshi, Kouhoku-ku, Yokohama, Kanagawa 223-8521, Japan
| | - Mariko Kondo
- Misaki Marine Biological Station, Graduate School of Science, The University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa 238-0225, Japan
| | - Hiroshi Wada
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan
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16
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Liu F, Wang L, Fu JL, Xiao Y, Gong X, Liu Y, Nie Q, Xiang JW, Yang L, Chen Z, Liu Y, Li DWC. Analysis of Non-Sumoylated and Sumoylated Isoforms of Pax-6, the Master Regulator for Eye and Brain Development in Ocular Cell Lines. Curr Mol Med 2019; 18:566-573. [PMID: 30636604 DOI: 10.2174/1566524019666190111153310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 11/21/2018] [Accepted: 01/07/2019] [Indexed: 11/22/2022]
Abstract
PURPOSE Pax-6 is a master regulator for eye and brain development. Previous studies including ours have shown that Pax-6 exists in 4 major isoforms. According to their sizes, they are named p48, p46, p43 and p32 with the corresponding molecular weight of 48, 46, 43 and 32 kd, respectively. While p48 and p46 is derived from alternative splicing, p32 Pax-6 is generated through an internal translation initiation site. As for 43 kd Pax-6, two resources have been reported. In bird, it was found that an alternative splicing can generate a p43 Pax-6. In human and mouse, we reported that the p43 kd Pax-6 is derived from sumoylation: addition of a 11 kd polypeptide SUMO1 into the p32 Pax-6 at the K91 residue. Whether other Pax-6 isoforms can be sumoylated or not remains to be explored. METHODS The 5 major ocular cell lines were cultured in Dulbecco's modified Eagle's medium (DMEM) containing fetal bovine serum (FBS) or rabbit serum (RBS) and 1% Penicillin- Streptomycin. The mRNA levels were analysed with qRT-PCR. The protein levels were determined with western blot analysis and quantitated with Image J. RESULTS Both non-sumoylated and sumoylated isoforms of Pax-6 exist in 6 major types of ocular cells among which five are lens epithelial cells, and one is retinal pigment epithelial cell. Our results revealed that the most abundant isoforms of Pax-6 are the p32 and p46 Pax-6. These two major isoforms can be sumoylated to generate p43 (mono-sumoylated p32 Pax-6), p57 and p68 Pax-6 (mono- and di-sumoylated p46 Pax-6). In addition, the splicing-generated p48 Pax-6 is also readily detected. CONCLUSION Our results for the first time, have determined the relative isoform abundance and also the sumoylation patterns of pax-6 in 6 major ocular cell lines.
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Affiliation(s)
- Fangyuan Liu
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Ling Wang
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Jia-Ling Fu
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Yuan Xiao
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Xiaodong Gong
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Yunfei Liu
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Qian Nie
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Jia-Wen Xiang
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Lan Yang
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Zhigang Chen
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Yizhi Liu
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - David Wan-Cheng Li
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
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17
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Reeves GT. The engineering principles of combining a transcriptional incoherent feedforward loop with negative feedback. J Biol Eng 2019; 13:62. [PMID: 31333758 PMCID: PMC6617889 DOI: 10.1186/s13036-019-0190-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/24/2019] [Indexed: 12/30/2022] Open
Abstract
Background Regulation of gene expression is of paramount importance in all living systems. In the past two decades, it has been discovered that certain motifs, such as the feedforward motif, are overrepresented in gene regulatory circuits. Feedforward loops are also ubiquitous in process control engineering, and are nearly always structured so that one branch has the opposite effect of the other, which is a structure known as an “incoherent” feedforward loop in biology. In engineered systems, feedforward control loops are subject to several engineering constraints, including that (1) they are finely-tuned so that the system returns to the original steady state after a disturbance occurs (perfect adaptation), (2) they are typically only implemented in the combination with negative feedback, and (3) they can greatly improve the stability and dynamical characteristics of the conjoined negative feedback loop. On the other hand, in biology, incoherent feedforward loops can serve many purposes, one of which may be perfect adaptation. It is an open question as to whether those that achieve perfect adaptation are subject to the above engineering principles. Results We analyzed an incoherent feedforward gene regulatory motif from the standpoint of the above engineering principles. In particular, we showed that an incoherent feedforward loop Type 1 (I1-FFL), from within a gene regulatory circuit, can be finely-tuned for perfect adaptation after a stimulus, and that the robustness of this behavior is increased by the presence of moderate negative feedback. In addition, we analyzed the advantages of adding a feedforward loop to a system that already operated under negative feedback, and found that the dynamical properties of the combined feedforward/feedback system were superior. Conclusions Our analysis shows that many of the engineering principles used in engineering design of feedforward control are also applicable to feedforward loops in biological systems. We speculate that principles found in other domains of engineering may also be applicable to analogous structures in biology. Electronic supplementary material The online version of this article (10.1186/s13036-019-0190-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gregory T Reeves
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695 USA
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18
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Yasuoka Y, Tando Y, Kubokawa K, Taira M. Evolution of cis-regulatory modules for the head organizer gene goosecoid in chordates: comparisons between Branchiostoma and Xenopus. Zoological Lett 2019; 5:27. [PMID: 31388442 PMCID: PMC6679436 DOI: 10.1186/s40851-019-0143-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 07/12/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND In cephalochordates (amphioxus), the notochord runs along the dorsal to the anterior tip of the body. In contrast, the vertebrate head is formed anterior to the notochord, as a result of head organizer formation in anterior mesoderm during early development. A key gene for the vertebrate head organizer, goosecoid (gsc), is broadly expressed in the dorsal mesoderm of amphioxus gastrula. Amphioxus gsc expression subsequently becomes restricted to the posterior notochord from the early neurula. This has prompted the hypothesis that a change in expression patterns of gsc led to development of the vertebrate head during chordate evolution. However, molecular mechanisms of head organizer evolution involving gsc have never been elucidated. RESULTS To address this question, we compared cis-regulatory modules of vertebrate organizer genes between amphioxus, Branchiostoma japonicum, and frogs, Xenopus laevis and Xenopus tropicalis. Here we show conservation and diversification of gene regulatory mechanisms through cis-regulatory modules for gsc, lim1/lhx1, and chordin in Branchiostoma and Xenopus. Reporter analysis using Xenopus embryos demonstrates that activation of gsc by Nodal/FoxH1 signal through the 5' upstream region, that of lim1 by Nodal/FoxH1 signal through the first intron, and that of chordin by Lim1 through the second intron, are conserved between amphioxus and Xenopus. However, activation of gsc by Lim1 and Otx through the 5' upstream region in Xenopus are not conserved in amphioxus. Furthermore, the 5' region of amphioxus gsc recapitulated the amphioxus-like posterior mesoderm expression of the reporter gene in transgenic Xenopus embryos. CONCLUSIONS On the basis of this study, we propose a model, in which the gsc gene acquired the cis-regulatory module bound with Lim1 and Otx at its 5' upstream region to be activated persistently in anterior mesoderm, in the vertebrate lineage. Because Gsc globally represses trunk (notochord) genes in the vertebrate head organizer, this cooption of gsc in vertebrates appears to have resulted in inhibition of trunk genes and acquisition of the head organizer and its derivative prechordal plate.
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Affiliation(s)
- Yuuri Yasuoka
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495 Japan
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Yukiko Tando
- Center for Advance Marine Research, Ocean Research Institute, The University of Tokyo, 1-15-1, Minamidai, Nakano-ku, Tokyo, 164-8639 Japan
- Present address: Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Kaoru Kubokawa
- Center for Advance Marine Research, Ocean Research Institute, The University of Tokyo, 1-15-1, Minamidai, Nakano-ku, Tokyo, 164-8639 Japan
- Present address: SIRC, Teikyo University, 2-11-1, Itabashi-ku, Tokyo, 173-8605 Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
- Present address: Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551 Japan
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Jiang Y, Xie Q, Wang W, Yang J, Zhang X, Yu N, Zhou Y, Wang E. Medicago AP2-Domain Transcription Factor WRI5a Is a Master Regulator of Lipid Biosynthesis and Transfer during Mycorrhizal Symbiosis. Mol Plant 2018; 11:1344-1359. [PMID: 30292683 DOI: 10.1016/j.molp.2018.09.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/27/2018] [Accepted: 09/27/2018] [Indexed: 05/25/2023]
Abstract
Most land plants have evolved a mutualistic symbiosis with arbuscular mycorrhiza (AM) fungi that improve nutrient acquisition from the soil. In return, up to 20% of host plant photosynthate is transferred to the mycorrhizal fungus in the form of lipids and sugar. Nutrient exchange must be regulated by both partners in order to maintain a reliable symbiotic relationship. However, the mechanisms underlying the regulation of lipid transfer from the plant to the AM fungus remain elusive. Here, we show that the Medicago truncatula AP2/EREBP transcription factor WRI5a, and likely its two homologs WRI5b/Erf1 and WRI5c, are master regulators of AM symbiosis controlling lipid transfer and periarbuscular membrane formation. We found that WRI5a binds AW-box cis-regulatory elements in the promoters of M. truncatula STR, which encodes a periarbuscular membrane-localized ABC transporter required for lipid transfer from the plant to the AM fungus, and MtPT4, which encodes a phosphate transporter required for phosphate transfer from the AM fungus to the plant. The hairy roots of the M. truncatula wri5a mutant and RNAi composite plants displayed impaired arbuscule formation, whereas overexpression of WRI5a resulted in enhanced expression of STR and MtPT4, suggesting that WRI5a regulates bidirectional symbiotic nutrient exchange. Moreover, we found that WRI5a and RAM1 (Required for Arbuscular Mycorrhization symbiosis 1), which encodes a GRAS-domain transcription factor, regulate each other at the transcriptional level, forming a positive feedback loop for regulating AM symbiosis. Collectively, our data suggest a role for WRI5a in controlling bidirectional nutrient exchange and periarbuscular membrane formation via the regulation of genes involved in the biosynthesis of fatty acids and phosphate uptake in arbuscule-containing cells.
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Affiliation(s)
- Yina Jiang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Qiujin Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Wanxiao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiaowei Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Nan Yu
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yun Zhou
- Collaborative Innovation Center of Crop Stress Biology, Henan Province; Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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20
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Hughes AEO, Myers CA, Corbo JC. A massively parallel reporter assay reveals context-dependent activity of homeodomain binding sites in vivo. Genome Res 2018; 28:1520-1531. [PMID: 30158147 PMCID: PMC6169884 DOI: 10.1101/gr.231886.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 08/27/2018] [Indexed: 12/20/2022]
Abstract
Cone-rod homeobox (CRX) is a paired-like homeodomain transcription factor (TF) and a master regulator of photoreceptor development in vertebrates. The in vitro DNA binding preferences of CRX have been described in detail, but the degree to which in vitro binding affinity is correlated with in vivo enhancer activity is not known. In addition, paired-class homeodomain TFs can bind DNA cooperatively as both homodimers and heterodimers at inverted TAAT half-sites separated by 2 or 3 nucleotides. This dimeric configuration is thought to mediate target specificity, but whether monomeric and dimeric sites encode distinct levels of activity is not known. Here, we used a massively parallel reporter assay to determine how local sequence context shapes the regulatory activity of CRX binding sites in mouse photoreceptors. We assayed inactivating mutations in more than 1700 TF binding sites and found that dimeric CRX binding sites act as stronger enhancers than monomeric CRX binding sites. Furthermore, the activity of dimeric half-sites is cooperative, dependent on a strict 3-bp spacing, and tuned by the identity of the spacer nucleotides. Saturating single-nucleotide mutagenesis of 195 CRX binding sites showed that, on average, changes in TF binding site affinity are correlated with changes in regulatory activity, but this relationship is obscured when considering mutations across multiple cis-regulatory elements (CREs). Taken together, these results demonstrate that the activity of CRX binding sites is highly dependent on sequence context, providing insight into photoreceptor gene regulation and illustrating functional principles of homeodomain binding sites that may be conserved in other cell types.
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Affiliation(s)
- Andrew E O Hughes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Connie A Myers
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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21
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Boudjadi S, Chatterjee B, Sun W, Vemu P, Barr FG. The expression and function of PAX3 in development and disease. Gene 2018; 666:145-157. [PMID: 29730428 DOI: 10.1016/j.gene.2018.04.087] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 04/26/2018] [Accepted: 04/27/2018] [Indexed: 12/27/2022]
Abstract
The PAX3 gene encodes a member of the PAX family of transcription factors that is characterized by a highly conserved paired box motif. The PAX3 protein is a transcription factor consisting of an N-terminal DNA binding domain (containing a paired box and homeodomain) and a C-terminal transcriptional activation domain. This protein is expressed during development of skeletal muscle, central nervous system and neural crest derivatives, and regulates expression of target genes that impact on proliferation, survival, differentiation and motility in these lineages. Germline mutations of the murine Pax3 and human PAX3 genes cause deficiencies in these developmental lineages and result in the Splotch phenotype and Waardenburg syndrome, respectively. Somatic genetic rearrangements that juxtapose the PAX3 DNA binding domain to the transcriptional activation domain of other transcription factors deregulate PAX3 function and contribute to the pathogenesis of the soft tissue cancers alveolar rhabdomyosarcoma and biphenotypic sinonasal sarcoma. The wild-type PAX3 protein is also expressed in other cancers related to developmental lineages that normally express this protein and exerts phenotypic effects related to its normal developmental role.
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Affiliation(s)
- Salah Boudjadi
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | | | - Wenyue Sun
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Prasantha Vemu
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Frederic G Barr
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA.
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22
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Dong X, Zhang W, Wu H, Huang J, Zhang M, Wang P, Zhang H, Chen Z, Chen SJ, Meng G. Structural basis of DUX4/IGH-driven transactivation. Leukemia 2018; 32:1466-1476. [PMID: 29572508 PMCID: PMC5990521 DOI: 10.1038/s41375-018-0093-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 02/10/2018] [Accepted: 02/20/2018] [Indexed: 01/10/2023]
Abstract
Oncogenic fusions are major drivers in leukemogenesis and may serve as potent targets for treatment. DUX4/IGHs have been shown to trigger the abnormal expression of ERGalt through binding to DUX4-Responsive-Element (DRE), which leads to B-cell differentiation arrest and a full-fledged B-ALL. Here, we determined the crystal structures of Apo- and DNADRE-bound DUX4HD2 and revealed a clamp-like transactivation mechanism via the double homeobox domain. Biophysical characterization showed that mutations in the interacting interfaces significantly impaired the DNA binding affinity of DUX4 homeobox. These mutations, when introduced into DUX4/IGH, abrogated its transactivation activity in Reh cells. More importantly, the structure-based mutants significantly impaired the inhibitory effects of DUX4/IGH upon B-cell differentiation in mouse progenitor cells. All these results help to define a key DUX4/IGH-DRE recognition/step in B-ALL.
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Affiliation(s)
- Xue Dong
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China.,Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dong Chuan Road, Shanghai, 200240, China
| | - Weina Zhang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China.,Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dong Chuan Road, Shanghai, 200240, China
| | - Haiyan Wu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China.,Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dong Chuan Road, Shanghai, 200240, China
| | - Jinyan Huang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China.,Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dong Chuan Road, Shanghai, 200240, China
| | - Ming Zhang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China.,Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dong Chuan Road, Shanghai, 200240, China
| | - Pengran Wang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China.,Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dong Chuan Road, Shanghai, 200240, China
| | - Hao Zhang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China.,Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dong Chuan Road, Shanghai, 200240, China
| | - Zhu Chen
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China.,Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dong Chuan Road, Shanghai, 200240, China
| | - Sai-Juan Chen
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China. .,Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dong Chuan Road, Shanghai, 200240, China.
| | - Guoyu Meng
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China. .,Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dong Chuan Road, Shanghai, 200240, China.
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23
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Watanabe M, Yasuoka Y, Mawaribuchi S, Kuretani A, Ito M, Kondo M, Ochi H, Ogino H, Fukui A, Taira M, Kinoshita T. Conservatism and variability of gene expression profiles among homeologous transcription factors in Xenopus laevis. Dev Biol 2017; 426:301-324. [DOI: 10.1016/j.ydbio.2016.09.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 07/27/2016] [Accepted: 09/19/2016] [Indexed: 12/11/2022]
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24
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Hughes AE, Enright JM, Myers CA, Shen SQ, Corbo JC. Cell Type-Specific Epigenomic Analysis Reveals a Uniquely Closed Chromatin Architecture in Mouse Rod Photoreceptors. Sci Rep 2017; 7:43184. [PMID: 28256534 DOI: 10.1038/srep43184] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/19/2017] [Indexed: 12/24/2022] Open
Abstract
Rod photoreceptors are specialized neurons that mediate vision in dim light and are the predominant photoreceptor type in nocturnal mammals. The rods of nocturnal mammals are unique among vertebrate cell types in having an ‘inverted’ nuclear architecture, with a dense mass of heterochromatin in the center of the nucleus rather than dispersed clumps at the periphery. To test if this unique nuclear architecture is correlated with a unique epigenomic landscape, we performed ATAC-seq on mouse rods and their most closely related cell type, cone photoreceptors. We find that thousands of loci are selectively closed in rods relative to cones as well as >60 additional cell types. Furthermore, we find that the open chromatin profile of photoreceptors lacking the rod master regulator Nrl is nearly indistinguishable from that of native cones, indicating that Nrl is required for selective chromatin closure in rods. Finally, we identified distinct enrichments of transcription factor binding sites in rods and cones, revealing key differences in the cis-regulatory grammar of these cell types. Taken together, these data provide insight into the development and maintenance of photoreceptor identity, and highlight rods as an attractive system for studying the relationship between nuclear organization and local changes in gene regulation.
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25
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Pozzi S, Tan WH, Martinez-Barbera J. Characterization of a novel HESX1 mutation in a pediatric case of septo-optic dysplasia. Clin Case Rep 2017; 5:463-470. [PMID: 28396770 PMCID: PMC5378840 DOI: 10.1002/ccr3.868] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 08/13/2016] [Accepted: 01/29/2017] [Indexed: 11/08/2022] Open
Abstract
Septo‐optic dysplasia (SOD) is a rare condition for which the precise etiology is still unclear. Elucidating the genetic component of SOD is a difficult but necessary task for the future. We describe herein a novel HESX1 c.475C>T (p.R159W) mutation and demonstrate its potential pathogenicity in the development of this rare disease.
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Affiliation(s)
- Sara Pozzi
- Developmental Biology and Cancer Research Programme Birth Defects Research Centre UCL Great Ormond Street Institute of Child Health London UK
| | - Wen-Hann Tan
- Division of Genetics and Genomics Boston Children's Hospital Boston Massachusetts USA
| | - JuanPedro Martinez-Barbera
- Developmental Biology and Cancer Research Programme Birth Defects Research Centre UCL Great Ormond Street Institute of Child Health London UK
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26
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Abstract
SHOX deficiency is the most frequent genetic growth disorder associated with isolated and syndromic forms of short stature. Caused by mutations in the homeobox gene SHOX, its varied clinical manifestations include isolated short stature, Léri-Weill dyschondrosteosis, and Langer mesomelic dysplasia. In addition, SHOX deficiency contributes to the skeletal features in Turner syndrome. Causative SHOX mutations have allowed downstream pathology to be linked to defined molecular lesions. Expression levels of SHOX are tightly regulated, and almost half of the pathogenic mutations have affected enhancers. Clinical severity of SHOX deficiency varies between genders and ranges from normal stature to profound mesomelic skeletal dysplasia. Treatment options for children with SHOX deficiency are available. Two decades of research support the concept of SHOX as a transcription factor that integrates diverse aspects of bone development, growth plate biology, and apoptosis. Due to its absence in mouse, the animal models of choice have become chicken and zebrafish. These models, therefore, together with micromass cultures and primary cell lines, have been used to address SHOX function. Pathway and network analyses have identified interactors, target genes, and regulators. Here, we summarize recent data and give insight into the critical molecular and cellular functions of SHOX in the etiopathogenesis of short stature and limb development.
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Affiliation(s)
- Antonio Marchini
- Tumour Virology Division F010 (A.M.), German Cancer Research Center, 69120 Heidelberg, Germany; Department of Oncology (A.M.), Luxembourg Institute of Health 84, rue Val Fleuri L-1526, Luxembourg; Department of Pediatrics (T.O.), Hamamatsu University School of Medicine, Higashi-ku, Hamamatsu 431-3192, Japan; and Department of Human Molecular Genetics (G.A.R.), Institute of Human Genetics, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Tsutomu Ogata
- Tumour Virology Division F010 (A.M.), German Cancer Research Center, 69120 Heidelberg, Germany; Department of Oncology (A.M.), Luxembourg Institute of Health 84, rue Val Fleuri L-1526, Luxembourg; Department of Pediatrics (T.O.), Hamamatsu University School of Medicine, Higashi-ku, Hamamatsu 431-3192, Japan; and Department of Human Molecular Genetics (G.A.R.), Institute of Human Genetics, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Gudrun A Rappold
- Tumour Virology Division F010 (A.M.), German Cancer Research Center, 69120 Heidelberg, Germany; Department of Oncology (A.M.), Luxembourg Institute of Health 84, rue Val Fleuri L-1526, Luxembourg; Department of Pediatrics (T.O.), Hamamatsu University School of Medicine, Higashi-ku, Hamamatsu 431-3192, Japan; and Department of Human Molecular Genetics (G.A.R.), Institute of Human Genetics, Heidelberg University Hospital, 69120 Heidelberg, Germany
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27
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Clovis YM, Seo SY, Kwon JS, Rhee JC, Yeo S, Lee JW, Lee S, Lee SK. Chx10 Consolidates V2a Interneuron Identity through Two Distinct Gene Repression Modes. Cell Rep 2016; 16:1642-1652. [PMID: 27477290 DOI: 10.1016/j.celrep.2016.06.100] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 04/29/2016] [Accepted: 06/29/2016] [Indexed: 12/22/2022] Open
Abstract
During development, two cell types born from closely related progenitor pools often express identical transcriptional regulators despite their completely distinct characteristics. This phenomenon implies the need for a mechanism that operates to segregate the identities of the two cell types throughout differentiation after initial fate commitment. To understand this mechanism, we investigated the fate specification of spinal V2a interneurons, which share important developmental genes with motor neurons (MNs). We demonstrate that the paired homeodomain factor Chx10 functions as a critical determinant for V2a fate and is required to consolidate V2a identity in postmitotic neurons. Chx10 actively promotes V2a fate, downstream of the LIM-homeodomain factor Lhx3, while concomitantly suppressing the MN developmental program by preventing the MN-specific transcription complex from binding and activating MN genes. This dual activity enables Chx10 to effectively separate the V2a and MN pathways. Our study uncovers a widely applicable gene regulatory principle for segregating related cell fates.
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Affiliation(s)
- Yoanne M Clovis
- Pediatric Neuroscience Research Program, Papé Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239, USA
| | - So Yeon Seo
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 151-742, Korea
| | - Ji-Sun Kwon
- Pediatric Neuroscience Research Program, Papé Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239, USA
| | - Jennifer C Rhee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 151-742, Korea
| | - Sujeong Yeo
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 151-742, Korea
| | - Jae W Lee
- Pediatric Neuroscience Research Program, Papé Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239, USA
| | - Seunghee Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 151-742, Korea.
| | - Soo-Kyung Lee
- Pediatric Neuroscience Research Program, Papé Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239, USA; Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA.
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28
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Mirasierra M, Vallejo M. Glucose-dependent downregulation of glucagon gene expression mediated by selective interactions between ALX3 and PAX6 in mouse alpha cells. Diabetologia 2016; 59:766-75. [PMID: 26739814 DOI: 10.1007/s00125-015-3849-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 12/07/2015] [Indexed: 12/11/2022]
Abstract
AIMS/HYPOTHESIS The stimulation of glucagon secretion in response to decreased glucose levels has been studied extensively. In contrast, little is known about the regulation of glucagon gene expression in response to fluctuations in glucose concentration. Paired box 6 (PAX6) is a key transcription factor that regulates the glucagon promoter by binding to the G1 and G3 elements. Here, we investigated the role of the transcription factor aristaless-like homeobox 3 (ALX3) as a glucose-dependent modulator of PAX6 activity in alpha cells. METHODS Experiments were performed in wild-type or Alx3-deficient islets and alphaTC1 cells. We used chromatin immunoprecipitations and electrophoretic mobility shift assays for DNA binding, immunoprecipitations and pull-down assays for protein interactions, transfected cells for promoter activity, and small interfering RNA and quantitative RT-PCR for gene expression. RESULTS Elevated glucose concentration resulted in stimulated expression of Alx3 and decreased glucagon gene expression in wild-type islets. In ALX3-deficient islets, basal glucagon levels were non-responsive to changes in glucose concentration. In basal conditions ALX3 bound to the glucagon promoter at G3, but not at G1. ALX3 could form heterodimers with PAX6 that were permissive for binding to G3 but not to G1. Thus, increasing the levels of ALX3 in response to glucose resulted in the sequestration of PAX6 by ALX3 for binding to G1, thus reducing glucagon promoter activation and glucagon gene expression. CONCLUSIONS/INTERPRETATION Glucose-stimulated expression of ALX3 in alpha cells provides a regulatory mechanism for the downregulation of glucagon gene expression by interfering with PAX6-mediated transactivation on the glucagon G1 promoter element.
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Affiliation(s)
- Mercedes Mirasierra
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Calle Arturo Duperier 4, 28029, Madrid, Spain
| | - Mario Vallejo
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain.
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Calle Arturo Duperier 4, 28029, Madrid, Spain.
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29
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Zhang Y, Lee JK, Toso EA, Lee JS, Choi SH, Slattery M, Aihara H, Kyba M. DNA-binding sequence specificity of DUX4. Skelet Muscle 2016; 6:8. [PMID: 26823969 PMCID: PMC4730607 DOI: 10.1186/s13395-016-0080-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/08/2016] [Indexed: 11/10/2022] Open
Abstract
Background Misexpression of the double homeodomain transcription factor DUX4 results in facioscapulohumeral muscular dystrophy (FSHD). A DNA-binding consensus with two tandem TAAT motifs based on chromatin IP peaks has been discovered; however, the consensus has multiple variations (flavors) of unknown relative activity. In addition, not all peaks have this consensus, and the Pitx1 promoter, the first DUX4 target sequence mooted, has a different TAAT-rich sequence. Furthermore, it is not known whether and to what extent deviations from the consensus affect DNA-binding affinity and transcriptional activation potential. Results Here, we take both unbiased and consensus sequence-driven approaches to determine the DNA-binding specificity of DUX4 and its tolerance to mismatches at each site within its consensus sequence. We discover that the best binding and the greatest transcriptional activation are observed when the two TAAT motifs are separated by a C residue. The second TAAT motif in the consensus sequence is actually (T/C)AAT. We find that a T is preferred here. DUX4 has no transcriptional activity on “half-sites”, i.e., those bearing only a single TAAT motif. We further find that DUX4 does not bind to the TAATTA motif in the Pitx1 promoter, that Pitx1 sequences have no competitive band shift activity, and that the Pitx1 sequence is transcriptionally inactive, calling into question PITX1 as a DUX4 target gene. Finally, by multimerizing binding sites, we find that DUX4 transcriptional activation demonstrates tremendous synergy and that at low DNA concentrations, at least two motifs are necessary to detect a transcriptional response. Conclusions These studies illuminate the DNA-binding sequence preferences of DUX4. Electronic supplementary material The online version of this article (doi:10.1186/s13395-016-0080-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu Zhang
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455 USA ; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455 USA
| | - John K Lee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455 USA
| | - Erik A Toso
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455 USA ; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455 USA
| | - Joslynn S Lee
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812 USA
| | - Si Ho Choi
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455 USA ; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455 USA ; Research Center, Dongnam Institute of Radiological & Medical Sciences (DIRAMS), Busan, South Korea
| | - Matthew Slattery
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812 USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455 USA
| | - Michael Kyba
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455 USA ; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455 USA
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30
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Raymond A, Liu B, Liang H, Wei C, Guindani M, Lu Y, Liang S, St John LS, Molldrem J, Nagarajan L. A role for BMP-induced homeobox gene MIXL1 in acute myelogenous leukemia and identification of type I BMP receptor as a potential target for therapy. Oncotarget 2015; 5:12675-93. [PMID: 25544748 PMCID: PMC4350356 DOI: 10.18632/oncotarget.2564] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 10/02/2014] [Indexed: 01/03/2023] Open
Abstract
Mesoderm Inducer in Xenopus Like1 (MIXL1), a paired-type homeobox transcription factor induced by TGF-β family of ligands is required for early embryonic specification of mesoderm and endoderm. Retrovirally transduced Mixl1 is reported to induce acute myelogenous leukemia (AML) with a high penetrance. But the mechanistic underpinnings of MIXL1 mediated leukemogenesis are unknown. Here, we establish the protooncogene c-REL to be a transcriptional target of MIXL1 by genome wide chromatin immune precipitation. Accordingly, expression of c-REL and its downstream targets BCL2L1 and BCL2A2 are elevated in MIXL1 expressing cells. Notably, MIXL1 regulates c-REL through a zinc finger binding motif, potentially by a MIXL1–Zinc finger protein transcriptional complex. Furthermore, MIXL1 expression is detected in the cancer genome atlas (TCGA) AML samples in a pattern mutually exclusive from that of HOXA9, CDX2 and HLX suggesting the existence of a core, yet distinct HOX transcriptional program. Finally, we demonstrate MIXL1 to be induced by BMP4 and not TGF-β in primary human hematopoietic stem and progenitor cells. Consequently, MIXL1 expressing AML cells are preferentially sensitive to the BMPR1 kinase inhibitor LDN-193189. These findings support the existence of a novel MIXL1-c REL mediated survival axis in AML that can be targeted by BMPR1 inhibitors. (MIXL1- human gene, Mixl1- mouse ortholog, MIXL1- protein)
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Affiliation(s)
- Aaron Raymond
- Department of Genetics, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Graduate Program in Genes and Development, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bin Liu
- Department of Genetics, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Center for Cancer Genetics and Genomics, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hong Liang
- Department of Genetics, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Caimiao Wei
- Department of Biostatistics, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michele Guindani
- Department of Biostatistics, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yue Lu
- Dept. of Leukemia, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Dept. of Molecular Carcinogenesis, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shoudan Liang
- Dept. of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lisa S St John
- Section of Transplantation Immunology, Department of Stem Cell Transplantation and Cellular Therapy, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeff Molldrem
- Section of Transplantation Immunology, Department of Stem Cell Transplantation and Cellular Therapy, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lalitha Nagarajan
- Department of Genetics, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Graduate Program in Genes and Development, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Center for Cancer Genetics and Genomics, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Dept. of Leukemia, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Graduate Program in Human Molecular Genetics, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Center for Stem cell and Developmental biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Curto GG, Gard C, Ribes V. Structures and properties of PAX linked regulatory networks architecting and pacing the emergence of neuronal diversity. Semin Cell Dev Biol 2015; 44:75-86. [DOI: 10.1016/j.semcdb.2015.09.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 09/07/2015] [Accepted: 09/16/2015] [Indexed: 12/13/2022]
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Mayran A, Pelletier A, Drouin J. Pax factors in transcription and epigenetic remodelling. Semin Cell Dev Biol 2015; 44:135-44. [PMID: 26234816 DOI: 10.1016/j.semcdb.2015.07.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 07/22/2015] [Accepted: 07/24/2015] [Indexed: 11/25/2022]
Abstract
The nine Pax transcription factors that constitute the mammalian family of paired domain (PD) factors play key roles in many developmental processes. As DNA binding transcription factors, they exhibit tremendous variability and complexity in their DNA recognition patterns. This is ascribed to the presence of multiple DNA binding structural domains, namely helix-turn-helix (HTH) domains. The PD contains two HTH subdomains and four of the nine Pax factors have an additional HTH domain, the homeodomain (HD). We now review these diverse DNA binding modalities together with their properties as transcriptional activators and repressors. The action of Pax factors on gene expression is also exerted through recruitment of chromatin remodelling complexes that introduce either activating or repressive chromatin marks. Interestingly, the recent demonstration that Pax7 has pioneer activity, the unique property to "open" chromatin, further underlines the mechanistic versatility and the developmental importance of these factors.
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Affiliation(s)
- Alexandre Mayran
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Audrey Pelletier
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Jacques Drouin
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada.
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Abstract
Metastatic melanoma is an aggressive and deadly disease. The chemokine receptor CXCR4 is active in melanoma metastasis, although the mechanism for the promotion and maintenance of CXCR4 expression in these cells is mostly unknown. Here, we find melanoma cells express two CXCR4 isoforms, the common version and a variant that is normally restricted to cells during development or to mature blood cells. CXCR4 expression is driven through a highly conserved intronic enhancer element by the transcription factors PAX3 and FOXD3. Inhibition of these transcription factors slows melanoma cell growth, migration, and motility, as well as reduces CXCR4 expression. Overexpression of these transcription factors drives the production of increased CXCR4 levels. Loss of PAX3 and FOXD3 transcription factor activity results in a reduction in cell motility, migration, and chemotaxis, all of which are rescued by CXCR4 overexpression. Here, we discover a molecular pathway wherein PAX3 and FOXD3 promote CXCR4 gene expression in melanoma.
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Affiliation(s)
| | - Jason W Lui
- From the Department of Medicine, Section of Dermatology and
| | | | - Anton E Ludvik
- From the Department of Medicine, Section of Dermatology and
| | - Sasank Konda
- From the Department of Medicine, Section of Dermatology and
| | - Ravi Salgia
- Section of Hematology/Oncology, University of Chicago, Chicago, Illinois 60637 and
| | - Andrew E Aplin
- the Department of Cancer Biology and Kimmel Cancer Center, and Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Deborah Lang
- From the Department of Medicine, Section of Dermatology and
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34
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Manuel MN, Mi D, Mason JO, Price DJ. Regulation of cerebral cortical neurogenesis by the Pax6 transcription factor. Front Cell Neurosci 2015; 9:70. [PMID: 25805971 PMCID: PMC4354436 DOI: 10.3389/fncel.2015.00070] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/18/2015] [Indexed: 12/19/2022] Open
Abstract
Understanding brain development remains a major challenge at the heart of understanding what makes us human. The neocortex, in evolutionary terms the newest part of the cerebral cortex, is the seat of higher cognitive functions. Its normal development requires the production, positioning, and appropriate interconnection of very large numbers of both excitatory and inhibitory neurons. Pax6 is one of a relatively small group of transcription factors that exert high-level control of cortical development, and whose mutation or deletion from developing embryos causes major brain defects and a wide range of neurodevelopmental disorders. Pax6 is very highly conserved between primate and non-primate species, is expressed in a gradient throughout the developing cortex and is essential for normal corticogenesis. Our understanding of Pax6’s functions and the cellular processes that it regulates during mammalian cortical development has significantly advanced in the last decade, owing to the combined application of genetic and biochemical analyses. Here, we review the functional importance of Pax6 in regulating cortical progenitor proliferation, neurogenesis, and formation of cortical layers and highlight important differences between rodents and primates. We also review the pathological effects of PAX6 mutations in human neurodevelopmental disorders. We discuss some aspects of Pax6’s molecular actions including its own complex transcriptional regulation, the distinct molecular functions of its splice variants and some of Pax6’s known direct targets which mediate its actions during cortical development.
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Affiliation(s)
- Martine N Manuel
- Centre for Integrative Physiology, The University of Edinburgh, Edinburgh UK
| | - Da Mi
- Centre for Integrative Physiology, The University of Edinburgh, Edinburgh UK
| | - John O Mason
- Centre for Integrative Physiology, The University of Edinburgh, Edinburgh UK
| | - David J Price
- Centre for Integrative Physiology, The University of Edinburgh, Edinburgh UK
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35
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Chiu WT, Charney Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, Cho KWY. Genome-wide view of TGFβ/Foxh1 regulation of the early mesendoderm program. Development 2014; 141:4537-47. [PMID: 25359723 DOI: 10.1242/dev.107227] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Nodal/TGFβ signaling regulates diverse biological responses. By combining RNA-seq on Foxh1 and Nodal signaling loss-of-function embryos with ChIP-seq of Foxh1 and Smad2/3, we report a comprehensive genome-wide interaction between Foxh1 and Smad2/3 in mediating Nodal signaling during vertebrate mesendoderm development. This study significantly increases the total number of Nodal target genes regulated by Foxh1 and Smad2/3, and reinforces the notion that Foxh1-Smad2/3-mediated Nodal signaling directly coordinates the expression of a cohort of genes involved in the control of gene transcription, signaling pathway modulation and tissue morphogenesis during gastrulation. We also show that Foxh1 may function independently of Nodal signaling, in addition to its role as a transcription factor mediating Nodal signaling via Smad2/3. Finally, we propose an evolutionarily conserved interaction between Foxh1 and PouV, a mechanism observed in Pou5f1-mediated regulation of pluripotency in human embryonic stem and epiblast cells.
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Affiliation(s)
- William T Chiu
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697-2300, USA
| | - Rebekah Charney Le
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697-2300, USA
| | - Ira L Blitz
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697-2300, USA
| | - Margaret B Fish
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697-2300, USA
| | - Yi Li
- Department of Computer Science, University of California, Irvine, CA 92697-2300, USA
| | - Jacob Biesinger
- Department of Computer Science, University of California, Irvine, CA 92697-2300, USA
| | - Xiaohui Xie
- Department of Computer Science, University of California, Irvine, CA 92697-2300, USA
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697-2300, USA
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Monteiro CB, Costa MF, Reguenga C, Lima D, Castro DS, Monteiro FA. Paired related homeobox protein-like 1 (Prrxl1) controls its own expression by a transcriptional autorepression mechanism. FEBS Lett 2014; 588:3475-82. [PMID: 25131932 DOI: 10.1016/j.febslet.2014.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 07/21/2014] [Accepted: 08/08/2014] [Indexed: 10/24/2022]
Abstract
The homeodomain factor paired related homeobox protein-like 1 (Prrxl1) is crucial for proper assembly of dorsal root ganglia (DRG)-dorsal spinal cord (SC) pain-sensing circuit. By performing chromatin immunoprecipitation with either embryonic DRG or dorsal SC, we identified two evolutionarily conserved regions (i.e. proximal promoter and intron 4) of Prrxl1 locus that show tissue-specific binding of Prrxl1. Transcriptional assays confirm the identified regions can mediate repression by Prrxl1, while gain-of-function studies in Prrxl1 expressing ND7/23 cells indicate Prrxl1 can down-regulate its own expression. Altogether, our results suggest that Prrxl1 uses distinct regulatory regions to repress its own expression in DRG and dorsal SC.
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Affiliation(s)
- César B Monteiro
- Departamento de Biologia Experimental, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal; Morfofisiologia do Sistema Somatosensitivo, IBMC - Instituto de Biologia Celular e Molecular, 4150-180 Porto, Portugal.
| | - Mariana F Costa
- Departamento de Biologia Experimental, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal; Morfofisiologia do Sistema Somatosensitivo, IBMC - Instituto de Biologia Celular e Molecular, 4150-180 Porto, Portugal.
| | - Carlos Reguenga
- Departamento de Biologia Experimental, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal; Morfofisiologia do Sistema Somatosensitivo, IBMC - Instituto de Biologia Celular e Molecular, 4150-180 Porto, Portugal.
| | - Deolinda Lima
- Departamento de Biologia Experimental, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal; Morfofisiologia do Sistema Somatosensitivo, IBMC - Instituto de Biologia Celular e Molecular, 4150-180 Porto, Portugal.
| | - Diogo S Castro
- Molecular Neurobiology, IGC - Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal.
| | - Filipe A Monteiro
- Departamento de Biologia Experimental, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal; Morfofisiologia do Sistema Somatosensitivo, IBMC - Instituto de Biologia Celular e Molecular, 4150-180 Porto, Portugal.
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37
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Mahajan P, Leavey PJ, Galindo RL. PAX genes in childhood oncogenesis: developmental biology gone awry? Oncogene 2015; 34:2681-9. [PMID: 25043308 DOI: 10.1038/onc.2014.209] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 06/10/2014] [Accepted: 06/11/2014] [Indexed: 01/27/2023]
Abstract
Childhood solid tumors often arise from embryonal-like cells, which are distinct from the epithelial cancers observed in adults, and etiologically can be considered as 'developmental patterning gone awry'. Paired-box (PAX) genes encode a family of evolutionarily conserved transcription factors that are important regulators of cell lineage specification, migration and tissue patterning. PAX loss-of-function mutations are well known to cause potent developmental phenotypes in animal models and underlie genetic disease in humans, whereas dysregulation and/or genetic modification of PAX genes have been shown to function as critical triggers for human tumorigenesis. Consequently, exploring PAX-related pathobiology generates insights into both normal developmental biology and key molecular mechanisms that underlie pediatric cancer, which are the topics of this review.
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38
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Yasuoka Y, Suzuki Y, Takahashi S, Someya H, Sudou N, Haramoto Y, Cho KW, Asashima M, Sugano S, Taira M. Occupancy of tissue-specific cis-regulatory modules by Otx2 and TLE/Groucho for embryonic head specification. Nat Commun 2014; 5:4322. [PMID: 25005894 DOI: 10.1038/ncomms5322] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 06/06/2014] [Indexed: 12/11/2022] Open
Abstract
Head specification by the head-selector gene, orthodenticle (otx), is highly conserved among bilaterian lineages. However, the molecular mechanisms by which Otx and other transcription factors (TFs) interact with the genome to direct head formation are largely unknown. Here we employ ChIP-seq and RNA-seq approaches in Xenopus tropicalis gastrulae and find that occupancy of the corepressor, TLE/Groucho, is a better indicator of tissue-specific cis-regulatory modules (CRMs) than the coactivator p300, during early embryonic stages. On the basis of TLE binding and comprehensive CRM profiling, we define two distinct types of Otx2- and TLE-occupied CRMs. Using these devices, Otx2 and other head organizer TFs (for example, Lim1/Lhx1 (activator) or Goosecoid (repressor)) are able to upregulate or downregulate a large battery of target genes in the head organizer. An underlying principle is that Otx marks target genes for head specification to be regulated positively or negatively by partner TFs through specific types of CRMs.
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Xu X, Pulavarti SV, Eletsky A, Huang YJ, Acton TB, Xiao R, Everett JK, Montelione GT, Szyperski T. Solution NMR structures of homeodomains from human proteins ALX4, ZHX1, and CASP8AP2 contribute to the structural coverage of the Human Cancer Protein Interaction Network. J Struct Funct Genomics 2014; 15:201-7. [PMID: 24941917 DOI: 10.1007/s10969-014-9184-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 06/10/2014] [Indexed: 10/25/2022]
Abstract
High-quality solution NMR structures of three homeodomains from human proteins ALX4, ZHX1 and CASP8AP2 were solved. These domains were chosen as targets of a biomedical theme project pursued by the Northeast Structural Genomics Consortium. This project focuses on increasing the structural coverage of human proteins associated with cancer.
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40
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Aza-Carmona M, Barca-Tierno V, Hisado-Oliva A, Belinchón A, Gorbenko-del Blanco D, Rodriguez JI, Benito-Sanz S, Campos-Barros A, Heath KE. NPPB and ACAN, two novel SHOX2 transcription targets implicated in skeletal development. PLoS One 2014; 9:e83104. [PMID: 24421874 PMCID: PMC3885427 DOI: 10.1371/journal.pone.0083104] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 10/30/2013] [Indexed: 11/18/2022] Open
Abstract
SHOX and SHOX2 transcription factors are highly homologous, with even identical homeodomains. Genetic alterations in SHOX result in two skeletal dysplasias; Léri-Weill dyschondrosteosis (LWD) and Langer mesomelic dysplasia (LMD), while no human genetic disease has been linked to date with SHOX2. SHOX2 is, though, involved in skeletal development, as shown by different knockout mice models. Due to the high homology between SHOX and SHOX2, and their functional redundancy during heart development, we postulated that SHOX2 might have the same transcriptional targets and cofactors as SHOX in limb development. We selected two SHOX transcription targets regulated by different mechanisms: 1) the natriuretic peptide precursor B gene (NPPB) involved in the endochondral ossification signalling and directly activated by SHOX; and 2) Aggrecan (ACAN), a major component of cartilage extracellular matrix, regulated by the cooperation of SHOX with the SOX trio (SOX5, SOX6 and SOX9) via the protein interaction between SOX5/SOX6 and SHOX. Using the luciferase assay we have demonstrated that SHOX2, like SHOX, regulates NPPB directly whilst activates ACAN via its cooperation with the SOX trio. Subsequently, we have identified and characterized the protein domains implicated in the SHOX2 dimerization and also its protein interaction with SOX5/SOX6 and SHOX using the yeast-two hybrid and co-immunoprecipitation assays. Immunohistochemistry of human fetal growth plates from different time points demonstrated that SHOX2 is coexpressed with SHOX and the members of the SOX trio. Despite these findings, no mutation was identified in SHOX2 in a cohort of 83 LWD patients with no known molecular defect, suggesting that SHOX2 alterations do not cause LWD. In conclusion, our work has identified the first cofactors and two new transcription targets of SHOX2 in limb development, and we hypothesize a time- and tissue-specific functional redundancy between SHOX and SHOX2.
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Affiliation(s)
- Miriam Aza-Carmona
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
- Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto Carlos III, Madrid, Spain
| | - Veronica Barca-Tierno
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
- Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto Carlos III, Madrid, Spain
| | - Alfonso Hisado-Oliva
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
- Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto Carlos III, Madrid, Spain
| | - Alberta Belinchón
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
- Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto Carlos III, Madrid, Spain
| | - Darya Gorbenko-del Blanco
- Dept. Celular Biology, Immunology & Neurosciences, Facultad de Medicina, Universidad de Barcelona, Barcelona, Spain
| | | | - Sara Benito-Sanz
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
- Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto Carlos III, Madrid, Spain
| | - Angel Campos-Barros
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
- Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto Carlos III, Madrid, Spain
| | - Karen E. Heath
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
- Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto Carlos III, Madrid, Spain
- * E-mail:
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Regadas I, Matos MR, Monteiro FA, Gómez-Skarmeta JL, Lima D, Bessa J, Casares F, Reguenga C. Several cis-regulatory elements control mRNA stability, translation efficiency, and expression pattern of Prrxl1 (paired related homeobox protein-like 1). J Biol Chem 2013; 288:36285-301. [PMID: 24214975 DOI: 10.1074/jbc.m113.491993] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The homeodomain transcription factor Prrxl1/DRG11 has emerged as a crucial molecule in the establishment of the pain circuitry, in particular spinal cord targeting of dorsal root ganglia (DRG) axons and differentiation of nociceptive glutamatergic spinal cord neurons. Despite Prrxl1 importance in the establishment of the DRG-spinal nociceptive circuit, the molecular mechanisms that regulate its expression along development remain largely unknown. Here, we show that Prrxl1 transcription is regulated by three alternative promoters (named P1, P2, and P3), which control the expression of three distinct Prrxl1 5'-UTR variants, named 5'-UTR-A, 5'-UTR-B, and 5'-UTR-C. These 5'-UTR sequences confer distinct mRNA stability and translation efficiency to the Prrxl1 transcript. The most conserved promoter (P3) contains a TATA-box and displays in vivo enhancer activity in a pattern that overlaps with the zebrafish Prrxl1 homologue, drgx. Regulatory modules present in this sequence were identified and characterized, including a binding site for Phox2b. Concomitantly, we demonstrate that zebrafish Phox2b is required for the expression of drgx in the facial, glossopharyngeal, and vagal cranial ganglia.
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Affiliation(s)
- Isabel Regadas
- From the Departamento de Biologia Experimental, Faculdade de Medicina do Porto, Universidade do Porto, Porto 4200-319, Portugal
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Colasante G, Simonet JC, Calogero R, Crispi S, Sessa A, Cho G, Golden JA, Broccoli V. ARX regulates cortical intermediate progenitor cell expansion and upper layer neuron formation through repression of Cdkn1c. ACTA ACUST UNITED AC 2013; 25:322-35. [PMID: 23968833 DOI: 10.1093/cercor/bht222] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mutations in the Aristaless-related homeobox (ARX) gene are found in a spectrum of epilepsy and X-linked intellectual disability disorders. During development Arx is expressed in pallial ventricular zone (VZ) progenitor cells where the excitatory projection neurons of the cortex are born. Arx(-/Y) mice were shown to have decreased proliferation in the cortical VZ resulting in smaller brains; however, the basis for this reduced proliferation was not established. To determine the role of ARX on cell cycle dynamics in cortical progenitor cells, we generated cerebral cortex-specific Arx mouse mutants (cKO). The loss of pallial Arx resulted in the reduction of cortical progenitor cells, particularly the proliferation of intermediate progenitor cells (IPCs) was affected. Later in development and postnatally cKO brains showed a reduction of upper layer but not deeper layer neurons consistent with the IPC defect. Transcriptional profile analysis of E14.5 Arx-ablated cortices compared with control revealed that CDKN1C, an inhibitor of cell cycle progression, is overexpressed in the cortical VZ and SVZ of Arx KOs throughout corticogenesis. We also identified ARX as a direct regulator of Cdkn1c transcription. Together these data support a model where ARX regulates the expansion of cortical progenitor cells through repression of Cdkn1c.
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Affiliation(s)
- Gaia Colasante
- Department of Neuroscience, San Raffaele Scientific Institute, Milan 20132, Italy
| | - Jacqueline C Simonet
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raffaele Calogero
- Bioinformatics and Genomics Unit, MBC Centro di Biotecnologie Molecolari, Turin, Italy
| | - Stefania Crispi
- Institute of Genetics and Byophisics "A. B. T" CNR, Naples 80131, Italy and
| | - Alessandro Sessa
- Department of Neuroscience, San Raffaele Scientific Institute, Milan 20132, Italy
| | - Ginam Cho
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jeffrey A Golden
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Vania Broccoli
- Department of Neuroscience, San Raffaele Scientific Institute, Milan 20132, Italy
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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 DOI: 10.1007/s00018-013-1305-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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
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44
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Poeta L, Fusco F, Drongitis D, Shoubridge C, Manganelli G, Filosa S, Paciolla M, Courtney M, Collombat P, Lioi M, Gecz J, Ursini M, Miano M. A regulatory path associated with X-linked intellectual disability and epilepsy links KDM5C to the polyalanine expansions in ARX. Am J Hum Genet 2013; 92:114-25. [PMID: 23246292 DOI: 10.1016/j.ajhg.2012.11.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 06/07/2012] [Accepted: 11/13/2012] [Indexed: 10/27/2022] Open
Abstract
Intellectual disability (ID) and epilepsy often occur together and have a dramatic impact on the development and quality of life of the affected children. Polyalanine (polyA)-expansion-encoding mutations of aristaless-related homeobox (ARX) cause a spectrum of X-linked ID (XLID) diseases and chronic epilepsy, including infantile spasms. We show that lysine-specific demethylase 5C (KDM5C), a gene known to be mutated in XLID-affected children and involved in chromatin remodeling, is directly regulated by ARX through the binding in a conserved noncoding element. We have studied altered ARX carrying various polyA elongations in individuals with XLID and/or epilepsy. The changes in polyA repeats cause hypomorphic ARX alterations, which exhibit a decreased trans-activity and reduced, but not abolished, binding to the KDM5C regulatory region. The altered functioning of the mutants tested is likely to correlate with the severity of XLID and/or epilepsy. By quantitative RT-PCR, we observed a dramatic Kdm5c mRNA downregulation in murine Arx-knockout embryonic and neural stem cells. Such Kdm5c mRNA diminution led to a severe decrease in the KDM5C content during in vitro neuronal differentiation, which inversely correlated with an increase in H3K4me3 signal. We established that ARX polyA alterations damage the regulation of KDM5C expression, and we propose a potential ARX-dependent path acting via chromatin remodeling.
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Abstract
The understanding of cardiovascular development has begun a transformation from the descriptive science of anatomy and embryology to a molecular understanding of the cellular and subcellular events leading to proper cardiac morphogenesis. Powerful tools available to molecular geneticists have identified numerous examples of specific gene defects that result in predictable cardiovascular abnormalities. Not only have certain genes been "knocked out" (mutated by homologous recombination in embryonic stem cells), but also single gene defects have been found to underlie the cardiovascular derangements observed in certain inbred mouse lines. Such is the case for the mouse mutant Splotch, which was first described in 1954 as a spontaneously occurring mutation resulting in a white belly spot. More recently, the genetic defect of all of the various Splotch alleles has been found to be due to mutations or deletions of a gene called Pax-3. In the homozygous state, these mutations result in embryonic lethality at about day 13.5 of mouse embryogenesis (E13.5). These embryos display abnormalities strikingly reminiscent of human DiGeorge syndrome. These include outflow tract abnormalities of the heart, such as double-outlet right ventricle (DORV) and persistent truncus arteriosus (PTA), as well as abnormalities of the great vessels and the thyroid and parathyroid glands. These defects suggest an underlying abnormality of neural crest, including its contribution to the cardiovascular system. © 1996, Elsevier Science Inc. (Trends Cardiovasc Med 1996;6:255-261).
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Affiliation(s)
- J A Epstein
- Jonathan A. Epstein is at the Division of Cardiology, Hospital of the University of Pennsylvania,Philadelphia, PA 19104,USA
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Bulut-karslioglu A, Perrera V, Scaranaro M, de la Rosa-velazquez IA, van de Nobelen S, Shukeir N, Popow J, Gerle B, Opravil S, Pagani M, Meidhof S, Brabletz T, Manke T, Lachner M, Jenuwein T. A transcription factor–based mechanism for mouse heterochromatin formation. Nat Struct Mol Biol 2012; 19:1023-30. [PMID: 22983563 DOI: 10.1038/nsmb.2382] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 08/15/2012] [Indexed: 12/22/2022]
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Pereira LA, Wong MS, Mei Lim S, Stanley EG, Elefanty AG. The Mix family of homeobox genes—Key regulators of mesendoderm formation during vertebrate development. Dev Biol 2012; 367:163-77. [DOI: 10.1016/j.ydbio.2012.04.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 04/24/2012] [Accepted: 04/30/2012] [Indexed: 10/28/2022]
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Soleimani VD, Punch VG, Kawabe YI, Jones AE, Palidwor GA, Porter CJ, Cross JW, Carvajal JJ, Kockx CEM, van IJcken WFJ, Perkins TJ, Rigby PWJ, Grosveld F, Rudnicki MA. Transcriptional dominance of Pax7 in adult myogenesis is due to high-affinity recognition of homeodomain motifs. Dev Cell 2012; 22:1208-20. [PMID: 22609161 DOI: 10.1016/j.devcel.2012.03.014] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 01/20/2012] [Accepted: 03/28/2012] [Indexed: 01/08/2023]
Abstract
Pax3 and Pax7 regulate stem cell function in skeletal myogenesis. However, molecular insight into their distinct roles has remained elusive. Using gene expression data combined with genome-wide binding-site analysis, we show that both Pax3 and Pax7 bind identical DNA motifs and jointly activate a large panel of genes involved in muscle stem cell function. Surprisingly, in adult myoblasts Pax3 binds a subset (6.4%) of Pax7 targets. Despite a significant overlap in their transcriptional network, Pax7 regulates distinct panels of genes involved in the promotion of proliferation and inhibition of myogenic differentiation. We show that Pax7 has a higher binding affinity to the homeodomain-binding motif relative to Pax3, suggesting that intrinsic differences in DNA binding contribute to the observed functional difference between Pax3 and Pax7 binding in myogenesis. Together, our data demonstrate distinct attributes of Pax7 function and provide mechanistic insight into the nonredundancy of Pax3 and Pax7 in muscle development.
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Affiliation(s)
- Vahab D Soleimani
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, and Department of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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Shaham O, Menuchin Y, Farhy C, Ashery-Padan R. Pax6: a multi-level regulator of ocular development. Prog Retin Eye Res 2012; 31:351-76. [PMID: 22561546 DOI: 10.1016/j.preteyeres.2012.04.002] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 04/19/2012] [Accepted: 04/24/2012] [Indexed: 02/08/2023]
Abstract
Eye development has been a paradigm for the study of organogenesis, from the demonstration of lens induction through epithelial tissue morphogenesis, to neuronal specification and differentiation. The transcription factor Pax6 has been shown to play a key role in each of these processes. Pax6 is required for initiation of developmental pathways, patterning of epithelial tissues, activation of tissue-specific genes and interaction with other regulatory pathways. Herein we examine the data accumulated over the last few decades from extensive analyses of biochemical modules and genetic manipulation of the Pax6 gene. Specifically, we describe the regulation of Pax6's expression pattern, the protein's DNA-binding properties, and its specific roles and mechanisms of action at all stages of lens and retinal development. Pax6 functions at multiple levels to integrate extracellular information and execute cell-intrinsic differentiation programs that culminate in the specification and differentiation of a distinct ocular lineage.
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Affiliation(s)
- Ohad Shaham
- Sackler Faculty of Medicine, Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
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Shukla S, Mishra R. Predictions on impact of missense mutations on structure function relationship of PAX6 and its alternatively spliced isoform PAX6(5a). Interdiscip Sci 2012; 4:54-73. [PMID: 22392277 DOI: 10.1007/s12539-012-0114-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 04/11/2011] [Accepted: 05/17/2011] [Indexed: 05/31/2023]
Abstract
The PAX6 contains two DNA-binding domains, paired domain (PD), homeodomain (HD), and a transactivation domain (TD). Only the crystal structure of PD and the solution structure of HD of PAX6 are known. Mutations in PAX6 show variable penetrance, and expressivity of ocular and neural diseases, but the mechanism is poorly understood. Its alternatively spliced isoform PAX6(5a), is also required in a specific ratio for optimal functions. To understand impact of missense mutations on stability, and conformation of PAX6, whose functional analyses are described in PAX6 allelic variant database, were considered. Representative mutations like PAX6-L46R, -C52R, -V126D, -R128C, -R242T, -P375Q, -Q422R, -V256E, and -S259P from PD, HD, and TD of PAX6 were explored. The secondary structures were analyzed through PSIPRED, and relative solvent accessibilities (RSA) of the mutant and the wild type amino acid residues were compared through SABLE. The change in the contact residues and calculations of energy level were studied through SVMcon, MUpro, and FoldX, respectively. The 3D modeling was performed with the help of MODELLER and models were visualized in Chimera. Predictions suggest mutation induced alterations in local conformation or misfolding in DNA-binding domains of PAX6 and PAX6(5a). The predicted impact of mutations via secondary structure, changes in free energy, stability, conformation, and experimental reports on DNA-binding and transactivation, necessarily provides a strong background to explain structure-function relationship of PAX6 and PAX6(5a). However, because of their predictive nature, these findings need to be validated with other experimental evidences when structure of full length PAX6 is available.
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Affiliation(s)
- Sachin Shukla
- Department of Zoology, Banaras Hindu University, Varanasi, 221005, India
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