1
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Nguyen TT, Mitchell JM, Kiel MD, Kenny CP, Li H, Jones KL, Cornell RA, Williams TJ, Nichols JT, Van Otterloo E. TFAP2 paralogs regulate midfacial development in part through a conserved ALX genetic pathway. Development 2024; 151:dev202095. [PMID: 38063857 PMCID: PMC10820886 DOI: 10.1242/dev.202095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023]
Abstract
Cranial neural crest development is governed by positional gene regulatory networks (GRNs). Fine-tuning of the GRN components underlies facial shape variation, yet how those networks in the midface are connected and activated remain poorly understood. Here, we show that concerted inactivation of Tfap2a and Tfap2b in the murine neural crest, even during the late migratory phase, results in a midfacial cleft and skeletal abnormalities. Bulk and single-cell RNA-seq profiling reveal that loss of both TFAP2 family members dysregulates numerous midface GRN components involved in midface morphogenesis, patterning and differentiation. Notably, Alx1, Alx3 and Alx4 (ALX) transcript levels are reduced, whereas ChIP-seq analyses suggest TFAP2 family members directly and positively regulate ALX gene expression. Tfap2a, Tfap2b and ALX co-expression in midfacial neural crest cells of both mouse and zebrafish implies conservation of this regulatory axis across vertebrates. Consistent with this notion, tfap2a zebrafish mutants present with abnormal alx3 expression patterns, Tfap2a binds ALX loci and tfap2a-alx3 genetic interactions are observed. Together, these data demonstrate TFAP2 paralogs regulate vertebrate midfacial development in part by activating expression of ALX transcription factor genes.
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Affiliation(s)
- Timothy T. Nguyen
- Iowa Institute for Oral Health Research, College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA 52242, USA
- Department of Periodontics, College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA 52242, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA
| | - Jennyfer M. Mitchell
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michaela D. Kiel
- Iowa Institute for Oral Health Research, College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA 52242, USA
- Department of Periodontics, College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA 52242, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Colin P. Kenny
- Department of Surgery, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Hong Li
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kenneth L. Jones
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO 80045, USA
| | - Robert A. Cornell
- Department of Oral Health Sciences, University of Washington, School of Dentistry, Seattle, WA 98195, USA
| | - Trevor J. Williams
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO 80045, USA
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - James T. Nichols
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Eric Van Otterloo
- Iowa Institute for Oral Health Research, College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA 52242, USA
- Department of Periodontics, College of Dentistry and Dental Clinics, University of Iowa, Iowa City, IA 52242, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA
- Craniofacial Anomalies Research Center, University of Iowa, Iowa City, IA 52242, USA
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2
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Nguyen TT, Mitchell JM, Kiel MD, Jones KL, Williams TJ, Nichols JT, Van Otterloo E. TFAP2 paralogs regulate midfacial development in part through a conserved ALX genetic pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545376. [PMID: 37398373 PMCID: PMC10312788 DOI: 10.1101/2023.06.16.545376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Cranial neural crest development is governed by positional gene regulatory networks (GRNs). Fine-tuning of the GRN components underly facial shape variation, yet how those in the midface are connected and activated remain poorly understood. Here, we show that concerted inactivation of Tfap2a and Tfap2b in the murine neural crest even during the late migratory phase results in a midfacial cleft and skeletal abnormalities. Bulk and single-cell RNA-seq profiling reveal that loss of both Tfap2 members dysregulated numerous midface GRN components involved in midface fusion, patterning, and differentiation. Notably, Alx1/3/4 (Alx) transcript levels are reduced, while ChIP-seq analyses suggest TFAP2 directly and positively regulates Alx gene expression. TFAP2 and ALX co-expression in midfacial neural crest cells of both mouse and zebrafish further implies conservation of this regulatory axis across vertebrates. Consistent with this notion, tfap2a mutant zebrafish present abnormal alx3 expression patterns, and the two genes display a genetic interaction in this species. Together, these data demonstrate a critical role for TFAP2 in regulating vertebrate midfacial development in part through ALX transcription factor gene expression.
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Affiliation(s)
- Timothy T Nguyen
- Iowa Institute for Oral Health Research, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Periodontics, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52242, USA
| | - Jennyfer M Mitchell
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michaela D Kiel
- Iowa Institute for Oral Health Research, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Periodontics, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Kenneth L Jones
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children’s Hospital Colorado, Aurora, CO 80045, USA
| | - Trevor J Williams
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children’s Hospital Colorado, Aurora, CO 80045, USA
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - James T Nichols
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Eric Van Otterloo
- Iowa Institute for Oral Health Research, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Periodontics, College of Dentistry & Dental Clinics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52242, USA
- Craniofacial Anomalies Research Center, University of Iowa, Iowa City, IA, 52242, USA
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3
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Fabian P, Crump JG. Reassessing the embryonic origin and potential of craniofacial ectomesenchyme. Semin Cell Dev Biol 2023; 138:45-53. [PMID: 35331627 PMCID: PMC9489819 DOI: 10.1016/j.semcdb.2022.03.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/28/2022] [Accepted: 03/14/2022] [Indexed: 11/27/2022]
Abstract
Of all the cell types arising from the neural crest, ectomesenchyme is likely the most unusual. In contrast to the neuroglial cells generated by neural crest throughout the embryo, consistent with its ectodermal origin, cranial neural crest-derived cells (CNCCs) generate many connective tissue and skeletal cell types in common with mesoderm. Whether this ectoderm-derived mesenchyme (ectomesenchyme) potential reflects a distinct developmental origin from other CNCC lineages, and/or epigenetic reprogramming of the ectoderm, remains debated. Whereas decades of lineage tracing studies have defined the potential of CNCC ectomesenchyme, these are being revisited by modern genetic techniques. Recent work is also shedding light on the extent to which intrinsic and extrinsic cues determine ectomesenchyme potential, and whether maintenance or reacquisition of CNCC multipotency influences craniofacial repair.
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Affiliation(s)
- Peter Fabian
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - J Gage Crump
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA.
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4
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Vetrivel S, Truong DJJ, Wurst W, Graw J, Giesert F. Identification of ocular regulatory functions of core histone variant H3.2. Exp Eye Res 2023; 226:109346. [PMID: 36529279 DOI: 10.1016/j.exer.2022.109346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/05/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
The posttranscriptional modifications (PTM) of the Histone H3 family play an important role in ocular system differentiation. However, there has been no study on the nature of specific Histone H3 subtype carrying these modifications. Fortuitously, we had previously identified a dominant small-eye mutant Aey69 mouse with a mutation in the H3.2 encoding Hist2h3c1 gene (Vetrivel et al., 2019). In continuation, in the present study, the role of Histone H3.2 with relation to the microphtalmic Aey69 has been elaborated. Foremost, a transgenic mouse line expressing the fusion protein H3.2-GFP was generated using Crispr/Cas9. The approach was intended to confer a unique tag to the Hist2h3c1 gene which is similar in sequence and encoded protein structure to other histones. The GFP tag was then used for ChIP Seq analysis of the genes regulated by H3.2. The approach revealed ocular specific H3.2 targets including Ephrin family genes. Altered enrichment of H3.2 was found in the mutant Aey69 mouse, specifically around the ligand Efna5 and the receptor Ephb2. The effect of this altered enrichment on Ephrin signaling was further analysed by QPCR and immunohistochemistry. This study identifies Hist2h3c1 encoded H3.2 as an important epigenetic player in ocular development. By binding to specific regions of ocular developmental factors Histone H3.2 facilitates the function of these genes for successful early ocular development.
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Affiliation(s)
- Sharmilee Vetrivel
- Department of Endocrinology, Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-University, Munich, Germany.
| | - Dong-Jiunn Jeffery Truong
- Institute of Developmental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, D-85764, Neuherberg, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, D-85764, Neuherberg, Germany
| | - Jochen Graw
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Florian Giesert
- Institute of Developmental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, D-85764, Neuherberg, Germany.
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5
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Okeke C, Paulding D, Riedel A, Paudel S, Phelan C, Teng CS, Barske L. Control of cranial ectomesenchyme fate by Nr2f nuclear receptors. Development 2022; 149:dev201133. [PMID: 36367707 PMCID: PMC10114104 DOI: 10.1242/dev.201133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022]
Abstract
Certain cranial neural crest cells are uniquely endowed with the ability to make skeletal cell types otherwise only derived from mesoderm. As these cells migrate into the pharyngeal arches, they downregulate neural crest specifier genes and upregulate so-called ectomesenchyme genes that are characteristic of skeletal progenitors. Although both external and intrinsic factors have been proposed as triggers of this transition, the details remain obscure. Here, we report the Nr2f nuclear receptors as intrinsic activators of the ectomesenchyme program: zebrafish nr2f5 single and nr2f2;nr2f5 double mutants show marked delays in upregulation of ectomesenchyme genes, such as dlx2a, prrx1a, prrx1b, sox9a, twist1a and fli1a, and in downregulation of sox10, which is normally restricted to early neural crest and non-ectomesenchyme lineages. Mutation of sox10 fully rescued skeletal development in nr2f5 single but not nr2f2;nr2f5 double mutants, but the initial ectomesenchyme delay persisted in both. Sox10 perdurance thus antagonizes the recovery but does not explain the impaired ectomesenchyme transition. Unraveling the mechanisms of Nr2f function will help solve the enduring puzzle of how cranial neural crest cells transition to the skeletal progenitor state.
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Affiliation(s)
- Chukwuebuka Okeke
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - David Paulding
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Alexa Riedel
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Sandhya Paudel
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Conrad Phelan
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Camilla S. Teng
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Lindsey Barske
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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6
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Ash2l, an obligatory component of H3K4 methylation complexes, regulates neural crest development. Dev Biol 2022; 492:14-24. [PMID: 36162552 DOI: 10.1016/j.ydbio.2022.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/29/2022] [Accepted: 09/20/2022] [Indexed: 02/05/2023]
Abstract
The vertebrate nervous system develops from embryonic neural plate and neural crest. Although genetic mechanisms governing vertebrate neural development have been investigated in depth, epigenetic regulation of this process remains less understood. Redundancy of epigenetic factors and early lethality of animals deficient in critical epigenetic components pose major challenges in characterization of epigenetic factors in vertebrate neural development. In this study, we use the amphibian model Xenopus laevis to investigate the roles of non-redundant, obligatory components of all histone H3K4 activating methylation complexes (COMPASS, also known as SET1/MLL complexes) in early neural development. The two genes that we focus on, Ash2l and Dpy30, regulate mesendodermal differentiation in mouse embryonic stem cells and cause early embryonic lethality when removed from mouse embryos. Using targeted knockdown of the genes in dorsal ectoderm of Xenopus that gives rise to future nervous system, we show here that ash2l and dpy30 are required for neural and neural crest marker expression in Xenopus late neurula embryos but are dispensable for early neural and neural plate border gene expression. Co-immunoprecipitation assays reveal that Dpy30 and Ash2L associate with the neural plate border transcription factors, such as Msx1 and Tfap2a. Chromatin immunoprecipitation (ChIP) assay further demonstrates that Ash2L and the H3K4me3 active histone mark accumulate at the promoter regions of the neural crest gene sox10 in a Tfap2a-dependent manner. Collectively, our data suggest that Ash2l and Dpy30 interact with specific transcription factors to recruit COMPASS complexes to the regulatory regions of neural crest specification genes to control their expression and influence development of the nervous system during vertebrate embryogenesis.
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7
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Postmitotic accumulation of histone variant H3.3 in new cortical neurons establishes neuronal chromatin, transcriptome, and identity. Proc Natl Acad Sci U S A 2022; 119:e2116956119. [PMID: 35930666 PMCID: PMC9371731 DOI: 10.1073/pnas.2116956119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Histone variants, which can be expressed outside of S-phase and deposited DNA synthesis-independently, provide long-term histone replacement in postmitotic cells, including neurons. Beyond replenishment, histone variants also play active roles in gene regulation by modulating chromatin states or enabling nucleosome turnover. Here, we uncover crucial roles for the histone H3 variant H3.3 in neuronal development. We find that newborn cortical excitatory neurons, which have only just completed replication-coupled deposition of canonical H3.1 and H3.2, substantially accumulate H3.3 immediately postmitosis. Codeletion of H3.3-encoding genes H3f3a and H3f3b from newly postmitotic neurons abrogates H3.3 accumulation, markedly alters the histone posttranslational modification landscape, and causes widespread disruptions to the establishment of the neuronal transcriptome. These changes coincide with developmental phenotypes in neuronal identities and axon projections. Thus, preexisting, replication-dependent histones are insufficient for establishing neuronal chromatin and transcriptome; de novo H3.3 is required. Stage-dependent deletion of H3f3a and H3f3b from 1) cycling neural progenitor cells, 2) neurons immediately postmitosis, or 3) several days later, reveals the first postmitotic days to be a critical window for de novo H3.3. After H3.3 accumulation within this developmental window, codeletion of H3f3a and H3f3b does not lead to immediate H3.3 loss, but causes progressive H3.3 depletion over several months without widespread transcriptional disruptions or cellular phenotypes. Our study thus uncovers key developmental roles for de novo H3.3 in establishing neuronal chromatin, transcriptome, identity, and connectivity immediately postmitosis that are distinct from its role in maintaining total histone H3 levels over the neuronal lifespan.
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8
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Candido-Ferreira IL, Lukoseviciute M, Sauka-Spengler T. Multi-layered transcriptional control of cranial neural crest development. Semin Cell Dev Biol 2022; 138:1-14. [PMID: 35941042 DOI: 10.1016/j.semcdb.2022.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 07/23/2022] [Accepted: 07/23/2022] [Indexed: 11/28/2022]
Abstract
The neural crest (NC) is an emblematic population of embryonic stem-like cells with remarkable migratory ability. These distinctive attributes have inspired the curiosity of developmental biologists for over 150 years, however only recently the regulatory mechanisms controlling the complex features of the NC have started to become elucidated at genomic scales. Regulatory control of NC development is achieved through combinatorial transcription factor binding and recruitment of associated transcriptional complexes to distal cis-regulatory elements. Together, they regulate when, where and to what extent transcriptional programmes are actively deployed, ultimately shaping ontogenetic processes. Here, we discuss how transcriptional networks control NC ontogeny, with a special emphasis on the molecular mechanisms underlying specification of the cephalic NC. We also cover emerging properties of transcriptional regulation revealed in diverse developmental systems, such as the role of three-dimensional conformation of chromatin, and how they are involved in the regulation of NC ontogeny. Finally, we highlight how advances in deciphering the NC transcriptional network have afforded new insights into the molecular basis of human diseases.
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Affiliation(s)
- Ivan L Candido-Ferreira
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Martyna Lukoseviciute
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Tatjana Sauka-Spengler
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK.
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9
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Kori Y, Lund PJ, Trovato M, Sidoli S, Yuan ZF, Noh KM, Garcia BA. Multi-omic profiling of histone variant H3.3 lysine 27 methylation reveals a distinct role from canonical H3 in stem cell differentiation. Mol Omics 2022; 18:296-314. [PMID: 35044400 PMCID: PMC9098674 DOI: 10.1039/d1mo00352f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Histone variants, such as histone H3.3, replace canonical histones within the nucleosome to alter chromatin accessibility and gene expression. Although the biological roles of selected histone post-translational modifications (PTMs) have been extensively characterized, the potential differences in the function of a given PTM on different histone variants is almost always elusive. By applying proteomics and genomics techniques, we investigate the role of lysine 27 tri-methylation specifically on the histone variant H3.3 (H3.3K27me3) in the context of mouse embryonic stem cell pluripotency and differentiation as a model system for development. We demonstrate that while the steady state overall levels of methylation on both H3K27 and H3.3K27 decrease during differentiation, methylation dynamics studies indicate that methylation on H3.3K27 is maintained more than on H3K27. Using a custom-made antibody, we identify a unique enrichment of H3.3K27me3 at lineage-specific genes, such as olfactory receptor genes, and at binding motifs for the transcription factors FOXJ2/3. REST, a predicted FOXJ2/3 target that acts as a transcriptional repressor of terminal neuronal genes, was identified with H3.3K27me3 at its promoter region. H3.3K27A mutant cells confirmed an upregulation of FOXJ2/3 targets upon the loss of methylation at H3.3K27. Thus, while canonical H3K27me3 has been characterized to regulate the expression of transcription factors that play a general role in differentiation, our work suggests H3.3K27me3 is essential for regulating distinct terminal differentiation genes. This work highlights the importance of understanding the effects of PTMs not only on canonical histones but also on specific histone variants, as they may exhibit distinct roles.
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Affiliation(s)
- Yekaterina Kori
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peder J Lund
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
| | - Matteo Trovato
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.,Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Zuo-Fei Yuan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kyung-Min Noh
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
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10
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Histone modifications in neurodifferentiation of embryonic stem cells. Heliyon 2022; 8:e08664. [PMID: 35028451 PMCID: PMC8741459 DOI: 10.1016/j.heliyon.2021.e08664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/25/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022] Open
Abstract
Post-translational modifications of histone proteins regulate a long cascade of downstream cellular activities, including transcription and replication. Cellular lineage differentiation involves large-scale intracellular signaling and extracellular context. In particular, histone modifications play instructive and programmatic roles in central nervous system development. Deciphering functions of histone could offer feasible molecular strategies for neural diseases caused by histone modifications. Here, we review recent advances of in vitro and in vivo studies on histone modifications in neural differentiation.
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11
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Choe CP, Choi SY, Kee Y, Kim MJ, Kim SH, Lee Y, Park HC, Ro H. Transgenic fluorescent zebrafish lines that have revolutionized biomedical research. Lab Anim Res 2021; 37:26. [PMID: 34496973 PMCID: PMC8424172 DOI: 10.1186/s42826-021-00103-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/26/2021] [Indexed: 12/22/2022] Open
Abstract
Since its debut in the biomedical research fields in 1981, zebrafish have been used as a vertebrate model organism in more than 40,000 biomedical research studies. Especially useful are zebrafish lines expressing fluorescent proteins in a molecule, intracellular organelle, cell or tissue specific manner because they allow the visualization and tracking of molecules, intracellular organelles, cells or tissues of interest in real time and in vivo. In this review, we summarize representative transgenic fluorescent zebrafish lines that have revolutionized biomedical research on signal transduction, the craniofacial skeletal system, the hematopoietic system, the nervous system, the urogenital system, the digestive system and intracellular organelles.
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Affiliation(s)
- Chong Pyo Choe
- Division of Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea.,Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Seok-Yong Choi
- Department of Biomedical Sciences, Chonnam National University Medical School, Hwasun, 58128, Republic of Korea
| | - Yun Kee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
| | - Min Jung Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Seok-Hyung Kim
- Department of Marine Life Sciences and Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea
| | - Yoonsung Lee
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Hae-Chul Park
- Department of Biomedical Sciences, College of Medicine, Korea University, Ansan, 15355, Republic of Korea
| | - Hyunju Ro
- Department of Biological Sciences, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
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12
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Farmer DT, Patel P, Choi R, Liu CY, Crump JG. A comprehensive series of Irx cluster mutants reveals diverse roles in facial cartilage development. Development 2021; 148:271157. [PMID: 34338288 DOI: 10.1242/dev.197244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 07/21/2021] [Indexed: 12/28/2022]
Abstract
Proper function of the vertebrate skeleton requires the development of distinct articulating embryonic cartilages. Irx transcription factors are arranged in co-regulated clusters that are expressed in the developing skeletons of the face and appendages. IrxB cluster genes are required for the separation of toes in mice and formation of the hyoid joint in zebrafish, yet whether Irx genes have broader roles in skeletal development remains unclear. Here, we perform a comprehensive loss-of-function analysis of all 11 Irx genes in zebrafish. We uncover conserved requirements for IrxB genes in formation of the fish and mouse scapula. In the face, we find a requirement for IrxAb genes and irx7 in formation of anterior neural crest precursors of the jaw, and for IrxBa genes in formation of endodermal pouches and gill cartilages. We also observe extensive joint loss and cartilage fusions in animals with combinatorial losses of Irx clusters, with in vivo imaging revealing that at least some of these fusions arise through inappropriate chondrogenesis. Our analysis reveals diverse roles for Irx genes in the formation and later segmentation of the facial skeleton.
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Affiliation(s)
- D'Juan T Farmer
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Punam Patel
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Rachelle Choi
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Chih-Yu Liu
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - J Gage Crump
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
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13
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Dilshat R, Vu HN, Steingrímsson E. Epigenetic regulation during melanocyte development and homeostasis. Exp Dermatol 2021; 30:1033-1050. [PMID: 34003523 DOI: 10.1111/exd.14391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 04/09/2021] [Accepted: 05/09/2021] [Indexed: 12/26/2022]
Abstract
Melanocytes originate in the neural crest as precursor cells which then migrate and proliferate to reach their destination where they differentiate into pigment-producing cells. Melanocytes not only determine the colour of hair, skin and eyes but also protect against the harmful effects of UV irradiation. The establishment of the melanocyte lineage is regulated by a defined set of transcription factors and signalling pathways that direct the specific gene expression programmes underpinning melanoblast specification, survival, migration, proliferation and differentiation. In addition, epigenetic modifiers and replacement histones play key roles in regulating gene expression and its timing during the different steps of this process. Here, we discuss the evidence for the role of epigenetic regulators in melanocyte development and function and how they interact with transcription factors and signalling pathways to establish and maintain this important cell lineage.
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Affiliation(s)
- Ramile Dilshat
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavik, Iceland
| | - Hong Nhung Vu
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavik, Iceland
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavik, Iceland
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14
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Bryant L, Li D, Cox SG, Marchione D, Joiner EF, Wilson K, Janssen K, Lee P, March ME, Nair D, Sherr E, Fregeau B, Wierenga KJ, Wadley A, Mancini GMS, Powell-Hamilton N, van de Kamp J, Grebe T, Dean J, Ross A, Crawford HP, Powis Z, Cho MT, Willing MC, Manwaring L, Schot R, Nava C, Afenjar A, Lessel D, Wagner M, Klopstock T, Winkelmann J, Catarino CB, Retterer K, Schuette JL, Innis JW, Pizzino A, Lüttgen S, Denecke J, Strom TM, Monaghan KG, Yuan ZF, Dubbs H, Bend R, Lee JA, Lyons MJ, Hoefele J, Günthner R, Reutter H, Keren B, Radtke K, Sherbini O, Mrokse C, Helbig KL, Odent S, Cogne B, Mercier S, Bezieau S, Besnard T, Kury S, Redon R, Reinson K, Wojcik MH, Õunap K, Ilves P, Innes AM, Kernohan KD, Costain G, Meyn MS, Chitayat D, Zackai E, Lehman A, Kitson H, Martin MG, Martinez-Agosto JA, Nelson SF, Palmer CGS, Papp JC, Parker NH, Sinsheimer JS, Vilain E, Wan J, Yoon AJ, Zheng A, Brimble E, Ferrero GB, Radio FC, Carli D, Barresi S, Brusco A, Tartaglia M, Thomas JM, Umana L, Weiss MM, Gotway G, Stuurman KE, Thompson ML, McWalter K, Stumpel CTRM, Stevens SJC, Stegmann APA, Tveten K, Vøllo A, Prescott T, Fagerberg C, Laulund LW, Larsen MJ, Byler M, Lebel RR, Hurst AC, Dean J, Schrier Vergano SA, Norman J, Mercimek-Andrews S, Neira J, Van Allen MI, Longo N, Sellars E, Louie RJ, Cathey SS, Brokamp E, Heron D, Snyder M, Vanderver A, Simon C, de la Cruz X, Padilla N, Crump JG, Chung W, Garcia B, Hakonarson HH, Bhoj EJ. Histone H3.3 beyond cancer: Germline mutations in Histone 3 Family 3A and 3B cause a previously unidentified neurodegenerative disorder in 46 patients. SCIENCE ADVANCES 2020; 6:eabc9207. [PMID: 33268356 PMCID: PMC7821880 DOI: 10.1126/sciadv.abc9207] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/19/2020] [Indexed: 05/07/2023]
Abstract
Although somatic mutations in Histone 3.3 (H3.3) are well-studied drivers of oncogenesis, the role of germline mutations remains unreported. We analyze 46 patients bearing de novo germline mutations in histone 3 family 3A (H3F3A) or H3F3B with progressive neurologic dysfunction and congenital anomalies without malignancies. Molecular modeling of all 37 variants demonstrated clear disruptions in interactions with DNA, other histones, and histone chaperone proteins. Patient histone posttranslational modifications (PTMs) analysis revealed notably aberrant local PTM patterns distinct from the somatic lysine mutations that cause global PTM dysregulation. RNA sequencing on patient cells demonstrated up-regulated gene expression related to mitosis and cell division, and cellular assays confirmed an increased proliferative capacity. A zebrafish model showed craniofacial anomalies and a defect in Foxd3-derived glia. These data suggest that the mechanism of germline mutations are distinct from cancer-associated somatic histone mutations but may converge on control of cell proliferation.
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Affiliation(s)
- Laura Bryant
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Dong Li
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Samuel G Cox
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, CA 90033, USA
| | - Dylan Marchione
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Evan F Joiner
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Khadija Wilson
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kevin Janssen
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pearl Lee
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael E March
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Divya Nair
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elliott Sherr
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Brieana Fregeau
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Klaas J Wierenga
- Department of Clinical Genomics, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Alexandrea Wadley
- Department of Clinical Genomics, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, Netherlands
| | - Nina Powell-Hamilton
- Department of Medical Genetics, Alfred I. duPont Hospital for Children, Wilmington, DE 19810, USA
| | | | - Theresa Grebe
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ 85016, USA
| | - John Dean
- Department of Medical Genetics, Aberdeen Royal Infirmary, Aberdeen, Scotland, UK
| | - Alison Ross
- Department of Medical Genetics, Aberdeen Royal Infirmary, Aberdeen, Scotland, UK
| | - Heather P Crawford
- Clinical and Metabolic Genetics, Cook Children's Medical Center, Fort Worth, TX 76104, USA
| | - Zoe Powis
- Department of Emerging Genetic Medicine, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Megan T Cho
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Marcia C Willing
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Linda Manwaring
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Rachel Schot
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, Netherlands
| | - Caroline Nava
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, Paris, France
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013 Paris, France
| | - Alexandra Afenjar
- Service de génétique, CRMR des malformations et maladies congénitales du cervelet et CRMR déficience intellectuelle, hôpital Trousseau, AP-HP, France
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Undiagnosed Disease Program at the University Medical Center Hamburg-Eppendorf (UDP-UKE), Martinistrasse 52, 20246 Hamburg, Germany
| | - Matias Wagner
- Institut für Neurogenomik, Helmholtz Zentrum München, Munich, Germany
- Institut für Humangenetik, Helmholtz Zentrum München, Munich, Germany
- Institut für Humangenetik, Technische Universität München, Munich, Germany
| | - Thomas Klopstock
- Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians University, Ziemssenstr. 1a, 80336 Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
| | - Juliane Winkelmann
- Institut für Neurogenomik, Helmholtz Zentrum München, Munich, Germany
- Institut für Humangenetik, Technische Universität München, Munich, Germany
- Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
- Klinik und Poliklinik für Neurologie, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Claudia B Catarino
- Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians University, Ziemssenstr. 1a, 80336 Munich, Germany
| | - Kyle Retterer
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Jane L Schuette
- Division of Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeffrey W Innis
- Division of Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amy Pizzino
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Sabine Lüttgen
- Department of Pediatrics, University Medical Center Eppendorf, 20246 Hamburg, Germany
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Eppendorf, 20246 Hamburg, Germany
| | - Tim M Strom
- Institut für Neurogenomik, Helmholtz Zentrum München, Munich, Germany
- Institut für Humangenetik, Technische Universität München, Munich, Germany
| | | | - Zuo-Fei Yuan
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Holly Dubbs
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Renee Bend
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | | | | | - Julia Hoefele
- Institut für Humangenetik, Technische Universität München, Munich, Germany
| | - Roman Günthner
- Department of Nephrology, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany
| | - Heiko Reutter
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University Hospital Bonn & Institute of Human Genetics, University Hospital Bonn, Bonn, Germany
| | - Boris Keren
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013 Paris, France
| | - Kelly Radtke
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Omar Sherbini
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Cameron Mrokse
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Katherine L Helbig
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Sylvie Odent
- CHU Rennes, Service de Génétique Clinique, CNRS UMR6290, University Rennes1, Rennes, France
| | - Benjamin Cogne
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Sandra Mercier
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Stephane Bezieau
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Thomas Besnard
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Sebastien Kury
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Richard Redon
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Karit Reinson
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Monica H Wojcik
- Division of Genetics and Genomics and Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute, Cambridge, MA 02142, USA
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Pilvi Ilves
- Radiology Department of Tartu University Hospital and Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - A Micheil Innes
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H8L1, Canada
- Newborn Screening Ontario (NSO), Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Gregory Costain
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - M Stephen Meyn
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Center for Human Genomics and Precision Medicine, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, Wisconsin 53705, USA
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Elaine Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Hilary Kitson
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
| | - Martin G Martin
- Division of Gastroenterology and Nutrition, Department of Pediatrics, Mattel Children's Hospital, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research and the David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Stan F Nelson
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Christina G S Palmer
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- Institute for Society and Genetics, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Jeanette C Papp
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Neil H Parker
- David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Janet S Sinsheimer
- Institute for Society and Genetics, Departments of Human Genetics, Biomathematics, and Biostatistics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Eric Vilain
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA
| | - Jijun Wan
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Amanda J Yoon
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Allison Zheng
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Elise Brimble
- Department of Neurology and Neurological Sciences, Stanford Medicine, Stanford, CA 94305, USA
| | | | | | - Diana Carli
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - Sabina Barresi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Jennifer Muncy Thomas
- Pediatrics and Neurology and Neurotherapeutics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Luis Umana
- Genetics and Metabolism, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Marjan M Weiss
- Department of Clinical Genetics, VU Medical Center, Amsterdam, Netherlands
| | - Garrett Gotway
- Genetics and Metabolism, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - K E Stuurman
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, Netherlands
| | | | | | - Constance T R M Stumpel
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Arve Vøllo
- Department of Pediatrics, Hospital of Østfold, 1714 Grålum, Norway
| | - Trine Prescott
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | | | - Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Melissa Byler
- SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | | | - Anna C Hurst
- University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Joy Dean
- University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Samantha A Schrier Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk VA 23507, USA
| | | | - Saadet Mercimek-Andrews
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Juanita Neira
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Margot I Van Allen
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- Medical Genetics Programs, Provincial Health Shared Services BC and Vancouver Island Health Shared Services BC, Canada
| | - Nicola Longo
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, UT 84112, USA
| | - Elizabeth Sellars
- University of Arkansas for Medical Sciences, Little Rock, AR 72701, USA
| | | | | | | | - Delphine Heron
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013 Paris, France
| | - Molly Snyder
- Child Neurology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adeline Vanderver
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Celeste Simon
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Xavier de la Cruz
- Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Natália Padilla
- Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - J Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, CA 90033, USA
| | - Wendy Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Benjamin Garcia
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, CA 90033, USA
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hakon H Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elizabeth J Bhoj
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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15
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Cavalieri V. Histones, Their Variants and Post-translational Modifications in Zebrafish Development. Front Cell Dev Biol 2020; 8:456. [PMID: 32582716 PMCID: PMC7289917 DOI: 10.3389/fcell.2020.00456] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/15/2020] [Indexed: 01/01/2023] Open
Abstract
Complex multi-cellular organisms are shaped starting from a single-celled zygote, owing to elaborate developmental programs. These programs involve several layers of regulation to orchestrate the establishment of progressively diverging cell type-specific gene expression patterns. In this scenario, epigenetic modifications of chromatin are central in influencing spatiotemporal patterns of gene transcription. In fact, it is generally recognized that epigenetic changes of chromatin states impact on the accessibility of genomic DNA to regulatory proteins. Several lines of evidence highlighted that zebrafish is an excellent vertebrate model for research purposes in the field of developmental epigenetics. In this review, I focus on the dynamic roles recently emerged for histone post-translational modifications (PTMs), histone modifying enzymes, histone variants and histone themselves in the coordination between the precise execution of transcriptional programs and developmental progression in zebrafish. In particular, I first outline a synopsis of the current state of knowledge in this field during early embryogenesis. Then, I present a survey of histone-based epigenetic mechanisms occurring throughout morphogenesis, with a stronger emphasis on cardiac formation. Undoubtedly, the issues addressed in this review take on particular importance in the emerging field of comparative biology of epigenetics, as well as in translational research.
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Affiliation(s)
- Vincenzo Cavalieri
- Laboratory of Molecular Biology and Functional Genomics, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy.,Zebrafish Laboratory, Advanced Technologies Network (ATeN) Center, University of Palermo, Palermo, Italy
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16
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Nzirorera N, Jabado N, Majewska L. Investigating the Effects of Histone H3.3 Point Mutations in Neural Crest Cells and Craniofacial Development. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.09571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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Raja DA, Subramaniam Y, Aggarwal A, Gotherwal V, Babu A, Tanwar J, Motiani RK, Sivasubbu S, Gokhale RS, Natarajan VT. Histone variant dictates fate biasing of neural crest cells to melanocyte lineage. Development 2020; 147:dev.182576. [PMID: 32098766 DOI: 10.1242/dev.182576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/24/2020] [Indexed: 11/20/2022]
Abstract
In the neural crest lineage, progressive fate restriction and stem cell assignment are crucial for both development and regeneration. Whereas fate commitment events have distinct transcriptional footprints, fate biasing is often transitory and metastable, and is thought to be moulded by epigenetic programmes. Therefore, the molecular basis of specification is difficult to define. In this study, we established a role for a histone variant, H2a.z.2, in specification of the melanocyte lineage from multipotent neural crest cells. H2a.z.2 silencing reduces the number of melanocyte precursors in developing zebrafish embryos and from mouse embryonic stem cells in vitro We demonstrate that this histone variant occupies nucleosomes in the promoter of the key melanocyte determinant mitf, and enhances its induction. CRISPR/Cas9-based targeted mutagenesis of this gene in zebrafish drastically reduces adult melanocytes, as well as their regeneration. Thereby, our study establishes the role of a histone variant upstream of the core gene regulatory network in the neural crest lineage. This epigenetic mark is a key determinant of cell fate and facilitates gene activation by external instructive signals, thereby establishing melanocyte fate identity.
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Affiliation(s)
- Desingu Ayyappa Raja
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Yogaspoorthi Subramaniam
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Ayush Aggarwal
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Vishvabandhu Gotherwal
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Aswini Babu
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Jyoti Tanwar
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Rajender K Motiani
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Sridhar Sivasubbu
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Rajesh S Gokhale
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Vivek T Natarajan
- Pigment Cell Biology Group, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India .,Academy of Scientific and Innovative Research, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
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18
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Balasubramanian S, Raghunath A, Perumal E. Role of epigenetics in zebrafish development. Gene 2019; 718:144049. [DOI: 10.1016/j.gene.2019.144049] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 02/07/2023]
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19
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Narboux-Neme N, Ekker M, Levi G, Heude E. Posterior axis formation requires Dlx5/Dlx6 expression at the neural plate border. PLoS One 2019; 14:e0214063. [PMID: 30889190 PMCID: PMC6424422 DOI: 10.1371/journal.pone.0214063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 03/06/2019] [Indexed: 11/18/2022] Open
Abstract
Neural tube defects (NTDs), one of the most common birth defects in human, present a multifactorial etiology with a poorly defined genetic component. The Dlx5 and Dlx6 bigenic cluster encodes two evolutionary conserved homeodomain transcription factors, which are necessary for proper vertebrate development. It has been shown that Dlx5/6 genes are essential for anterior neural tube closure, however their role in the formation of the posterior structures has never been described. Here, we show that Dlx5/6 expression is required during vertebrate posterior axis formation. Dlx5 presents a similar expression pattern in neural plate border cells during posterior neurulation of zebrafish and mouse. Dlx5/6-inactivation in the mouse results in a phenotype reminiscent of NTDs characterized by open thoracic and lumbar vertebral arches and failure of epaxial muscle formation at the dorsal midline. The dlx5a/6a zebrafish morphants present posterior NTDs associated with abnormal delamination of neural crest cells showing altered expression of cell adhesion molecules and defects of motoneuronal development. Our findings provide new molecular leads to decipher the mechanisms of vertebrate posterior neurulation and might help to gather a better understanding of human congenital NTDs etiology.
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Affiliation(s)
- Nicolas Narboux-Neme
- Département Adaptations du Vivant, Centre National de la Recherche Scientifique UMR 7221, Muséum National d’Histoire Naturelle, Paris, France
| | - Marc Ekker
- Department of Biology, Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, Canada
| | - Giovanni Levi
- Département Adaptations du Vivant, Centre National de la Recherche Scientifique UMR 7221, Muséum National d’Histoire Naturelle, Paris, France
| | - Eglantine Heude
- Département Adaptations du Vivant, Centre National de la Recherche Scientifique UMR 7221, Muséum National d’Histoire Naturelle, Paris, France
- * E-mail:
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20
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Teng CS, Ting MC, Farmer DT, Brockop M, Maxson RE, Crump JG. Altered bone growth dynamics prefigure craniosynostosis in a zebrafish model of Saethre-Chotzen syndrome. eLife 2018; 7:37024. [PMID: 30375332 PMCID: PMC6207424 DOI: 10.7554/elife.37024] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 10/14/2018] [Indexed: 01/09/2023] Open
Abstract
Cranial sutures separate the skull bones and house stem cells for bone growth and repair. In Saethre-Chotzen syndrome, mutations in TCF12 or TWIST1 ablate a specific suture, the coronal. This suture forms at a neural-crest/mesoderm interface in mammals and a mesoderm/mesoderm interface in zebrafish. Despite this difference, we show that combinatorial loss of TCF12 and TWIST1 homologs in zebrafish also results in specific loss of the coronal suture. Sequential bone staining reveals an initial, directional acceleration of bone production in the mutant skull, with subsequent localized stalling of bone growth prefiguring coronal suture loss. Mouse genetics further reveal requirements for Twist1 and Tcf12 in both the frontal and parietal bones for suture patency, and to maintain putative progenitors in the coronal region. These findings reveal conservation of coronal suture formation despite evolutionary shifts in embryonic origins, and suggest that the coronal suture might be especially susceptible to imbalances in progenitor maintenance and osteoblast differentiation. Some of the most common birth defects involve improper development of the head and face. One such birth defect is called craniosynostosis. Normally, an infant’s skull bones are not fully fused together. Instead, they are held together by soft tissue that allows the baby’s skull to more easily pass through the birth canal. This tissue also houses specialized cells called stem cells that allow the brain and skull to grow with the child. But in craniosynostosis these stem cells behave abnormally, which fuses the skull bones together and prevents the skull and brain from growing properly during childhood. One form of craniosynostosis called Saethre-Chotzen syndrome is caused by mutations in one of two genes that ensure the proper separation of two bones in the roof of the skull. Mice with mutations in the mouse versions of these genes develop the same problem and are used to study this condition. Mouse studies have looked mostly at what happens after birth. Studies looking at what happens in embryos with these mutations could help scientists learn more. One way to do so would be to genetically engineer zebrafish with the equivalent mutations. This is because zebrafish embryos are transparent and grow outside their mother’s body, making it easier for scientists to watch them develop. Now, Teng et al. have grown zebrafish with mutations in the zebrafish versions of the genes that cause Saethre-Chotzen syndrome. In the experiments, imaging tools were used to observe the live fish as they developed. This showed that the stem cells in their skulls become abnormal much earlier than previous studies had suggested. Teng et al. also showed that similar stem cells are responsible for growth of the skull in zebrafish and mice. Babies with craniosynostosis often need multiple, risky surgeries to separate their skull bones and allow their brain and head to grow. Unfortunately, these bones often fuse again because they have abnormal stem cells. Teng et al. provide new information on what goes wrong in these stem cells. Hopefully, this new information will help scientists to one day correct the defective stem cells in babies with craniosynostosis, thus reducing the number of surgeries needed to correct the problem.
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Affiliation(s)
- Camilla S Teng
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, United States.,Department of Biochemistry, Keck School of Medicine, University of Southern California, Los Angeles, United States
| | - Man-Chun Ting
- Department of Biochemistry, Keck School of Medicine, University of Southern California, Los Angeles, United States
| | - D'Juan T Farmer
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, United States
| | - Mia Brockop
- Department of Biochemistry, Keck School of Medicine, University of Southern California, Los Angeles, United States
| | - Robert E Maxson
- Department of Biochemistry, Keck School of Medicine, University of Southern California, Los Angeles, United States
| | - J Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, United States
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21
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Affiliation(s)
- Seth M. Weinberg
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Anthropology, University of Pittsburgh, Pittsburgh, Pennsylvania, United Staes of America
- * E-mail:
| | - Robert Cornell
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, United States America
| | - Elizabeth J. Leslie
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
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22
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Bano D, Piazzesi A, Salomoni P, Nicotera P. The histone variant H3.3 claims its place in the crowded scene of epigenetics. Aging (Albany NY) 2017; 9:602-614. [PMID: 28284043 PMCID: PMC5391221 DOI: 10.18632/aging.101194] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/26/2017] [Indexed: 12/16/2022]
Abstract
Histones are evolutionarily conserved DNA-binding proteins. As scaffolding molecules, they significantly regulate the DNA packaging into the nucleus of all eukaryotic cells. As docking units, they influence the recruitment of the transcriptional machinery, thus establishing unique gene expression patterns that ultimately promote different biological outcomes. While canonical histones H3.1 and H3.2 are synthetized and loaded during DNA replication, the histone variant H3.3 is expressed and deposited into the chromatin throughout the cell cycle. Recent findings indicate that H3.3 replaces the majority of canonical H3 in non-dividing cells, reaching almost saturation levels in a time-dependent manner. Consequently, H3.3 incorporation and turnover represent an additional layer in the regulation of the chromatin landscape during aging. In this respect, work from our group and others suggest that H3.3 plays an important function in age-related processes throughout evolution. Here, we summarize the current knowledge on H3.3 biology and discuss the implications of its aberrant dynamics in the establishment of cellular states that may lead to human pathology. Critically, we review the importance of H3.3 turnover as part of epigenetic events that influence senescence and age-related processes. We conclude with the emerging evidence that H3.3 is required for proper neuronal function and brain plasticity.
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Affiliation(s)
- Daniele Bano
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Antonia Piazzesi
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Paolo Salomoni
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Pierluigi Nicotera
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
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23
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Mllt10 knockout mouse model reveals critical role of Af10-dependent H3K79 methylation in midfacial development. Sci Rep 2017; 7:11922. [PMID: 28931923 PMCID: PMC5607342 DOI: 10.1038/s41598-017-11745-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/30/2017] [Indexed: 01/04/2023] Open
Abstract
Epigenetic regulation is required to ensure the precise spatial and temporal pattern of gene expression that is necessary for embryonic development. Although the roles of some epigenetic modifications in embryonic development have been investigated in depth, the role of methylation at lysine 79 (H3K79me) is poorly understood. Dot1L, a unique methyltransferase for H3K79, forms complexes with distinct sets of co-factors. To further understand the role of H3K79me in embryogenesis, we generated a mouse knockout of Mllt10, the gene encoding Af10, one Dot1L complex co-factor. We find homozygous Mllt10 knockout mutants (Mllt10-KO) exhibit midline facial cleft. The midfacial defects of Mllt10-KO embryos correspond to hyperterolism and are associated with reduced proliferation of mesenchyme in developing nasal processes and adjacent tissue. We demonstrate that H3K79me level is significantly decreased in nasal processes of Mllt10-KO embryos. Importantly, we find that expression of AP2α, a gene critical for midfacial development, is directly regulated by Af10-dependent H3K79me, and expression AP2α is reduced specifically in nasal processes of Mllt10-KO embryos. Suppression of H3K79me completely mimicked the Mllt10-KO phenotype. Together these data are the first to demonstrate that Af10-dependent H3K79me is essential for development of nasal processes and adjacent tissues, and consequent midfacial formation.
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24
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Brooks EP, Nichols JT. Shifting Zebrafish Lethal Skeletal Mutant Penetrance by Progeny Testing. J Vis Exp 2017. [PMID: 28892034 DOI: 10.3791/56200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Zebrafish mutant phenotypes are often incompletely penetrant, only manifesting in some mutants. Interesting phenotypes that inconsistently appear can be difficult to study, and can lead to confounding results. The protocol described here is a straightforward breeding paradigm to increase and decrease penetrance in lethal zebrafish skeletal mutants. Because lethal mutants cannot be selectively bred directly, the classic selective breeding strategy of progeny testing is employed. This method also includes protocols for Kompetitive Allele Specific PCR (KASP) genotyping zebrafish and staining larval zebrafish cartilage and bone. Applying the husbandry strategy described here can increase the penetrance of an interesting skeletal phenotype enabling more reproducible results in downstream applications. In addition, decreasing the mutant penetrance through this selective breeding strategy can reveal the developmental processes that most crucially require the function of the mutated gene. While the skeleton is specifically considered here, we propose that this methodology will be useful for all zebrafish mutant lines.
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Affiliation(s)
- Elliott P Brooks
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus
| | - James T Nichols
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus;
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25
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Gupta N, Shastri S, Singh PK, Jana M, Mridha A, Verma G, Kabra M. Nasopharyngeal teratoma, congenital diaphragmatic hernia and Dandy-Walker malformation - a yet uncharacterized syndrome. Clin Genet 2016; 90:470-471. [PMID: 27506516 DOI: 10.1111/cge.12830] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 07/05/2016] [Accepted: 07/06/2016] [Indexed: 11/28/2022]
Abstract
An association of congenital diaphragmatic hernia, dandy walker malformation and nasopharyngeal teratoma is very rare. Here, we report a fourth case with this association where chromosomal microarray and whole exome sequencing (WES) was performed to understand the underlying genetic basis. Findings of few variants especially a novel variation in HIRA provided some insights. An association of congenital diaphragmatic hernia, dandy walker malformation and nasopharyngeal teratoma is very rare. Here, we report a fourth case with this association where chromosomal microarray and whole exome sequencing (WES) was performed to understand the underlying genetic basis. Findings of few variants especially a novel variation in HIRA provided some insights.
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Affiliation(s)
- N Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India.
| | - S Shastri
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - P K Singh
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - M Jana
- Department of Radiodiagnosis, All India Institute of Medical Sciences, New Delhi, India
| | - A Mridha
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - G Verma
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - M Kabra
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
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26
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Wenderski W, Maze I. Histone turnover and chromatin accessibility: Critical mediators of neurological development, plasticity, and disease. Bioessays 2016; 38:410-9. [PMID: 26990528 DOI: 10.1002/bies.201500171] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In postmitotic neurons, nucleosomal turnover was long considered to be a static process that is inconsequential to transcription. However, our recent studies in human and rodent brain indicate that replication-independent (RI) nucleosomal turnover, which requires the histone variant H3.3, is dynamic throughout life and is necessary for activity-dependent gene expression, synaptic connectivity, and cognition. H3.3 turnover also facilitates cellular lineage specification and plays a role in suppressing the expression of heterochromatic repetitive elements, including mutagenic transposable sequences, in mouse embryonic stem cells. In this essay, we review mechanisms and functions for RI nucleosomal turnover in brain and present the hypothesis that defects in histone dynamics may represent a common mechanism underlying neurological aging and disease.
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Affiliation(s)
- Wendy Wenderski
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Ian Maze
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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27
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Abstract
The formation of the face and skull involves a complex series of developmental events mediated by cells derived from the neural crest, endoderm, mesoderm, and ectoderm. Although vertebrates boast an enormous diversity of adult facial morphologies, the fundamental signaling pathways and cellular events that sculpt the nascent craniofacial skeleton in the embryo have proven to be highly conserved from fish to man. The zebrafish Danio rerio, a small freshwater cyprinid fish from eastern India, has served as a popular model of craniofacial development since the 1990s. Unique strengths of the zebrafish model include a simplified skeleton during larval stages, access to rapidly developing embryos for live imaging, and amenability to transgenesis and complex genetics. In this chapter, we describe the anatomy of the zebrafish craniofacial skeleton; its applications as models for the mammalian jaw, middle ear, palate, and cranial sutures; the superior imaging technology available in fish that has provided unprecedented insights into the dynamics of facial morphogenesis; the use of the zebrafish to decipher the genetic underpinnings of craniofacial biology; and finally a glimpse into the most promising future applications of zebrafish craniofacial research.
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28
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Snyers L, Zupkovitz G, Almeder M, Fliesser M, Stoisser A, Weipoltshammer K, Schöfer C. Distinct chromatin signature of histone H3 variant H3.3 in human cells. Nucleus 2015; 5:449-61. [PMID: 25482197 PMCID: PMC4164487 DOI: 10.4161/nucl.36229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Actively transcribed regions of the genome have been found enriched for the histone H3 variant H3.3. This variant is incorporated into nucleosomes throughout the cell cycle whereas the canonical isoforms are predominately deposited in association with replication. In order to obtain a global picture of the deposition pattern at the single cell level we expressed H3.3 in both normal and malignant human cells and analyzed nuclei using conventional and structured illumination imaging (SIM). We found that the distribution pattern of H3.3 in interphase differs from that of the canonical histone H3 variants and this difference is conveyed to mitotic chromosomes which display a distinct H3.3 banding pattern. Histone H3.3 localization positively correlated with markers for transcriptionally active chromatin and, notably, H3.3 was almost completely absent from the inactive X chromosome. Collectively, our data show that histone variant H3.3 occupies distinct intranuclear chromatin domains and that these genomic loci are associated with gene expression.
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Affiliation(s)
- Luc Snyers
- a Department for Cell and Developmental Biology; Medical Imaging Cluster; Medical University of Vienna; Vienna, Austria
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29
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Jang CW, Shibata Y, Starmer J, Yee D, Magnuson T. Histone H3.3 maintains genome integrity during mammalian development. Genes Dev 2015; 29:1377-92. [PMID: 26159997 PMCID: PMC4511213 DOI: 10.1101/gad.264150.115] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 06/16/2015] [Indexed: 12/19/2022]
Abstract
Histone H3.3 is a highly conserved histone H3 replacement variant in metazoans and has been implicated in many important biological processes, including cell differentiation and reprogramming. Germline and somatic mutations in H3.3 genomic incorporation pathway components or in H3.3 encoding genes have been associated with human congenital diseases and cancers, respectively. However, the role of H3.3 in mammalian development remains unclear. To address this question, we generated H3.3-null mouse models through classical genetic approaches. We found that H3.3 plays an essential role in mouse development. Complete depletion of H3.3 leads to developmental retardation and early embryonic lethality. At the cellular level, H3.3 loss triggers cell cycle suppression and cell death. Surprisingly, H3.3 depletion does not dramatically disrupt gene regulation in the developing embryo. Instead, H3.3 depletion causes dysfunction of heterochromatin structures at telomeres, centromeres, and pericentromeric regions of chromosomes, leading to mitotic defects. The resulting karyotypical abnormalities and DNA damage lead to p53 pathway activation. In summary, our results reveal that an important function of H3.3 is to support chromosomal heterochromatic structures, thus maintaining genome integrity during mammalian development.
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Affiliation(s)
- Chuan-Wei Jang
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| | - Yoichiro Shibata
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| | - Joshua Starmer
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| | - Della Yee
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| | - Terry Magnuson
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
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30
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Point mutations in an epigenetic factor lead to multiple types of bone tumors: role of H3.3 histone variant in bone development and disease. BONEKEY REPORTS 2015; 4:715. [PMID: 26157578 DOI: 10.1038/bonekey.2015.84] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 04/24/2015] [Indexed: 12/27/2022]
Abstract
Coordinated post-translational modifications (PTMs) of nucleosomal histones emerge as a key mechanism of gene regulation by defining chromatin configuration. Patterns of histone modifications vary in different cells and constitute core elements of cell-specific epigenomes. Recently, in addition to canonical histone proteins produced during the S phase of cell cycle, several non-canonical histone variants have been identified and shown to express in a DNA replication-independent manner. These histone variants generate diversity in nucleosomal structures and add further complexity to mechanisms of epigenetic regulation. Cell-specific functions of histone variants remain to be determined. Several recent studies reported an association between some point mutations in the non-canonical histone H3.3 and particular types of brain and bone tumors. This suggests a possibility of differential physiological effects of histone variants in different cells and tissues, including bone. In this review, we outline the roles of histone variants and their PTMs in the epigenetic regulation of chromatin structure and discuss possible mechanisms of biological effects of the non-canonical histone mutations found in bone tumors on tumorigenesis in differentiating bone stem cells.
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31
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Pentimento: Neural Crest and the origin of mesectoderm. Dev Biol 2015; 401:37-61. [DOI: 10.1016/j.ydbio.2014.12.035] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/28/2014] [Accepted: 12/30/2014] [Indexed: 11/17/2022]
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32
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Choe CP, Crump JG. Dynamic epithelia of the developing vertebrate face. Curr Opin Genet Dev 2015; 32:66-72. [PMID: 25748249 DOI: 10.1016/j.gde.2015.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 01/29/2015] [Accepted: 02/01/2015] [Indexed: 10/23/2022]
Abstract
A segmental series of endoderm-derived pouch and ectoderm-derived cleft epithelia act as signaling centers in the developing face. Their precise morphogenesis is therefore essential for proper patterning of the vertebrate head. Intercellular adhesion and polarity are highly dynamic within developing facial epithelial cells, with signaling from the adjacent mesenchyme controlling both epithelial character and directional migration. Endodermal and ectodermal epithelia fuse to form the primary mouth and gill slits, which involves basement membrane dissolution, cell intercalations, and apoptosis, as well as undergo further morphogenesis to generate the middle ear cavity and glands of the neck. Recent studies of facial epithelia are revealing both core programs of epithelial morphogenesis and insights into the coordinated assembly of the vertebrate head.
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Affiliation(s)
- Chong Pyo Choe
- Broad California Institute of Regenerative Medicine Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - J Gage Crump
- Broad California Institute of Regenerative Medicine Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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33
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Chemical “Diversity” of Chromatin Through Histone Variants and Histone Modifications. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s40610-015-0005-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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34
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Filipescu D, Müller S, Almouzni G. Histone H3 Variants and Their Chaperones During Development and Disease: Contributing to Epigenetic Control. Annu Rev Cell Dev Biol 2014; 30:615-46. [DOI: 10.1146/annurev-cellbio-100913-013311] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dan Filipescu
- Institut Curie, Centre de Recherche, Paris, F-75248 France; , ,
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35
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Lin CJ, Koh FM, Wong P, Conti M, Ramalho-Santos M. Hira-mediated H3.3 incorporation is required for DNA replication and ribosomal RNA transcription in the mouse zygote. Dev Cell 2014; 30:268-79. [PMID: 25087892 DOI: 10.1016/j.devcel.2014.06.022] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 05/09/2014] [Accepted: 06/25/2014] [Indexed: 10/25/2022]
Abstract
Extensive chromatin reprogramming occurs at fertilization and is thought to be under the control of maternal factors, but the underlying mechanisms remain poorly understood. We report that maternal Hira, a chaperone for the histone variant H3.3, is required for mouse development past the zygote stage. Male pronucleus formation is inhibited upon deletion of Hira due to a lack of nucleosome assembly in the sperm genome. Hira mutant oocytes are incapable of developing parthenogenetically, indicative of a role for Hira in the female genome. Both parental genomes show highly reduced levels of DNA replication and transcription in the mutants. It has long been thought that transcription is not required for zygote development. Surprisingly, we found that Hira/H3.3-dependent transcription of ribosomal RNA is required for first cleavage. Our results demonstrate that Hira-mediated H3.3 incorporation is essential for parental genome reprogramming and reveal an unexpected role for rRNA transcription in the mouse zygote.
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Affiliation(s)
- Chih-Jen Lin
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Fong Ming Koh
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Priscilla Wong
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Marco Conti
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA.
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Every amino acid matters: essential contributions of histone variants to mammalian development and disease. Nat Rev Genet 2014; 15:259-71. [PMID: 24614311 DOI: 10.1038/nrg3673] [Citation(s) in RCA: 233] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite a conserved role for histones as general DNA packaging agents, it is now clear that another key function of these proteins is to confer variations in chromatin structure to ensure dynamic patterns of transcriptional regulation in eukaryotes. The incorporation of histone variants is particularly important to this process. Recent knockdown and knockout studies in various cellular systems, as well as direct mutational evidence from human cancers, now suggest a crucial role for histone variant regulation in processes as diverse as differentiation and proliferation, meiosis and nuclear reprogramming. In this Review, we provide an overview of histone variants in the context of their unique functions during mammalian germ cell and embryonic development, and examine the consequences of aberrant histone variant regulation in human disease.
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Coelho-Aguiar JM, Le Douarin NM, Dupin E. Environmental factors unveil dormant developmental capacities in multipotent progenitors of the trunk neural crest. Dev Biol 2013; 384:13-25. [DOI: 10.1016/j.ydbio.2013.09.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 09/27/2013] [Accepted: 09/28/2013] [Indexed: 12/13/2022]
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Banaszynski LA, Wen D, Dewell S, Whitcomb SJ, Lin M, Diaz N, Elsässer SJ, Chapgier A, Goldberg AD, Canaani E, Rafii S, Zheng D, Allis CD. Hira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells. Cell 2013; 155:107-20. [PMID: 24074864 DOI: 10.1016/j.cell.2013.08.061] [Citation(s) in RCA: 205] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 07/08/2013] [Accepted: 08/28/2013] [Indexed: 11/15/2022]
Abstract
Polycomb repressive complex 2 (PRC2) regulates gene expression during lineage specification through trimethylation of lysine 27 on histone H3 (H3K27me3). In Drosophila, polycomb binding sites are dynamic chromatin regions enriched with the histone variant H3.3. Here, we show that, in mouse embryonic stem cells (ESCs), H3.3 is required for proper establishment of H3K27me3 at the promoters of developmentally regulated genes. Upon H3.3 depletion, these promoters show reduced nucleosome turnover measured by deposition of de novo synthesized histones and reduced PRC2 occupancy. Further, we show H3.3-dependent interaction of PRC2 with the histone chaperone, Hira, and that Hira localization to chromatin requires H3.3. Our data demonstrate the importance of H3.3 in maintaining a chromatin landscape in ESCs that is important for proper gene regulation during differentiation. Moreover, our findings support the emerging notion that H3.3 has multiple functions in distinct genomic locations that are not always correlated with an "active" chromatin state.
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Affiliation(s)
- Laura A Banaszynski
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, New York, 10065 USA
| | - Duancheng Wen
- Howard Hughes Medical Institute, Ansary Stem Cell Institute, and Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, 10065 USA
| | - Scott Dewell
- Genomics Resource Center, The Rockefeller University, New York, New York, 10065 USA
| | - Sarah J Whitcomb
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, New York, 10065 USA
| | - Mingyan Lin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, 10461 USA
| | - Nichole Diaz
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, New York, 10065 USA
| | - Simon J Elsässer
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, New York, 10065 USA
| | - Ariane Chapgier
- Molecular Medicine Unit, Institute of Child Health, London WC1N 1EH, UK
| | - Aaron D Goldberg
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, New York, 10065 USA
| | - Eli Canaani
- The Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Isreal
| | - Shahin Rafii
- Howard Hughes Medical Institute, Ansary Stem Cell Institute, and Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, 10065 USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, 10461 USA.,Departments of Neurology and Neuroscience, Albert Einstein College of Medicine, Bronx, New York, 10461 USA
| | - C David Allis
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, New York, 10065 USA
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Yuen BTK, Knoepfler PS. Histone H3.3 mutations: a variant path to cancer. Cancer Cell 2013; 24:567-74. [PMID: 24229707 PMCID: PMC3882088 DOI: 10.1016/j.ccr.2013.09.015] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 09/11/2013] [Accepted: 09/24/2013] [Indexed: 12/31/2022]
Abstract
A host of cancer types exhibit aberrant histone modifications. Recently, distinct and recurrent mutations in a specific histone variant, histone H3.3, have been implicated in a high proportion of malignant pediatric brain cancers. The presence of mutant H3.3 histone disrupts epigenetic posttranslational modifications near genes involved in cancer processes and in brain function. Here, we review possible mechanisms by which mutant H3.3 histones may act to promote tumorigenesis. Furthermore, we discuss how perturbations in normal H3.3 chromatin-related and epigenetic functions may more broadly contribute to the formation of human cancers.
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Affiliation(s)
- Benjamin T K Yuen
- Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, 4303 Tupper Hall, Davis, CA 95616, USA; Genome Center, University of California Davis School of Medicine, 451 Health Sciences Drive, Davis, CA 95616, USA; Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, 2425 Stockton Boulevard, Sacramento, CA 95817, USA
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40
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Simões-Costa M, Bronner ME. Insights into neural crest development and evolution from genomic analysis. Genome Res 2013; 23:1069-80. [PMID: 23817048 PMCID: PMC3698500 DOI: 10.1101/gr.157586.113] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The neural crest is an excellent model system for the study of cell type diversification during embryonic development due to its multipotency, motility, and ability to form a broad array of derivatives ranging from neurons and glia, to cartilage, bone, and melanocytes. As a uniquely vertebrate cell population, it also offers important clues regarding vertebrate origins. In the past 30 yr, introduction of recombinant DNA technology has facilitated the dissection of the genetic program controlling neural crest development and has provided important insights into gene regulatory mechanisms underlying cell migration and differentiation. More recently, new genomic approaches have provided a platform and tools that are changing the depth and breadth of our understanding of neural crest development at a “systems” level. Such advances provide an insightful view of the regulatory landscape of neural crest cells and offer a new perspective on developmental as well as stem cell and cancer biology.
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Affiliation(s)
- Marcos Simões-Costa
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
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41
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Lin CJ, Conti M, Ramalho-Santos M. Histone variant H3.3 maintains a decondensed chromatin state essential for mouse preimplantation development. Development 2013; 140:3624-34. [PMID: 23903189 DOI: 10.1242/dev.095513] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Histone variants can replace canonical histones in the nucleosome and modify chromatin structure and gene expression. The histone variant H3.3 preferentially associates with active chromatin and has been implicated in the regulation of a diverse range of developmental processes. However, the mechanisms by which H3.3 may regulate gene activity are unclear and gene duplication has hampered an analysis of H3.3 function in mouse. Here, we report that the specific knockdown of H3.3 in fertilized mouse zygotes leads to developmental arrest at the morula stage. This phenotype can be rescued by exogenous H3.3 but not by canonical H3.1 mRNA. Loss of H3.3 leads to over-condensation and mis-segregation of chromosomes as early as the two-cell stage, with corresponding high levels of aneuploidy, but does not appear to affect zygotic gene activation at the two-cell stage or lineage gene transcription at the morula stage. H3.3-deficient embryos have significantly reduced levels of markers of open chromatin, such as H3K36me2 and H4K16Ac. Importantly, a mutation in H3.3K36 that disrupts H3K36 methylation (H3.3K36R) does not rescue the H3.3 knockdown (KD) phenotype. In addition, H3.3 KD embryos have increased incorporation of linker H1. Knockdown of Mof (Kat8), an acetyltransferase specific for H4K16, similarly leads to excessive H1 incorporation. Remarkably, pan-H1 RNA interference (RNAi) partially rescues the chromosome condensation of H3.3 KD embryos and allows development to the blastocyst stage. These results reveal that H3.3 mediates a balance between open and condensed chromatin that is crucial for the fidelity of chromosome segregation during early mouse development.
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Affiliation(s)
- Chih-Jen Lin
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Obstetrics and Gynecology and Center for Reproductive Sciences, University of California San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
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42
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Filipescu D, Szenker E, Almouzni G. Developmental roles of histone H3 variants and their chaperones. Trends Genet 2013; 29:630-40. [PMID: 23830582 DOI: 10.1016/j.tig.2013.06.002] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 05/14/2013] [Accepted: 06/03/2013] [Indexed: 11/27/2022]
Abstract
Animal development and lifetime potential exploit a balance between the stability and plasticity of cellular identity. Within the nucleus, this is controlled by an interplay involving lineage-specific transcription factors and chromatin dynamics. Histone H3 variants contribute to chromatin dynamics through the timing and sites of their incorporation, promoted by dedicated histone chaperones. Moreover, their individual modifications and binding partners provide distinct features at defined genomic loci. We highlight here the importance of the H3.3 replacement variant for the nuclear reprogramming that occurs during gametogenesis, fertilization, and germline establishment. Furthermore, we describe how the recently characterized H3.3 dynamics associated with gastrulation, myogenesis, or neurogenesis underline the role of chromatin changes in cell differentiation. Finally, we discuss the challenges of maintaining centromeric identity through propagation of the centromeric CenH3 variant in different cell types. Future challenges will be to gain a comprehensive picture of H3 variants and their chaperones during development and differentiation.
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Affiliation(s)
- Dan Filipescu
- Institut Curie, Centre de Recherche, Paris F-75248 Cedex 05, France; CNRS, UMR218, Paris F-75248 Cedex 05, France
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Endogenous mammalian histone H3.3 exhibits chromatin-related functions during development. Epigenetics Chromatin 2013; 6:7. [PMID: 23570311 PMCID: PMC3635903 DOI: 10.1186/1756-8935-6-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 03/22/2013] [Indexed: 12/21/2022] Open
Abstract
Background The histone variant H3.3 plays key roles in regulating chromatin states and transcription. However, the role of endogenous H3.3 in mammalian cells and during development has been less thoroughly investigated. To address this gap, we report the production and phenotypic analysis of mice and cells with targeted disruption of the H3.3-encoding gene, H3f3b. Results H3f3b knockout (KO) mice exhibit a semilethal phenotype traceable at least in part to defective cell division and chromosome segregation. H3f3b KO cells have widespread ectopic CENP-A protein localization suggesting one possible mechanism for defective chromosome segregation. KO cells have abnormal karyotypes and cell cycle profiles as well. The transcriptome and euchromatin-related epigenome were moderately affected by loss of H3f3b in mouse embryonic fibroblasts (MEFs) with ontology most notably pointing to changes in chromatin regulatory and histone coding genes. Reduced numbers of H3f3b KO mice survive to maturity and almost all survivors from both sexes are infertile. Conclusions Taken together, our studies suggest that endogenous mammalian histone H3.3 has important roles in regulating chromatin and chromosome functions that in turn are important for cell division, genome integrity, and development.
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Mahajan K, Mahajan NP. WEE1 tyrosine kinase, a novel epigenetic modifier. Trends Genet 2013; 29:394-402. [PMID: 23537585 DOI: 10.1016/j.tig.2013.02.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 12/26/2012] [Accepted: 02/25/2013] [Indexed: 11/30/2022]
Abstract
The cell cycle requires cells to duplicate their chromatin, DNA, and histones, while retaining a subset of epigenetic marks, in a highly coordinated manner. The WEE1 kinase was identified as an important regulator during S phase, preventing entry into mitosis until DNA replication has been completed. Interestingly, WEE1 has also emerged as a key player in regulating histone synthesis. It phosphorylates histone H2B at tyrosine 37 in the nucleosomes found upstream of the histone gene cluster, and this suppresses histone transcription in late S phase. These observations highlight a dual role for WEE1 as both a mitotic gatekeeper and a surveyor of chromatin synthesis, providing a direct link between epigenetics and cell-cycle progression. Importantly, this link has implications for the design of novel epigenetic inhibitors targeting cancers that display elevated expression of this kinase.
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Affiliation(s)
- Kiran Mahajan
- Drug Discovery Department, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.
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