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Yuan D, Zhang X, Yang Y, Wei L, Li H, Zhao T, Guo M, Li Z, Huang Z, Wang M, Dai Z, Li P, Xia Q, Qian W, Cheng D. Schlank orchestrates insect developmental transition by switching H3K27 acetylation to trimethylation in the prothoracic gland. Proc Natl Acad Sci U S A 2024; 121:e2401861121. [PMID: 39167603 PMCID: PMC11363265 DOI: 10.1073/pnas.2401861121] [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: 01/30/2024] [Accepted: 07/22/2024] [Indexed: 08/23/2024] Open
Abstract
Insect developmental transitions are precisely coordinated by ecdysone and juvenile hormone (JH). We previously revealed that accumulated H3K27 trimethylation (H3K27me3) at the locus encoding JH signal transducer Hairy is involved in the larval-pupal transition in insects, but the underlying mechanism remains to be fully defined. Here, we show in Drosophila and Bombyx that Rpd3-mediated H3K27 deacetylation in the prothoracic gland during the last larval instar promotes ecdysone biosynthesis and the larval-pupal transition by enabling H3K27me3 accumulation at the Hairy locus to induce its transcriptional repression. Importantly, we find that the homeodomain transcription factor Schlank acts to switch active H3K27 acetylation (H3K27ac) to repressive H3K27me3 at the Hairy locus by directly binding to the Hairy promoter and then recruiting the histone deacetylase Rpd3 and the histone methyltransferase PRC2 component Su(z)12 through physical interactions. Moreover, Schlank inhibits Hairy transcription to facilitate the larval-pupal transition, and the Schlank signaling cascade is suppressed by JH but regulated in a positive feedback manner by ecdysone. Together, our data uncover that Schlank mediates epigenetic reprogramming of H3K27 modifications in hormone actions during insect developmental transition.
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Affiliation(s)
- Dongqin Yuan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Xing Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Yan Yang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Ling Wei
- School of Life Sciences, Southwest University, Chongqing400715, China
| | - Hao Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Tujing Zhao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Mengge Guo
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Zheng Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Zhu Huang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Min Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Zongcai Dai
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Peixin Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Qingyou Xia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Wenliang Qian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Daojun Cheng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
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2
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Nicoletti P, Zafer S, Matok L, Irron I, Patrick M, Haklai R, Evangelista JE, Marino GB, Ma’ayan A, Sewda A, Holmes G, Britton SR, Lee WJ, Wu M, Ru Y, Arnaud E, Botto L, Brody LC, Byren JC, Caggana M, Carmichael SL, Cilliers D, Conway K, Crawford K, Cuellar A, Di Rocco F, Engel M, Fearon J, Feldkamp ML, Finnell R, Fisher S, Freudlsperger C, Garcia-Fructuoso G, Hagge R, Heuzé Y, Harshbarger RJ, Hobbs C, Howley M, Jenkins MM, Johnson D, Justice CM, Kane A, Kay D, Gosain AK, Langlois P, Legal-Mallet L, Lin AE, Mills JL, Morton JE, Noons P, Olshan A, Persing J, Phipps JM, Redett R, Reefhuis J, Rizk E, Samson TD, Shaw GM, Sicko R, Smith N, Staffenberg D, Stoler J, Sweeney E, Taub PJ, Timberlake AT, Topczewska J, Wall SA, Wilson AF, Wilson LC, Boyadjiev SA, Wilkie AO, Richtsmeier JT, Jabs EW, Romitti PA, Karasik D, Birnbaum RY, Peter I. Regulatory elements in SEM1-DLX5-DLX6 (7q21.3) locus contribute to genetic control of coronal nonsyndromic craniosynostosis and bone density-related traits. GENETICS IN MEDICINE OPEN 2024; 2:101851. [PMID: 39345948 PMCID: PMC11434253 DOI: 10.1016/j.gimo.2024.101851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Purpose The etiopathogenesis of coronal nonsyndromic craniosynostosis (cNCS), a congenital condition defined by premature fusion of 1 or both coronal sutures, remains largely unknown. Methods We conducted the largest genome-wide association study of cNCS followed by replication, fine mapping, and functional validation of the most significant region using zebrafish animal model. Results Genome-wide association study identified 6 independent genome-wide-significant risk alleles, 4 on chromosome 7q21.3 SEM1-DLX5-DLX6 locus, and their combination conferred over 7-fold increased risk of cNCS. The top variants were replicated in an independent cohort and showed pleiotropic effects on brain and facial morphology and bone mineral density. Fine mapping of 7q21.3 identified a craniofacial transcriptional enhancer (eDlx36) within the linkage region of the top variant (rs4727341; odds ratio [95% confidence interval], 0.48[0.39-0.59]; P = 1.2E-12) that was located in SEM1 intron and enriched in 4 rare risk variants. In zebrafish, the activity of the transfected human eDlx36 enhancer was observed in the frontonasal prominence and calvaria during skull development and was reduced when the 4 rare risk variants were introduced into the sequence. Conclusion Our findings support a polygenic nature of cNCS risk and functional role of craniofacial enhancers in cNCS susceptibility with potential broader implications for bone health.
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Affiliation(s)
- Paola Nicoletti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Samreen Zafer
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Lital Matok
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Inbar Irron
- Department of Life Sciences, Faculty of Natural Sciences and The Center for Evolutionarily Genomics and Medicine, Ben Gurion University, Beer Sheva, Israel
| | - Meidva Patrick
- Department of Life Sciences, Faculty of Natural Sciences and The Center for Evolutionarily Genomics and Medicine, Ben Gurion University, Beer Sheva, Israel
| | - Rotem Haklai
- Department of Life Sciences, Faculty of Natural Sciences and The Center for Evolutionarily Genomics and Medicine, Ben Gurion University, Beer Sheva, Israel
| | - John Erol Evangelista
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Giacomo B. Marino
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Avi Ma’ayan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Anshuman Sewda
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Greg Holmes
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sierra R. Britton
- Department of Population Health Sciences, Weill Cornell Medical College of Cornell University New York, NY
| | - Won Jun Lee
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Meng Wu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ying Ru
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Eric Arnaud
- Department of Neurosurgery, Necker Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Lorenzo Botto
- Department of Pediatrics, Division of Medical Genetics, University of Utah, Salt Lake City, Utah
| | - Lawrence C. Brody
- Social and Behavioral Research Branch, National Human Genome Research Institute, Bethesda, MD
| | - Jo C. Byren
- Craniofacial Unit, Department of Plastic Surgery, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Michele Caggana
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY
| | - Suzan L. Carmichael
- Department of Pediatrics, Department of Obstetrics and Gynecology, Stanford University, Stanford, CA
| | - Deirdre Cilliers
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Kristin Conway
- Department of Epidemiology, University of Iowa, Iowa City, IA
| | - Karen Crawford
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Araceli Cuellar
- Department of Pediatrics, University of California, Davis, CA
| | - Federico Di Rocco
- Hôpital Femme Mère Enfant Hospices Civils de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Michael Engel
- Department of Oral and Cranio-Maxillofacial Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Jeffrey Fearon
- The Craniofacial Center, Medical City Children’s Hospital Dallas, Dallas, TX
| | - Marcia L. Feldkamp
- Department of Pediatrics, Division of Medical Genetics, University of Utah, Salt Lake City, Utah
| | - Richard Finnell
- Center for Precision Environmental Health, Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, Texas
| | - Sarah Fisher
- Birth Defects Registry, New York State Department of Health, Albany, NY
| | - Christian Freudlsperger
- Department of Oral and Cranio-Maxillofacial Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Rhinda Hagge
- Department of Epidemiology, University of Iowa, Iowa City, IA
| | - Yann Heuzé
- Université de Bordeaux, CNRS, Ministère de la Culture, PACEA, Pessac, France
| | | | - Charlotte Hobbs
- Rady Children’s Institute for Genomic Medicine, San Diego, CA
| | - Meredith Howley
- Birth Defects Registry, New York State Department of Health, Albany, NY
| | - Mary M. Jenkins
- Division of Birth Defects and Infant Disorders, Centers for Disease Control and Prevention, Atlanta, GA
| | - David Johnson
- Craniofacial Unit, Department of Plastic Surgery, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Cristina M. Justice
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Baltimore, MD
| | - Alex Kane
- Department of Plastic Surgery, UT Southwestern Medical Center, Dallas, TX
| | - Denise Kay
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY
| | - Arun Kumar Gosain
- Department of Surgery, Division of Pediatric Plastic Surgery, Children’s Hospital of Chicago, Northwestern University, Chicago, IL
| | - Peter Langlois
- Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Austin Campus, Austin, TX
| | - Laurence Legal-Mallet
- Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia, Université de Paris Cité, Imagine Institute, INSERM U1163, Paris, France
| | - Angela E. Lin
- Medical Genetics, Mass General Hospital for Children, Harvard Medical School, Boston, MA
| | - James L. Mills
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD
| | - Jenny E.V. Morton
- Birmingham Health Partners, Birmingham Women’s and Children’s Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Peter Noons
- Birmingham Craniofacial Unit, Birmingham Women’s and Children’s Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Andrew Olshan
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC
| | - John Persing
- Division of Plastic and Reconstructive Surgery, Yale School of Medicine, New Haven, CT
| | - Julie M. Phipps
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Richard Redett
- Department of Plastic and Reconstructive Surgery, Johns Hopkins University, Baltimore, MD
| | - Jennita Reefhuis
- Division of Birth Defects and Infant Disorders, Centers for Disease Control and Prevention, Atlanta, GA
| | - Elias Rizk
- Department of Neurosurgery, Pennsylvania State University Medical Center, Hershey, PA
| | - Thomas D. Samson
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Pennsylvania State University Medical Center, Hershey, PA
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University, Stanford, CA
| | - Robert Sicko
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY
| | - Nataliya Smith
- Neuroscience Institute, Pennsylvania State University, College of Medicine, Hershey Medical Center, Hershey, PA
| | - David Staffenberg
- Hansjörg Wyss Department of Plastic Surgery, NYU Langone Medical Center, Hassenfeld Children’s Hospital, New York, NY
| | - Joan Stoler
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA
| | - Elizabeth Sweeney
- Department of Clinical Genetics, Liverpool Women’s Hospital NHS Trust, Liverpool, United Kingdom
| | - Peter J. Taub
- Division of Plastic and Reconstructive Surgery, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Andrew T. Timberlake
- Hansjörg Wyss Department of Plastic Surgery, NYU Langone Medical Center, Hassenfeld Children’s Hospital, New York, NY
| | - Jolanta Topczewska
- Department of Surgery, Division of Pediatric Plastic Surgery, Children’s Hospital of Chicago, Northwestern University, Chicago, IL
| | - Steven A. Wall
- Craniofacial Unit, Department of Plastic Surgery, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Alexander F. Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Baltimore, MD
| | - Louise C. Wilson
- Clinical Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | | | - Andrew O.M. Wilkie
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Joan T. Richtsmeier
- Department of Anthropology, Pennsylvania State University, University Park, PA
| | - Ethylin Wang Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Paul A. Romitti
- Department of Epidemiology, University of Iowa, Iowa City, IA
| | - David Karasik
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Ramon Y. Birnbaum
- Department of Life Sciences, Faculty of Natural Sciences and The Center for Evolutionarily Genomics and Medicine, Ben Gurion University, Beer Sheva, Israel
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
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Schneider S, Anderson JB, Bradley RP, Beigel K, Wright CM, Maguire BA, Yan G, Taylor DM, Harbour JW, Heuckeroth RO. BAP1 is required prenatally for differentiation and maintenance of postnatal murine enteric nervous system. J Clin Invest 2024; 134:e177771. [PMID: 38690732 PMCID: PMC11060734 DOI: 10.1172/jci177771] [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: 11/20/2023] [Accepted: 03/05/2024] [Indexed: 05/03/2024] Open
Abstract
Epigenetic regulatory mechanisms are underappreciated, yet are critical for enteric nervous system (ENS) development and maintenance. We discovered that fetal loss of the epigenetic regulator Bap1 in the ENS lineage caused severe postnatal bowel dysfunction and early death in Tyrosinase-Cre Bap1fl/fl mice. Bap1-depleted ENS appeared normal in neonates; however, by P15, Bap1-deficient enteric neurons were largely absent from the small and large intestine of Tyrosinase-Cre Bap1fl/fl mice. Bowel motility became markedly abnormal with disproportionate loss of cholinergic neurons. Single-cell RNA sequencing at P5 showed that fetal Bap1 loss in Tyrosinase-Cre Bap1fl/fl mice markedly altered the composition and relative proportions of enteric neuron subtypes. In contrast, postnatal deletion of Bap1 did not cause enteric neuron loss or impaired bowel motility. These findings suggest that BAP1 is critical for postnatal enteric neuron differentiation and for early enteric neuron survival, a finding that may be relevant to the recently described human BAP1-associated neurodevelopmental disorder.
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Affiliation(s)
- Sabine Schneider
- Children’s Hospital of Philadelphia Research Institute, Abramson Research Center, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Neurology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jessica B. Anderson
- Children’s Hospital of Philadelphia Research Institute, Abramson Research Center, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rebecca P. Bradley
- Children’s Hospital of Philadelphia Research Institute, Abramson Research Center, Philadelphia, Pennsylvania, USA
| | - Katherine Beigel
- Children’s Hospital of Philadelphia Research Institute, Abramson Research Center, Philadelphia, Pennsylvania, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia Research Institute, Abramson Research Center, Philadelphia, Pennsylvania, USA
| | - Christina M. Wright
- Children’s Hospital of Philadelphia Research Institute, Abramson Research Center, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Beth A. Maguire
- Children’s Hospital of Philadelphia Research Institute, Abramson Research Center, Philadelphia, Pennsylvania, USA
| | - Guang Yan
- Children’s Hospital of Philadelphia Research Institute, Abramson Research Center, Philadelphia, Pennsylvania, USA
| | - Deanne M. Taylor
- Children’s Hospital of Philadelphia Research Institute, Abramson Research Center, Philadelphia, Pennsylvania, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia Research Institute, Abramson Research Center, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - J. William Harbour
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Robert O. Heuckeroth
- Children’s Hospital of Philadelphia Research Institute, Abramson Research Center, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Kim S, Morgunova E, Naqvi S, Goovaerts S, Bader M, Koska M, Popov A, Luong C, Pogson A, Swigut T, Claes P, Taipale J, Wysocka J. DNA-guided transcription factor cooperativity shapes face and limb mesenchyme. Cell 2024; 187:692-711.e26. [PMID: 38262408 PMCID: PMC10872279 DOI: 10.1016/j.cell.2023.12.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/23/2023] [Accepted: 12/27/2023] [Indexed: 01/25/2024]
Abstract
Transcription factors (TFs) can define distinct cellular identities despite nearly identical DNA-binding specificities. One mechanism for achieving regulatory specificity is DNA-guided TF cooperativity. Although in vitro studies suggest that it may be common, examples of such cooperativity remain scarce in cellular contexts. Here, we demonstrate how "Coordinator," a long DNA motif composed of common motifs bound by many basic helix-loop-helix (bHLH) and homeodomain (HD) TFs, uniquely defines the regulatory regions of embryonic face and limb mesenchyme. Coordinator guides cooperative and selective binding between the bHLH family mesenchymal regulator TWIST1 and a collective of HD factors associated with regional identities in the face and limb. TWIST1 is required for HD binding and open chromatin at Coordinator sites, whereas HD factors stabilize TWIST1 occupancy at Coordinator and titrate it away from HD-independent sites. This cooperativity results in the shared regulation of genes involved in cell-type and positional identities and ultimately shapes facial morphology and evolution.
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Affiliation(s)
- Seungsoo Kim
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Ekaterina Morgunova
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Seppe Goovaerts
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium; Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Maram Bader
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mervenaz Koska
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Christy Luong
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Angela Pogson
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Peter Claes
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium; Department of Human Genetics, KU Leuven, Leuven, Belgium; Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Jussi Taipale
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden; Department of Biochemistry, University of Cambridge, Cambridge, UK; Applied Tumor Genomics Program, University of Helsinki, Helsinki, Finland
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA.
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5
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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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6
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Smeriglio P, Zalc A. Cranial Neural Crest Cells Contribution to Craniofacial Bone Development and Regeneration. Curr Osteoporos Rep 2023; 21:624-631. [PMID: 37421571 DOI: 10.1007/s11914-023-00804-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/14/2023] [Indexed: 07/10/2023]
Abstract
PURPOSE OF REVIEW This review aims to summarize (i) the latest evidence on cranial neural crest cells (CNCC) contribution to craniofacial development and ossification; (ii) the recent discoveries on the mechanisms responsible for their plasticity; and (iii) the newest procedures to ameliorate maxillofacial tissue repair. RECENT FINDINGS CNCC display a remarkable differentiation potential that exceeds the capacity of their germ layer of origin. The mechanisms by which they expand their plasticity was recently described. Their ability to participate to craniofacial bone development and regeneration open new perspectives for treatments of traumatic craniofacial injuries or congenital syndromes. These conditions can be life-threatening, require invasive maxillofacial surgery and can leave deep sequels on our health or quality of life. With accumulating evidence showing how CNCC-derived stem cells potential can ameliorate craniofacial reconstruction and tissue repair, we believe a deeper understanding of the mechanisms regulating CNCC plasticity is essential to ameliorate endogenous regeneration and improve tissue repair therapies.
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Affiliation(s)
- Piera Smeriglio
- Centre de Recherche en Myologie, Institut de Myologie, INSERM, Sorbonne Université, 75013, Paris, France.
| | - Antoine Zalc
- Institut Cochin, CNRS, INSERM, Université Paris Cité, 75014, Paris, France.
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7
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Selleri L, Rijli FM. Shaping faces: genetic and epigenetic control of craniofacial morphogenesis. Nat Rev Genet 2023; 24:610-626. [PMID: 37095271 DOI: 10.1038/s41576-023-00594-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2023] [Indexed: 04/26/2023]
Abstract
Major differences in facial morphology distinguish vertebrate species. Variation of facial traits underlies the uniqueness of human individuals, and abnormal craniofacial morphogenesis during development leads to birth defects that significantly affect quality of life. Studies during the past 40 years have advanced our understanding of the molecular mechanisms that establish facial form during development, highlighting the crucial roles in this process of a multipotent cell type known as the cranial neural crest cell. In this Review, we discuss recent advances in multi-omics and single-cell technologies that enable genes, transcriptional regulatory networks and epigenetic landscapes to be closely linked to the establishment of facial patterning and its variation, with an emphasis on normal and abnormal craniofacial morphogenesis. Advancing our knowledge of these processes will support important developments in tissue engineering, as well as the repair and reconstruction of the abnormal craniofacial complex.
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Affiliation(s)
- Licia Selleri
- Program in Craniofacial Biology, Department of Orofacial Sciences, School of Dentistry, University of California, San Francisco, CA, USA.
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA.
| | - Filippo M Rijli
- Laboratory of Developmental Neuroepigenetics, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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8
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Wu Y, Lan Y, Mao J, Shen J, Kang T, Xie Z. The interaction between the nervous system and the stomatognathic system: from development to diseases. Int J Oral Sci 2023; 15:34. [PMID: 37580325 PMCID: PMC10425412 DOI: 10.1038/s41368-023-00241-4] [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: 03/29/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023] Open
Abstract
The crosstalk between the nerve and stomatognathic systems plays a more important role in organismal health than previously appreciated with the presence of emerging concept of the "brain-oral axis". A deeper understanding of the intricate interaction between the nervous system and the stomatognathic system is warranted, considering their significant developmental homology and anatomical proximity, and the more complex innervation of the jawbone compared to other skeletons. In this review, we provide an in-depth look at studies concerning neurodevelopment, craniofacial development, and congenital anomalies that occur when the two systems develop abnormally. It summarizes the cross-regulation between nerves and jawbones and the effects of various states of the jawbone on intrabony nerve distribution. Diseases closely related to both the nervous system and the stomatognathic system are divided into craniofacial diseases caused by neurological illnesses, and neurological diseases caused by an aberrant stomatognathic system. The two-way relationships between common diseases, such as periodontitis and neurodegenerative disorders, and depression and oral diseases were also discussed. This review provides valuable insights into novel strategies for neuro-skeletal tissue engineering and early prevention and treatment of orofacial and neurological diseases.
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Affiliation(s)
- Yuzhu Wu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, China
| | - Yanhua Lan
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, China
| | - Jiajie Mao
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, China
| | - Jiahui Shen
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, China
| | - Ting Kang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, China.
| | - Zhijian Xie
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, China.
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9
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Yankee TN, Oh S, Winchester EW, Wilderman A, Robinson K, Gordon T, Rosenfeld JA, VanOudenhove J, Scott DA, Leslie EJ, Cotney J. Integrative analysis of transcriptome dynamics during human craniofacial development identifies candidate disease genes. Nat Commun 2023; 14:4623. [PMID: 37532691 PMCID: PMC10397224 DOI: 10.1038/s41467-023-40363-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/25/2023] [Indexed: 08/04/2023] Open
Abstract
Craniofacial disorders arise in early pregnancy and are one of the most common congenital defects. To fully understand how craniofacial disorders arise, it is essential to characterize gene expression during the patterning of the craniofacial region. To address this, we performed bulk and single-cell RNA-seq on human craniofacial tissue from 4-8 weeks post conception. Comparisons to dozens of other human tissues revealed 239 genes most strongly expressed during craniofacial development. Craniofacial-biased developmental enhancers were enriched +/- 400 kb surrounding these craniofacial-biased genes. Gene co-expression analysis revealed that regulatory hubs are enriched for known disease causing genes and are resistant to mutation in the normal healthy population. Combining transcriptomic and epigenomic data we identified 539 genes likely to contribute to craniofacial disorders. While most have not been previously implicated in craniofacial disorders, we demonstrate this set of genes has increased levels of de novo mutations in orofacial clefting patients warranting further study.
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Affiliation(s)
- Tara N Yankee
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington, CT, 06030, USA
| | - Sungryong Oh
- University of Connecticut School of Medicine, Department of Genetics and Genome Sciences, Farmington, CT, 06030, USA
| | | | - Andrea Wilderman
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington, CT, 06030, USA
| | - Kelsey Robinson
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Tia Gordon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics Laboratory, Houston, TX, 77021, USA
| | - Jennifer VanOudenhove
- University of Connecticut School of Medicine, Department of Genetics and Genome Sciences, Farmington, CT, 06030, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Justin Cotney
- University of Connecticut School of Medicine, Department of Genetics and Genome Sciences, Farmington, CT, 06030, USA.
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA.
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10
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Sui BD, Zheng CX, Zhao WM, Xuan K, Li B, Jin Y. Mesenchymal condensation in tooth development and regeneration: a focus on translational aspects of organogenesis. Physiol Rev 2023; 103:1899-1964. [PMID: 36656056 DOI: 10.1152/physrev.00019.2022] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 12/26/2022] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
The teeth are vertebrate-specific, highly specialized organs performing fundamental functions of mastication and speech, the maintenance of which is crucial for orofacial homeostasis and is further linked to systemic health and human psychosocial well-being. However, with limited ability for self-repair, the teeth can often be impaired by traumatic, inflammatory, and progressive insults, leading to high prevalence of tooth loss and defects worldwide. Regenerative medicine holds the promise to achieve physiological restoration of lost or damaged organs, and in particular an evolving framework of developmental engineering has pioneered functional tooth regeneration by harnessing the odontogenic program. As a key event of tooth morphogenesis, mesenchymal condensation dictates dental tissue formation and patterning through cellular self-organization and signaling interaction with the epithelium, which provides a representative to decipher organogenetic mechanisms and can be leveraged for regenerative purposes. In this review, we summarize how mesenchymal condensation spatiotemporally assembles from dental stem cells (DSCs) and sequentially mediates tooth development. We highlight condensation-mimetic engineering efforts and mechanisms based on ex vivo aggregation of DSCs, which have achieved functionally robust and physiologically relevant tooth regeneration after implantation in animals and in humans. The discussion of this aspect will add to the knowledge of development-inspired tissue engineering strategies and will offer benefits to propel clinical organ regeneration.
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Affiliation(s)
- Bing-Dong Sui
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi International Joint Research Center for Oral Diseases, Center for Tissue Engineering, School of Stomatology, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Chen-Xi Zheng
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi International Joint Research Center for Oral Diseases, Center for Tissue Engineering, School of Stomatology, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Wan-Min Zhao
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi International Joint Research Center for Oral Diseases, Center for Tissue Engineering, School of Stomatology, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Kun Xuan
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi International Joint Research Center for Oral Diseases, Center for Tissue Engineering, School of Stomatology, Fourth Military Medical University, Xi'an, Shaanxi, China
- Department of Preventive Dentistry, School of Stomatology, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Bei Li
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi International Joint Research Center for Oral Diseases, Center for Tissue Engineering, School of Stomatology, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Yan Jin
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi International Joint Research Center for Oral Diseases, Center for Tissue Engineering, School of Stomatology, Fourth Military Medical University, Xi'an, Shaanxi, China
- Xi'an Institute of Tissue Engineering and Regenerative Medicine, Xi'an, Shaanxi, China
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11
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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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12
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Kessler S, Minoux M, Joshi O, Ben Zouari Y, Ducret S, Ross F, Vilain N, Salvi A, Wolff J, Kohler H, Stadler MB, Rijli FM. A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest. Nat Commun 2023; 14:3242. [PMID: 37277355 DOI: 10.1038/s41467-023-38953-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 05/19/2023] [Indexed: 06/07/2023] Open
Abstract
Enhancer-promoter interactions preferentially occur within boundary-insulated topologically associating domains (TADs), limiting inter-TAD interactions. Enhancer clusters in linear proximity, termed super-enhancers (SEs), ensure high target gene expression levels. Little is known about SE topological regulatory impact during craniofacial development. Here, we identify 2232 genome-wide putative SEs in mouse cranial neural crest cells (CNCCs), 147 of which target genes establishing CNCC positional identity during face formation. In second pharyngeal arch (PA2) CNCCs, a multiple SE-containing region, partitioned into Hoxa Inter-TAD Regulatory Element 1 and 2 (HIRE1 and HIRE2), establishes long-range inter-TAD interactions selectively with Hoxa2, that is required for external and middle ear structures. HIRE2 deletion in a Hoxa2 haploinsufficient background results in microtia. HIRE1 deletion phenocopies the full homeotic Hoxa2 knockout phenotype and induces PA3 and PA4 CNCC abnormalities correlating with Hoxa2 and Hoxa3 transcriptional downregulation. Thus, SEs can overcome TAD insulation and regulate anterior Hoxa gene collinear expression in a CNCC subpopulation-specific manner during craniofacial development.
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Affiliation(s)
- Sandra Kessler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Maryline Minoux
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
- INSERM UMR 1121, Université de Strasbourg, Faculté de Chirurgie Dentaire, 8, rue Sainte Elisabeth, 67 000, Strasbourg, France
| | - Onkar Joshi
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Yousra Ben Zouari
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Sebastien Ducret
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Fiona Ross
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Nathalie Vilain
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Adwait Salvi
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Joachim Wolff
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Hubertus Kohler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Filippo M Rijli
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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13
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Kim S, Morgunova E, Naqvi S, Bader M, Koska M, Popov A, Luong C, Pogson A, Claes P, Taipale J, Wysocka J. DNA-guided transcription factor cooperativity shapes face and limb mesenchyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.541540. [PMID: 37398193 PMCID: PMC10312427 DOI: 10.1101/2023.05.29.541540] [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
Transcription factors (TFs) can define distinct cellular identities despite nearly identical DNA-binding specificities. One mechanism for achieving regulatory specificity is DNA-guided TF cooperativity. Although in vitro studies suggest it may be common, examples of such cooperativity remain scarce in cellular contexts. Here, we demonstrate how 'Coordinator', a long DNA motif comprised of common motifs bound by many basic helix-loop-helix (bHLH) and homeodomain (HD) TFs, uniquely defines regulatory regions of embryonic face and limb mesenchyme. Coordinator guides cooperative and selective binding between the bHLH family mesenchymal regulator TWIST1 and a collective of HD factors associated with regional identities in the face and limb. TWIST1 is required for HD binding and open chromatin at Coordinator sites, while HD factors stabilize TWIST1 occupancy at Coordinator and titrate it away from HD-independent sites. This cooperativity results in shared regulation of genes involved in cell-type and positional identities, and ultimately shapes facial morphology and evolution.
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Affiliation(s)
- Seungsoo Kim
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
- Howard Hughes Medical Institute, Stanford, CA 94305
| | - Ekaterina Morgunova
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
- Department of Genetics, Stanford University, Stanford, CA 94305
| | - Maram Bader
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
| | - Mervenaz Koska
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
| | | | - Christy Luong
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305
| | - Angela Pogson
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
| | - Peter Claes
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Jussi Taipale
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Applied Tumor Genomics Program, University of Helsinki, Helsinki, Finland
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
- Howard Hughes Medical Institute, Stanford, CA 94305
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14
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Schock EN, York JR, LaBonne C. The developmental and evolutionary origins of cellular pluripotency in the vertebrate neural crest. Semin Cell Dev Biol 2023; 138:36-44. [PMID: 35534333 DOI: 10.1016/j.semcdb.2022.04.008] [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: 10/30/2021] [Revised: 03/28/2022] [Accepted: 04/10/2022] [Indexed: 11/30/2022]
Abstract
Neural crest cells are central to vertebrate development and evolution, endowing vertebrates with a "new head" that resulted in morphological, physiological, and behavioral features that allowed vertebrates to become active predators. One remarkable feature of neural crest cells is their multi-germ layer potential that allows for the formation of both ectodermal (pigmentation, peripheral glia, sensory neurons) and mesenchymal (connective tissue, cartilage/bone, dermis) cell types. Understanding the cellular and evolutionary origins of this broad cellular potential in the neural crest has been a long-standing focus for developmental biologists. Here, we review recent work that has demonstrated that neural crest cells share key features with pluripotent blastula stem cells, including expression of the Yamanaka stem cell factors (Oct3/4, Klf4, Sox2, c-Myc). These shared features suggest that pluripotency is either retained in the neural crest from blastula stages or subsequently reactivated as the neural crest forms. We highlight the cellular and molecular parallels between blastula stem cells and neural crest cells and discuss the work that has led to current models for the cellular origins of broad potential in the crest. Finally, we explore how these themes can provide new insights into how and when neural crest cells and pluripotency evolved in vertebrates and the evolutionary relationship between these populations.
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Affiliation(s)
| | | | - Carole LaBonne
- Dept. of Molecular Biosciences; NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, United States.
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15
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Liu H, Liu Y, Jin SG, Johnson J, Xuan H, Lu D, Li J, Zhai L, Li X, Zhao Y, Liu M, Craig SEL, Floramo JS, Molchanov V, Li J, Li JD, Krawczyk C, Shi X, Pfeifer GP, Yang T. TRIM28 secures skeletal stem cell fate during skeletogenesis by silencing neural gene expression and repressing GREM1/AKT/mTOR signaling axis. Cell Rep 2023; 42:112012. [PMID: 36680774 PMCID: PMC11339952 DOI: 10.1016/j.celrep.2023.112012] [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: 07/15/2022] [Revised: 11/16/2022] [Accepted: 01/04/2023] [Indexed: 01/21/2023] Open
Abstract
Long bones are generated by mesoderm-derived skeletal progenitor/stem cells (SSCs) through endochondral ossification, a process of sequential chondrogenic and osteogenic differentiation tightly controlled by the synergy between intrinsic and microenvironment cues. Here, we report that loss of TRIM28, a transcriptional corepressor, in mesoderm-derived cells expands the SSC pool, weakens SSC osteochondrogenic potential, and endows SSCs with properties of ectoderm-derived neural crest cells (NCCs), leading to severe defects of skeletogenesis. TRIM28 preferentially enhances H3K9 trimethylation and DNA methylation on chromatin regions more accessible in NCCs; loss of this silencing upregulates neural gene expression and enhances neurogenic potential. Moreover, TRIM28 loss causes hyperexpression of GREM1, which is an extracellular signaling factor promoting SSC self-renewal and SSC neurogenic potential by activating AKT/mTORC1 signaling. Our results suggest that TRIM28-mediated chromatin silencing establishes a barrier for maintaining the SSC lineage trajectory and preventing a transition to ectodermal fate by regulating both intrinsic and microenvironment cues.
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Affiliation(s)
- Huadie Liu
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ye Liu
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Seung-Gi Jin
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Jennifer Johnson
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Hongwen Xuan
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Di Lu
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Jianshuang Li
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Lukai Zhai
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Xianfeng Li
- Hunan International Scientific and Technological Cooperation Base of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Yaguang Zhao
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA; Hunan International Scientific and Technological Cooperation Base of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Minmin Liu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Sonya E L Craig
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Joseph S Floramo
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Vladimir Molchanov
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Jie Li
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Jia-Da Li
- Hunan International Scientific and Technological Cooperation Base of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Connie Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Xiaobing Shi
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Gerd P Pfeifer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Tao Yang
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA.
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16
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Gopinathan G, Zhang X, Luan X, Diekwisch TGH. Changes in Hox Gene Chromatin Organization during Odontogenic Lineage Specification. Genes (Basel) 2023; 14:198. [PMID: 36672939 PMCID: PMC9859321 DOI: 10.3390/genes14010198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Craniofacial tissues comprise highly evolved organs characterized by a relative lack of expression in the HOX family transcription factors. In the present study, we sought to define the epigenetic events that limit HOX gene expression from undifferentiated neural crest cells to semi-differentiated odontogenic progenitors and to explore the effects of elevated levels of HOX. The ChIP-chip data demonstrated high levels of repressive H3K27me3 marks on the HOX gene promoters in ES and cranial neural crest cells when compared to the H3K4me3 marks, while the K4/K27 ratio was less repressive in the odontogenic progenitors, dental follicle, dental pulp, periodontal ligament fibroblasts, alveolar bone osteoblasts, and cementoblasts. The gene expression of multiple HOX genes, especially those from the HOXA and HOXB clusters, was significantly elevated and many times higher in alveolar bone cells than in the dental follicle cells. In addition, the HOX levels in the skeletal osteoblasts were many times higher in the trunk osteoblasts compared to the alveolar bone osteoblasts, and the repressive mark H3K27me3 promoter occupancy was substantially and significantly elevated in the alveolar bone osteoblasts when compared to the trunk osteoblasts. To explore the effect of elevated HOX levels in craniofacial neural crest cells, HOX expression was induced by transfecting cells with the Cdx4 transcription factor, resulting in a significant decrease in the mineralization markers, RUNX2, OSX, and OCN upon HOX elevation. Promoting HOX gene expression in developing teeth using the small molecule EZH2 inhibitor GSK126 resulted in an increased number of patterning events, supernumerary cusp formation, and increased Hoxa4 and Hoxb6 gene expression when compared to the controls. Together, these studies illustrate the profound effects of epigenetic regulatory events at all stages of the differentiation of craniofacial peripheral tissues from the neural crest, including lineage specification, tissue differentiation, and patterning.
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Affiliation(s)
- Gokul Gopinathan
- Center for Craniofacial Research and Diagnosis, Texas A&M University, Dallas, TX 75246, USA
| | - Xinmin Zhang
- Bioinforx Inc., 510 Charmany Dr#275a, Madison, WI 53719, USA
| | - Xianghong Luan
- Center for Craniofacial Research and Diagnosis, Texas A&M University, Dallas, TX 75246, USA
| | - Thomas G. H. Diekwisch
- Center for Craniofacial Research and Diagnosis, Texas A&M University, Dallas, TX 75246, USA
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17
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Macrae TA, Fothergill-Robinson J, Ramalho-Santos M. Regulation, functions and transmission of bivalent chromatin during mammalian development. Nat Rev Mol Cell Biol 2023; 24:6-26. [PMID: 36028557 DOI: 10.1038/s41580-022-00518-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2022] [Indexed: 12/25/2022]
Abstract
Cells differentiate and progress through development guided by a dynamic chromatin landscape that mediates gene expression programmes. During development, mammalian cells display a paradoxical chromatin state: histone modifications associated with gene activation (trimethylated histone H3 Lys4 (H3K4me3)) and with gene repression (trimethylated H3 Lys27 (H3K27me3)) co-occur at promoters of developmental genes. This bivalent chromatin modification state is thought to poise important regulatory genes for expression or repression during cell-lineage specification. In this Review, we discuss recent work that has expanded our understanding of the molecular basis of bivalent chromatin and its contributions to mammalian development. We describe the factors that establish bivalency, especially histone-lysine N-methyltransferase 2B (KMT2B) and Polycomb repressive complex 2 (PRC2), and consider evidence indicating that PRC1 shapes bivalency and may contribute to its transmission between generations. We posit that bivalency is a key feature of germline and embryonic stem cells, as well as other types of stem and progenitor cells. Finally, we discuss the relevance of bivalent chromtin to human development and cancer, and outline avenues of future research.
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Affiliation(s)
- Trisha A Macrae
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA.
| | - Julie Fothergill-Robinson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Miguel Ramalho-Santos
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
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18
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Cell-type specific profiling of histone post-translational modifications in the adult mouse striatum. Nat Commun 2022; 13:7720. [PMID: 36513652 PMCID: PMC9747932 DOI: 10.1038/s41467-022-35384-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022] Open
Abstract
Epigenetic gene regulation in the heterogeneous brain remains challenging to decipher with current strategies. Bulk tissue analysis from pooled subjects reflects the average of cell-type specific changes across cell-types and individuals, which obscures causal relationships between epigenetic modifications, regulation of gene expression, and complex pathology. To address these limitations, we optimized a hybrid protocol, ICuRuS, for the isolation of nuclei tagged in specific cell-types and histone post translational modification profiling from the striatum of a single mouse. We combined affinity-based isolation of the medium spiny neuron subtypes, Adenosine 2a Receptor or Dopamine Receptor D1, with cleavage of histone-DNA complexes using an antibody-targeted micrococcal nuclease to release DNA complexes for paired end sequencing. Unlike fluorescence activated cell sorting paired with chromatin immunoprecipitation, ICuRuS allowed for robust epigenetic profiling at cell-type specific resolution. Our analysis provides a framework to understand combinatorial relationships between neuronal-subtype-specific epigenetic modifications and gene expression.
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19
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Jing J, Zhang M, Guo T, Pei F, Yang Y, Chai Y. Rodent incisor as a model to study mesenchymal stem cells in tissue homeostasis and repair. FRONTIERS IN DENTAL MEDICINE 2022. [DOI: 10.3389/fdmed.2022.1068494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
The homeostasis of adult tissues, such as skin, hair, blood, and bone, requires continuous generation of differentiated progeny of stem cells. The rodent incisor undergoes constant renewal and can provide an extraordinary model for studying stem cells and their progeny in adult tissue homeostasis, cell differentiation and injury-induced regeneration. Meanwhile, cellular heterogeneity in the mouse incisor also provides an opportunity to study cell-cell communication between different cell types, including interactions between stem cells and their niche environment. More importantly, the molecular and cellular regulatory mechanisms revealed by the mouse incisor have broad implications for other organs. Here we review recent findings and advances using the mouse incisor as a model, including perspectives on the heterogeneity of cells in the mesenchyme, the niche environment, and signaling networks that regulate stem cell behavior. The progress from this field will not only expand the knowledge of stem cells and organogenesis, but also bridge a gap between animal models and tissue regeneration.
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20
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Chen Q, Dai J, Bian Q. Integration of 3D genome topology and local chromatin features uncovers enhancers underlying craniofacial-specific cartilage defects. SCIENCE ADVANCES 2022; 8:eabo3648. [PMID: 36417512 PMCID: PMC9683718 DOI: 10.1126/sciadv.abo3648] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Aberrations in tissue-specific enhancers underlie many developmental defects. Disrupting a noncoding region distal from the human SOX9 gene causes the Pierre Robin sequence (PRS) characterized by the undersized lower jaw. Such a craniofacial-specific defect has been previously linked to enhancers transiently active in cranial neural crest cells (CNCCs). We demonstrate that the PRS region also strongly regulates Sox9 in CNCC-derived Meckel's cartilage (MC), but not in limb cartilages, even after decommissioning of CNCC enhancers. Such an MC-specific regulatory effect correlates with the MC-specific chromatin contacts between the PRS region and Sox9, highlighting the importance of lineage-dependent chromatin topology in instructing enhancer usage. By integrating the enhancer signatures and chromatin topology, we uncovered >10,000 enhancers that function differentially between MC and limb cartilages and demonstrated their association with human diseases. Our findings provide critical insights for understanding the choreography of gene regulation during development and interpreting the genetic basis of craniofacial pathologies.
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Affiliation(s)
- Qiming Chen
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
| | - Jiewen Dai
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
- Corresponding author. (J.D.); (Q.B.)
| | - Qian Bian
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai Institute of Precision Medicine, Shanghai, 200125, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Corresponding author. (J.D.); (Q.B.)
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21
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Xu J, Liu H, Lan Y, Jiang R. The transcription factors Foxf1 and Foxf2 integrate the SHH, HGF and TGFβ signaling pathways to drive tongue organogenesis. Development 2022; 149:dev200667. [PMID: 36227576 PMCID: PMC10655918 DOI: 10.1242/dev.200667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 09/26/2022] [Indexed: 11/19/2023]
Abstract
The tongue is a highly specialized muscular organ with diverse cellular origins, which provides an excellent model for understanding mechanisms controlling tissue-tissue interactions during organogenesis. Previous studies showed that SHH signaling is required for tongue morphogenesis and tongue muscle organization, but little is known about the underlying mechanisms. Here we demonstrate that the Foxf1/Foxf2 transcription factors act in the cranial neural crest cell (CNCC)-derived mandibular mesenchyme to control myoblast migration into the tongue primordium during tongue initiation, and thereafter continue to regulate intrinsic tongue muscle assembly and lingual tendon formation. We performed chromatin immunoprecipitation sequencing analysis and identified Hgf, Tgfb2 and Tgfb3 among the target genes of Foxf2 in the embryonic tongue. Through genetic analyses of mice with CNCC-specific inactivation of Smo or both Foxf1 and Foxf2, we show that Foxf1 and Foxf2 mediate hedgehog signaling-mediated regulation of myoblast migration during tongue initiation and intrinsic tongue muscle formation by regulating the activation of the HGF and TGFβ signaling pathways. These data uncover the molecular network integrating the SHH, HGF and TGFβ signaling pathways in regulating tongue organogenesis.
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Affiliation(s)
- Jingyue Xu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Han Liu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Yu Lan
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Division of Plastic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Departments of Pediatrics and Surgery, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Rulang Jiang
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Division of Plastic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Departments of Pediatrics and Surgery, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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22
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Zhao X, Tang L, Le TP, Nguyen BH, Chen W, Zheng M, Yamaguchi H, Dawson B, You S, Martinez-Traverso IM, Erhardt S, Wang J, Li M, Martin JF, Lee BH, Komatsu Y, Wang J. Yap and Taz promote osteogenesis and prevent chondrogenesis in neural crest cells in vitro and in vivo. Sci Signal 2022; 15:eabn9009. [PMID: 36282910 PMCID: PMC9938793 DOI: 10.1126/scisignal.abn9009] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Neural crest cells (NCCs) are multipotent stem cells that can differentiate into multiple cell types, including the osteoblasts and chondrocytes, and constitute most of the craniofacial skeleton. Here, we show through in vitro and in vivo studies that the transcriptional regulators Yap and Taz have redundant functions as key determinants of the specification and differentiation of NCCs into osteoblasts or chondrocytes. Primary and cultured NCCs deficient in Yap and Taz switched from osteogenesis to chondrogenesis, and NCC-specific deficiency for Yap and Taz resulted in bone loss and ectopic cartilage in mice. Yap bound to the regulatory elements of key genes that govern osteogenesis and chondrogenesis in NCCs and directly regulated the expression of these genes, some of which also contained binding sites for the TCF/LEF transcription factors that interact with the Wnt effector β-catenin. During differentiation of NCCs in vitro and NCC-derived osteogenesis in vivo, Yap and Taz promoted the expression of osteogenic genes such as Runx2 and Sp7 but repressed the expression of chondrogenic genes such as Sox9 and Col2a1. Furthermore, Yap and Taz interacted with β-catenin in NCCs to coordinately promote osteoblast differentiation and repress chondrogenesis. Together, our data indicate that Yap and Taz promote osteogenesis in NCCs and prevent chondrogenesis, partly through interactions with the Wnt-β-catenin pathway.
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Affiliation(s)
- Xiaolei Zhao
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Li Tang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Tram P. Le
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Bao H. Nguyen
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, US
| | - Wen Chen
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Mingjie Zheng
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Hiroyuki Yamaguchi
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Brian Dawson
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Shuangjie You
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
- MD Anderson Cancer Center and UT Health Graduate School of Biomedical Sciences, The University of Texas, Houston, Texas 77030, USA
| | - Idaliz M. Martinez-Traverso
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, US
| | - Shannon Erhardt
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
- MD Anderson Cancer Center and UT Health Graduate School of Biomedical Sciences, The University of Texas, Houston, Texas 77030, USA
| | - Jianxin Wang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Min Li
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - James F. Martin
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, US
- Texas Heart Institute, Houston, Texas 77030, USA
| | - Brendan H. Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Yoshihiro Komatsu
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
- MD Anderson Cancer Center and UT Health Graduate School of Biomedical Sciences, The University of Texas, Houston, Texas 77030, USA
| | - Jun Wang
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
- MD Anderson Cancer Center and UT Health Graduate School of Biomedical Sciences, The University of Texas, Houston, Texas 77030, USA
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23
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Lin D, Xu W, Hong P, Wu C, Zhang Z, Zhang S, Xing L, Yang B, Zhou W, Xiao Q, Wang J, Wang C, He Y, Chen X, Cao X, Man J, Reheman A, Wu X, Hao X, Hu Z, Chen C, Cao Z, Yin R, Fu ZF, Zhou R, Teng Z, Li G, Cao G. Decoding the spatial chromatin organization and dynamic epigenetic landscapes of macrophage cells during differentiation and immune activation. Nat Commun 2022; 13:5857. [PMID: 36195603 PMCID: PMC9532393 DOI: 10.1038/s41467-022-33558-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 09/22/2022] [Indexed: 11/09/2022] Open
Abstract
Immunocytes dynamically reprogram their gene expression profiles during differentiation and immunoresponse. However, the underlying mechanism remains elusive. Here, we develop a single-cell Hi-C method and systematically delineate the 3D genome and dynamic epigenetic atlas of macrophages during these processes. We propose "degree of disorder" to measure genome organizational patterns inside topologically-associated domains, which is correlated with the chromatin epigenetic states, gene expression, and chromatin structure variability in individual cells. Furthermore, we identify that NF-κB initiates systematic chromatin conformation reorganization upon Mycobacterium tuberculosis infection. The integrated Hi-C, eQTL, and GWAS analysis depicts the atlas of the long-range target genes of mycobacterial disease susceptible loci. Among these, the SNP rs1873613 is located in the anchor of a dynamic chromatin loop with LRRK2, whose inhibitor AdoCbl could be an anti-tuberculosis drug candidate. Our study provides comprehensive resources for the 3D genome structure of immunocytes and sheds insights into the order of genome organization and the coordinated gene transcription during immunoresponse.
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Affiliation(s)
- Da Lin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China
| | - Weize Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Ping Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, China
- College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Chengchao Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhihui Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Siheng Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Lingyu Xing
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Bing Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Wei Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Qin Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China
| | - Jinyue Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China
| | - Cong Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yu He
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xi Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xiaojian Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Jiangwei Man
- College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Aikebaier Reheman
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- College of Animal Science and Technology, Tarim University, Alar, China
| | - Xiaofeng Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xingjie Hao
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhe Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Chunli Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Guizhou University, Guiyang, China
| | - Zimeng Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China
- College of Animal Sciences, Yangtze River University, Jingzhou, China
| | - Rong Yin
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhen F Fu
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Rong Zhou
- Dapartment of Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhaowei Teng
- The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, China.
- College of Informatics, Huazhong Agricultural University, Wuhan, China.
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
- College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China.
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24
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Jing J, Feng J, Yuan Y, Guo T, Lei J, Pei F, Ho TV, Chai Y. Spatiotemporal single-cell regulatory atlas reveals neural crest lineage diversification and cellular function during tooth morphogenesis. Nat Commun 2022; 13:4803. [PMID: 35974052 PMCID: PMC9381504 DOI: 10.1038/s41467-022-32490-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 08/02/2022] [Indexed: 11/10/2022] Open
Abstract
Cranial neural crest cells are an evolutionary innovation of vertebrates for craniofacial development and function, yet the mechanisms that govern the cell fate decisions of postmigratory cranial neural crest cells remain largely unknown. Using the mouse molar as a model, we perform single-cell transcriptome profiling to interrogate the cell fate diversification of postmigratory cranial neural crest cells. We reveal the landscape of transcriptional heterogeneity and define the specific cellular domains during the progression of cranial neural crest cell-derived dental lineage diversification, and find that each domain makes a specific contribution to distinct molar mesenchymal tissues. Furthermore, IGF signaling-mediated cell-cell interaction between the cellular domains highlights the pivotal role of autonomous regulation of the dental mesenchyme. Importantly, we reveal cell-type-specific gene regulatory networks in the dental mesenchyme and show that Foxp4 is indispensable for the differentiation of periodontal ligament. Our single-cell atlas provides comprehensive mechanistic insight into the cell fate diversification process of the cranial neural crest cell-derived odontogenic populations.
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Affiliation(s)
- Junjun Jing
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA ,grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Chengdu, Sichuan 610041 China
| | - Jifan Feng
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA
| | - Yuan Yuan
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA
| | - Tingwei Guo
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA
| | - Jie Lei
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA
| | - Fei Pei
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA
| | - Thach-Vu Ho
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA
| | - Yang Chai
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA.
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25
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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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26
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Isbel L, Grand RS, Schübeler D. Generating specificity in genome regulation through transcription factor sensitivity to chromatin. Nat Rev Genet 2022; 23:728-740. [PMID: 35831531 DOI: 10.1038/s41576-022-00512-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2022] [Indexed: 12/11/2022]
Abstract
Cell type-specific gene expression relies on transcription factors (TFs) binding DNA sequence motifs embedded in chromatin. Understanding how motifs are accessed in chromatin is crucial to comprehend differential transcriptional responses and the phenotypic impact of sequence variation. Chromatin obstacles to TF binding range from DNA methylation to restriction of DNA access by nucleosomes depending on their position, composition and modification. In vivo and in vitro approaches now enable the study of TF binding in chromatin at unprecedented resolution. Emerging insights suggest that TFs vary in their ability to navigate chromatin states. However, it remains challenging to link binding and transcriptional outcomes to molecular characteristics of TFs or the local chromatin substrate. Here, we discuss our current understanding of how TFs access DNA in chromatin and novel techniques and directions towards a better understanding of this critical step in genome regulation.
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Affiliation(s)
- Luke Isbel
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Ralph S Grand
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. .,Faculty of Sciences, University of Basel, Basel, Switzerland.
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27
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Hirsch N, Dahan I, D'haene E, Avni M, Vergult S, Vidal-García M, Magini P, Graziano C, Severi G, Bonora E, Nardone AM, Brancati F, Fernández-Jaén A, Rory OJ, Hallgrímsson B, Birnbaum RY. HDAC9 structural variants disrupting TWIST1 transcriptional regulation lead to craniofacial and limb malformations. Genome Res 2022; 32:1242-1253. [PMID: 35710300 PMCID: PMC9341515 DOI: 10.1101/gr.276196.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 06/02/2022] [Indexed: 11/25/2022]
Abstract
Structural variants (SVs) can affect protein-coding sequences as well as gene regulatory elements. However, SVs disrupting protein-coding sequences that also function as cis-regulatory elements remain largely uncharacterized. Here, we show that craniosynostosis patients with SVs containing the histone deacetylase 9 (HDAC9) protein-coding sequence are associated with disruption of TWIST1 regulatory elements that reside within the HDAC9 sequence. Based on SVs within the HDAC9-TWIST1 locus, we defined the 3'-HDAC9 sequence as a critical TWIST1 regulatory region, encompassing craniofacial TWIST1 enhancers and CTCF sites. Deletions of either Twist1 enhancers (eTw5-7Δ/Δ) or CTCF site (CTCF-5Δ/Δ) within the Hdac9 protein-coding sequence led to decreased Twist1 expression and altered anterior/posterior limb expression patterns of SHH pathway genes. This decreased Twist1 expression results in a smaller sized and asymmetric skull and polydactyly that resembles Twist1+/- mouse phenotype. Chromatin conformation analysis revealed that the Twist1 promoter interacts with Hdac9 sequences that encompass Twist1 enhancers and a CTCF site, and that interactions depended on the presence of both regulatory regions. Finally, a large inversion of the entire Hdac9 sequence (Hdac9 INV/+) in mice that does not disrupt Hdac9 expression but repositions Twist1 regulatory elements showed decreased Twist1 expression and led to a craniosynostosis-like phenotype and polydactyly. Thus, our study elucidates essential components of TWIST1 transcriptional machinery that reside within the HDAC9 sequence. It suggests that SVs encompassing protein-coding sequences could lead to a phenotype that is not attributed to its protein function but rather to a disruption of the transcriptional regulation of a nearby gene.
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Affiliation(s)
- Naama Hirsch
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Center of Evolutionary Genomics and Medicine, The Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Idit Dahan
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Center of Evolutionary Genomics and Medicine, The Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Eva D'haene
- Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium
| | - Matan Avni
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Center of Evolutionary Genomics and Medicine, The Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium
| | - Marta Vidal-García
- Department of Cell Biology and Anatomy, Alberta Children's Hospital Research Institute, University of Calgary, T2N 1N4, Calgary, Alberta, Canada
| | - Pamela Magini
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy
| | - Claudio Graziano
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy
| | - Giulia Severi
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy
| | - Elena Bonora
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, 40126, Bologna, Italy
| | - Anna Maria Nardone
- Medical Genetics Unit, Policlinico Tor Vergata University Hospital, 00133, Rome, Italy
| | - Francesco Brancati
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
- Human Functional Genomics Laboratory, San Raffaele Pisana, 00167, Rome, Italy
| | - Alberto Fernández-Jaén
- Department of Pediatrics and Neurology, Hospital Universitario Quirónsalud, School of Medicine, Universidad Europea de Madrid, 28223, Madrid, Spain
| | - Olson J Rory
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Benedikt Hallgrímsson
- Department of Cell Biology and Anatomy, Alberta Children's Hospital Research Institute, University of Calgary, T2N 1N4, Calgary, Alberta, Canada
| | - Ramon Y Birnbaum
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Center of Evolutionary Genomics and Medicine, The Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
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28
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Cellular plasticity in the neural crest and cancer. Curr Opin Genet Dev 2022; 75:101928. [PMID: 35749971 DOI: 10.1016/j.gde.2022.101928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 11/24/2022]
Abstract
In vertebrates, neural crest cells (NCCs) are a multipotent embryonic population generating both neural/neuronal and mesenchymal derivatives, and thus the neural crest (NC) is often referred to as the fourth germ layer. NC development is a dynamic process, where NCCs possess substantial plasticity in transcriptional and epigenomic profiles. Recent technical advances in single-cell and low-input sequencing have empowered fine-resolution characterisation of NC development. In this review, we summarise the latest models underlying NC-plasticity acquirement and cell-fate restriction, outline the connections between NC plasticity and NC-derived cancer and envision the new opportunities in studying NC plasticity and its link to cancer.
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29
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Quiat D, Kim SW, Zhang Q, Morton SU, Pereira AC, DePalma SR, Willcox JAL, McDonough B, DeLaughter DM, Gorham JM, Curran JJ, Tumblin M, Nicolau Y, Artunduaga MA, Quintanilla-Dieck L, Osorno G, Serrano L, Hamdan U, Eavey RD, Seidman CE, Seidman JG. An ancient founder mutation located between ROBO1 and ROBO2 is responsible for increased microtia risk in Amerindigenous populations. Proc Natl Acad Sci U S A 2022; 119:e2203928119. [PMID: 35584116 PMCID: PMC9173816 DOI: 10.1073/pnas.2203928119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/12/2022] [Indexed: 01/14/2023] Open
Abstract
Microtia is a congenital malformation that encompasses mild hypoplasia to complete loss of the external ear, or pinna. Although the contribution of genetic variation and environmental factors to microtia remains elusive, Amerindigenous populations have the highest reported incidence. Here, using both transmission disequilibrium tests and association studies in microtia trios (parents and affected child) and microtia cohorts enrolled in Latin America, we map an ∼10-kb microtia locus (odds ratio = 4.7; P = 6.78e-18) to the intergenic region between Roundabout 1 (ROBO1) and Roundabout 2 (ROBO2) (chr3: 78546526 to 78555137). While alleles at the microtia locus significantly increase the risk of microtia, their penetrance is low (<1%). We demonstrate that the microtia locus contains a polymorphic complex repeat element that is expanded in affected individuals. The locus is located near a chromatin loop region that regulates ROBO1 and ROBO2 expression in induced pluripotent stem cell–derived neural crest cells. Furthermore, we use single nuclear RNA sequencing to demonstrate ROBO1 and ROBO2 expression in both fibroblasts and chondrocytes of the mature human pinna. Because the microtia allele is enriched in Amerindigenous populations and is shared by some East Asian subjects with craniofacial malformations, we propose that both populations share a mutation that arose in a common ancestor prior to the ancient migration of Eurasian populations into the Americas and that the high incidence of microtia among Amerindigenous populations reflects the population bottleneck that occurred during the migration out of Eurasia.
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Affiliation(s)
- Daniel Quiat
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Seong Won Kim
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Qi Zhang
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Sarah U. Morton
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Division of Newborn Medicine, Department of Medicine, Boston Children’s Hospital, Boston, MA 02115
| | - Alexandre C. Pereira
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, Medical School of University of Sao Paulo, Sao Paulo, 05508-060, Brazil
| | | | | | | | | | - Joshua M. Gorham
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Justin J. Curran
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | | | | | | | - Lourdes Quintanilla-Dieck
- Department of Otolaryngology Head and Neck Surgery, Oregon Health & Science University, Portland, OR 97239
| | - Gabriel Osorno
- Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, 111321, Colombia
| | | | | | - Roland D. Eavey
- Department of Otolaryngology Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Cardiovascular Division, Brigham and Women’s Hospital, Boston, MA 02115
- HHMI, Chevy Chase, MD 20815
| | - J. G. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115
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30
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Kanai SM, Heffner C, Cox TC, Cunningham ML, Perez FA, Bauer AM, Reigan P, Carter C, Murray SA, Clouthier DE. Auriculocondylar syndrome 2 results from the dominant-negative action of PLCB4 variants. Dis Model Mech 2022; 15:dmm049320. [PMID: 35284927 PMCID: PMC9066496 DOI: 10.1242/dmm.049320] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/22/2022] [Indexed: 12/16/2022] Open
Abstract
Auriculocondylar syndrome 2 (ARCND2) is a rare autosomal dominant craniofacial malformation syndrome linked to multiple genetic variants in the coding sequence of phospholipase C β4 (PLCB4). PLCB4 is a direct signaling effector of the endothelin receptor type A (EDNRA)-Gq/11 pathway, which establishes the identity of neural crest cells (NCCs) that form lower jaw and middle ear structures. However, the functional consequences of PLCB4 variants on EDNRA signaling is not known. Here, we show, using multiple signaling reporter assays, that known PLCB4 variants resulting from missense mutations exert a dominant-negative interference over EDNRA signaling. In addition, using CRISPR/Cas9, we find that F0 mouse embryos modeling one PLCB4 variant have facial defects recapitulating those observed in hypomorphic Ednra mouse models, including a bone that we identify as an atavistic change in the posterior palate/oral cavity. Remarkably, we have identified a similar osseous phenotype in a child with ARCND2. Our results identify the disease mechanism of ARCND2, demonstrate that the PLCB4 variants cause craniofacial differences and illustrate how minor changes in signaling within NCCs may have driven evolutionary changes in jaw structure and function. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Stanley M. Kanai
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Timothy C. Cox
- Departments of Oral and Craniofacial Sciences and Pediatrics, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Michael L. Cunningham
- University of Washington, Department of Pediatrics, Division of Craniofacial Medicine and Seattle Children's Craniofacial Center, Seattle, WA 98105, USA
| | - Francisco A. Perez
- University of Washington, Department of Radiology and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Aaron M. Bauer
- Department of Biology, Villanova University, Villanova, PA 19085, USA
| | - Philip Reigan
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Cristan Carter
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - David E. Clouthier
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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31
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Van Otterloo E, Milanda I, Pike H, Thompson JA, Li H, Jones KL, Williams T. AP-2α and AP-2β cooperatively function in the craniofacial surface ectoderm to regulate chromatin and gene expression dynamics during facial development. eLife 2022; 11:e70511. [PMID: 35333176 PMCID: PMC9038197 DOI: 10.7554/elife.70511] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
The facial surface ectoderm is essential for normal development of the underlying cranial neural crest cell populations, providing signals that direct appropriate growth, patterning, and morphogenesis. Despite the importance of the ectoderm as a signaling center, the molecular cues and genetic programs implemented within this tissue are understudied. Here, we show that removal of two members of the AP-2 transcription factor family, AP-2α and AP-2ß, within the early embryonic ectoderm of the mouse leads to major alterations in the craniofacial complex. Significantly, there are clefts in both the upper face and mandible, accompanied by fusion of the upper and lower jaws in the hinge region. Comparison of ATAC-seq and RNA-seq analyses between controls and mutants revealed significant changes in chromatin accessibility and gene expression centered on multiple AP-2 binding motifs associated with enhancer elements within these ectodermal lineages. In particular, loss of these AP-2 proteins affects both skin differentiation as well as multiple signaling pathways, most notably the WNT pathway. We also determined that the mutant clefting phenotypes that correlated with reduced WNT signaling could be rescued by Wnt1 ligand overexpression in the ectoderm. Collectively, these findings highlight a conserved ancestral function for AP-2 transcription factors in ectodermal development and signaling, and provide a framework from which to understand the gene regulatory network operating within this tissue that directs vertebrate craniofacial development.
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Affiliation(s)
- Eric Van Otterloo
- Iowa Institute for Oral Health Research, College of Dentistry & Dental Clinics, University of IowaIowa CityUnited States
- Department of Periodontics, College of Dentistry & Dental Clinics, University of IowaIowa CityUnited States
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of IowaIowa CityUnited States
- Department of Craniofacial Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Isaac Milanda
- Department of Craniofacial Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Hamish Pike
- Department of Craniofacial Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Jamie A Thompson
- Iowa Institute for Oral Health Research, College of Dentistry & Dental Clinics, University of IowaIowa CityUnited States
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of IowaIowa CityUnited States
| | - Hong Li
- Department of Craniofacial Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Kenneth L Jones
- Department of Pediatrics, Section of Hematology, Oncology, and Bone Marrow Transplant, University of Colorado School of Medicine, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Trevor Williams
- Department of Craniofacial Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children's Hospital ColoradoAuroraUnited States
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32
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Liao J, Huang Y, Wang Q, Chen S, Zhang C, Wang D, Lv Z, Zhang X, Wu M, Chen G. Gene regulatory network from cranial neural crest cells to osteoblast differentiation and calvarial bone development. Cell Mol Life Sci 2022; 79:158. [PMID: 35220463 PMCID: PMC11072871 DOI: 10.1007/s00018-022-04208-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/02/2022] [Accepted: 02/14/2022] [Indexed: 11/03/2022]
Abstract
Calvarial bone is one of the most complex sequences of developmental events in embryology, featuring a uniquely transient, pluripotent stem cell-like population known as the cranial neural crest (CNC). The skull is formed through intramembranous ossification with distinct tissue lineages (e.g. neural crest derived frontal bone and mesoderm derived parietal bone). Due to CNC's vast cell fate potential, in response to a series of inductive secreted cues including BMP/TGF-β, Wnt, FGF, Notch, Hedgehog, Hippo and PDGF signaling, CNC enables generations of a diverse spectrum of differentiated cell types in vivo such as osteoblasts and chondrocytes at the craniofacial level. In recent years, since the studies from a genetic mouse model and single-cell sequencing, new discoveries are uncovered upon CNC patterning, differentiation, and the contribution to the development of cranial bones. In this review, we summarized the differences upon the potential gene regulatory network to regulate CNC derived osteogenic potential in mouse and human, and highlighted specific functions of genetic molecules from multiple signaling pathways and the crosstalk, transcription factors and epigenetic factors in orchestrating CNC commitment and differentiation into osteogenic mesenchyme and bone formation. Disorders in gene regulatory network in CNC patterning indicate highly close relevance to clinical birth defects and diseases, providing valuable transgenic mouse models for subsequent discoveries in delineating the underlying molecular mechanisms. We also emphasized the potential regenerative alternative through scientific discoveries from CNC patterning and genetic molecules in interfering with or alleviating clinical disorders or diseases, which will be beneficial for the molecular targets to be integrated for novel therapeutic strategies in the clinic.
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Affiliation(s)
- Junguang Liao
- College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Yuping Huang
- College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Qiang Wang
- College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Sisi Chen
- College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Chenyang Zhang
- College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Dan Wang
- College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Zhengbing Lv
- College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Xingen Zhang
- Department of Orthopedics, Jiaxing Key Laboratory for Minimally Invasive Surgery in Orthopaedics & Skeletal Regenerative Medicine, Zhejiang Rongjun Hospital, Jiaxing, 314001, China
| | - Mengrui Wu
- Institute of Genetics, College of Life Science, Zhejiang University, Hangzhou, 310058, China
| | - Guiqian Chen
- College of Life Science and Medicine, Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
- Institute of Genetics, College of Life Science, Zhejiang University, Hangzhou, 310058, China.
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33
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Xu R, Liu Y, Zhou Y, Lin W, Yuan Q, Zhou X, Yang Y. Gnas Loss Causes Chondrocyte Fate Conversion in Cranial Suture Formation. J Dent Res 2022; 101:931-941. [PMID: 35220829 DOI: 10.1177/00220345221075215] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Calvaria development is distinct from limb formation. Craniosynostosis is a skull deformity characterized by premature cranial suture fusion due to the loss of the GNAS gene and, consequently, its encoded protein Gαs. This birth defect requires surgery, with potential lethal consequences. So far, hardly any early-stage nonsurgical interventions for GNAS loss-related craniosynostosis are available. Here, we investigated the role of the Gnas gene in mice in guarding the distinctiveness of intramembranous ossification and how loss of Gnas triggered endochondral-like ossification within the cranial sutures. Single-cell RNA sequencing (scRNA-seq) of normal neonatal mice cranial suture chondrocytes showed a Hedgehog (Hh) inactivation pattern, which was associated with Gαs signaling activation. Loss of Gnas evoked chondrocyte-to-osteoblast fate conversion and resulted in cartilage heterotopic ossification (HO) within cranial sutures and fontanels of the mouse model, leading to a skull deformity resembling craniosynostosis in patients with loss of GNAS. Activation of ectopic Hh signaling within cranial chondrocytes stimulated the conversion of cell identity through a hypertrophy-like stage, which shared features of endochondral ossification in vivo. Reduction of Gli transcription activity by crossing with a loss-of-function Gli2 allele or injecting GLI1/2 antagonist hindered the progression of cartilage HO in neonatal stage mice. Our study uncovered the role of Gαs in maintaining cranial chondrocyte identity during neonatal calvaria development in mice and how reduction of Hh signaling could be a nonsurgical intervention to reduce skull deformity in craniosynostosis due to loss of GNAS.
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Affiliation(s)
- R. Xu
- Department of Developmental Biology, Harvard School of Dental Medicine, Harvard Stem Cell Institute, Boston, MA, USA
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Y. Liu
- Department of Developmental Biology, Harvard School of Dental Medicine, Harvard Stem Cell Institute, Boston, MA, USA
| | - Y. Zhou
- Department of Developmental Biology, Harvard School of Dental Medicine, Harvard Stem Cell Institute, Boston, MA, USA
| | - W. Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Q. Yuan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - X. Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Y. Yang
- Department of Developmental Biology, Harvard School of Dental Medicine, Harvard Stem Cell Institute, Boston, MA, USA
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34
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Kitazawa T, Minoux M, Ducret S, Rijli FM. Different Ectopic Hoxa2 Expression Levels in Mouse Cranial Neural Crest Cells Result in Distinct Craniofacial Anomalies and Homeotic Phenotypes. J Dev Biol 2022; 10:jdb10010009. [PMID: 35225962 PMCID: PMC8883995 DOI: 10.3390/jdb10010009] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 02/01/2023] Open
Abstract
Providing appropriate positional identity and patterning information to distinct rostrocaudal subpopulations of cranial neural crest cells (CNCCs) is central to vertebrate craniofacial morphogenesis. Hox genes are not expressed in frontonasal and first pharyngeal arch (PA1) CNCCs, whereas a single Hox gene, Hoxa2, is necessary to provide patterning information to second pharyngeal arch (PA2) CNCCs. In frog, chick and mouse embryos, ectopic expression of Hoxa2 in Hox-negative CNCCs induced hypoplastic phenotypes of CNCC derivatives of variable severity, associated or not with homeotic transformation of a subset of PA1 structures into a PA2-like identity. Whether these different morphological outcomes are directly related to distinct Hoxa2 overexpression levels is unknown. To address this issue, we selectively induced Hoxa2 overexpression in mouse CNCCs, using a panel of mouse lines expressing different Hoxa2 ectopic expression levels, including a newly generated Hoxa2 knocked-in mouse line. While ectopic Hoxa2 expression at only 60% of its physiological levels was sufficient for pinna duplication, ectopic Hoxa2 expression at 100% of its normal level was required for complete homeotic repatterning of a subset of PA1 skeletal elements into a duplicated set of PA2-like elements. On the other hand, ectopic Hoxa2 overexpression at non-physiological levels (200% of normal levels) led to an almost complete loss of craniofacial skeletal structures. Moreover, ectopic Hoxa5 overexpression in CNCCs, while also resulting in severe craniofacial defects, did not induce homeotic changes of PA1-derived CNCCs, indicating Hoxa2 specificity in repatterning a subset of Hox-negative CNCCs. These results reconcile some discrepancies in previously published experiments and indicate that distinct subpopulations of CNCCs are differentially sensitive to ectopic levels of Hox expression.
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Affiliation(s)
- Taro Kitazawa
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; (T.K.); (M.M.); (S.D.)
| | - Maryline Minoux
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; (T.K.); (M.M.); (S.D.)
- INSERM UMR 1121, Faculté de Chirurgie Dentaire, Université de Strasbourg, 8 rue Sainte Elisabeth, 67 000 Strasbourg, France
| | - Sebastien Ducret
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; (T.K.); (M.M.); (S.D.)
| | - Filippo M. Rijli
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; (T.K.); (M.M.); (S.D.)
- Departement Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
- Correspondence:
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35
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Dinsmore CJ, Soriano P. Differential regulation of cranial and cardiac neural crest by serum response factor and its cofactors. eLife 2022; 11:e75106. [PMID: 35044299 PMCID: PMC8806183 DOI: 10.7554/elife.75106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022] Open
Abstract
Serum response factor (SRF) is an essential transcription factor that influences many cellular processes including cell proliferation, migration, and differentiation. SRF directly regulates and is required for immediate early gene (IEG) and actin cytoskeleton-related gene expression. SRF coordinates these competing transcription programs through discrete sets of cofactors, the ternary complex factors (TCFs) and myocardin-related transcription factors (MRTFs). The relative contribution of these two programs to in vivo SRF activity and mutant phenotypes is not fully understood. To study how SRF utilizes its cofactors during development, we generated a knock-in SrfaI allele in mice harboring point mutations that disrupt SRF-MRTF-DNA complex formation but leave SRF-TCF activity unaffected. Homozygous SrfaI/aI mutants die at E10.5 with notable cardiovascular phenotypes, and neural crest conditional mutants succumb at birth to defects of the cardiac outflow tract but display none of the craniofacial phenotypes associated with complete loss of SRF in that lineage. Our studies further support an important role for MRTF mediating SRF function in cardiac neural crest and suggest new mechanisms by which SRF regulates transcription during development.
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Affiliation(s)
- Colin J Dinsmore
- Department of Cell, Development and Regenerative Biology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Philippe Soriano
- Department of Cell, Development and Regenerative Biology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
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Torres-Campana D, Horard B, Denaud S, Benoit G, Loppin B, Orsi GA. Three classes of epigenomic regulators converge to hyperactivate the essential maternal gene deadhead within a heterochromatin mini-domain. PLoS Genet 2022; 18:e1009615. [PMID: 34982772 PMCID: PMC8759638 DOI: 10.1371/journal.pgen.1009615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 01/14/2022] [Accepted: 12/10/2021] [Indexed: 11/24/2022] Open
Abstract
The formation of a diploid zygote is a highly complex cellular process that is entirely controlled by maternal gene products stored in the egg cytoplasm. This highly specialized transcriptional program is tightly controlled at the chromatin level in the female germline. As an extreme case in point, the massive and specific ovarian expression of the essential thioredoxin Deadhead (DHD) is critically regulated in Drosophila by the histone demethylase Lid and its partner, the histone deacetylase complex Sin3A/Rpd3, via yet unknown mechanisms. Here, we identified Snr1 and Mod(mdg4) as essential for dhd expression and investigated how these epigenomic effectors act with Lid and Sin3A to hyperactivate dhd. Using Cut&Run chromatin profiling with a dedicated data analysis procedure, we found that dhd is intriguingly embedded in an H3K27me3/H3K9me3-enriched mini-domain flanked by DNA regulatory elements, including a dhd promoter-proximal element essential for its expression. Surprisingly, Lid, Sin3a, Snr1 and Mod(mdg4) impact H3K27me3 and this regulatory element in distinct manners. However, we show that these effectors activate dhd independently of H3K27me3/H3K9me3, and that dhd remains silent in the absence of these marks. Together, our study demonstrates an atypical and critical role for chromatin regulators Lid, Sin3A, Snr1 and Mod(mdg4) to trigger tissue-specific hyperactivation within a unique heterochromatin mini-domain. Multicellular development depends on a tight control of gene expression in each cell type. This relies on the coordinated activities of nuclear proteins that interact with DNA or its histone scaffold to promote or restrict gene transcription. For example, we previously showed that the histone modifying enzymes Lid and Sin3A/Rpd3 are required in Drosophila ovaries for the massive expression of deadhead (dhd), a gene encoding for a thioredoxin that is essential for fertility. In this paper, we have further identified two additional dhd regulators, Snr1 and Mod(mdg4) and dissected the mechanism behind hyperactivation of this gene. Using the epigenomic profiling method Cut&Run with a dedicated data analysis approach, we unexpectedly found that dhd is embedded in an unusual chromatin mini-domain featuring repressive histone modifications H3K27me3 and H3K9me3 and flanked by two regulatory elements. However, we further showed that Lid, Sin3A, Snr1 and Mod(mdg4) behave like obligatory activators of dhd independently of this mini-domain. Our study unveils how multiple broad-acting epigenomic effectors operate in non-canonical manners to ensure a critical and specialized gene activation event. These findings challenge our knowledge on these regulatory mechanisms and their roles in development and pathology.
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Affiliation(s)
- Daniela Torres-Campana
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS UMR5239, École Normale Supérieure de Lyon, University of Lyon, Lyon, France
| | - Béatrice Horard
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS UMR5239, École Normale Supérieure de Lyon, University of Lyon, Lyon, France
| | - Sandrine Denaud
- Institute of Human Genetics, UMR 9002, CNRS, Université de Montpellier, Montpellier, France
| | - Gérard Benoit
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS UMR5239, École Normale Supérieure de Lyon, University of Lyon, Lyon, France
| | - Benjamin Loppin
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS UMR5239, École Normale Supérieure de Lyon, University of Lyon, Lyon, France
- * E-mail: (BL); (GAO)
| | - Guillermo A. Orsi
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS UMR5239, École Normale Supérieure de Lyon, University of Lyon, Lyon, France
- * E-mail: (BL); (GAO)
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Xia Z, Bi X, Yang S, Yang X, Song Z, Wei J, Xu P, Rink L, Min J, Wang F. Metal transporter Slc30a1 controls pharyngeal neural crest differentiation via the zinc-Snai2-Jag1 cascade. MedComm (Beijing) 2021; 2:778-797. [PMID: 34977877 PMCID: PMC8706747 DOI: 10.1002/mco2.91] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 02/07/2023] Open
Abstract
The pharyngeal arch (PA) is a neural crest (NC)-derived organ that is transiently developed during embryogenesis and is required for the subsequent development of various tissues. However, the role of zinc during PA differentiation from NC progenitor cells is unknown. Here, we found that the metal transporters Slc30a1a and Slc30a1b mediate zinc homeostasis during PA differentiation. Slc30a1-deficient zebrafish develop zinc accumulation in NC cells, with increased expression of stemness markers and PA dorsal genes, and SMART-seq analyses revealed that the genes snai2 and jag1b may serve as downstream targets. Furthermore, functional studies showed that knocking down either snai2 or jag1b rescues PA development in Slc30a1-deficient zebrafish. Notably, we identified the double zinc-finger domain in the transcription factor Snai2 as a zinc-responsive element that regulates jag1b expression. Our findings indicate that the Slc30a1/zinc-snai2-jag1b axis is an essential regulatory network controlling PA differentiation, shedding new light on the function of zinc homeostasis in maintaining NC cell stemness and multipotency in vertebrates.
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Affiliation(s)
- Zhidan Xia
- The First Affiliated HospitalSchool of Public HealthInstitute of Translational MedicineInstitute of GeneticsZhejiang University School of MedicineHangzhouChina
| | - Xinying Bi
- The First Affiliated HospitalSchool of Public HealthInstitute of Translational MedicineInstitute of GeneticsZhejiang University School of MedicineHangzhouChina
- The First Affiliated HospitalHengyang Medical SchoolUniversity of South ChinaHengyangChina
| | - Sisi Yang
- The First Affiliated HospitalSchool of Public HealthInstitute of Translational MedicineInstitute of GeneticsZhejiang University School of MedicineHangzhouChina
| | - Xiu Yang
- The First Affiliated HospitalSchool of Public HealthInstitute of Translational MedicineInstitute of GeneticsZhejiang University School of MedicineHangzhouChina
| | - Zijun Song
- The First Affiliated HospitalSchool of Public HealthInstitute of Translational MedicineInstitute of GeneticsZhejiang University School of MedicineHangzhouChina
| | - Jiayu Wei
- The First Affiliated HospitalSchool of Public HealthInstitute of Translational MedicineInstitute of GeneticsZhejiang University School of MedicineHangzhouChina
| | - Pengfei Xu
- The First Affiliated HospitalSchool of Public HealthInstitute of Translational MedicineInstitute of GeneticsZhejiang University School of MedicineHangzhouChina
| | - Lothar Rink
- Faculty of MedicineInstitute of ImmunologyRWTH Aachen UniversityAachenGermany
| | - Junxia Min
- The First Affiliated HospitalSchool of Public HealthInstitute of Translational MedicineInstitute of GeneticsZhejiang University School of MedicineHangzhouChina
| | - Fudi Wang
- The First Affiliated HospitalSchool of Public HealthInstitute of Translational MedicineInstitute of GeneticsZhejiang University School of MedicineHangzhouChina
- The First Affiliated HospitalHengyang Medical SchoolUniversity of South ChinaHengyangChina
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The effects of altered BMP4 signaling in first branchial-arch-derived murine embryonic orofacial tissues. Int J Oral Sci 2021; 13:40. [PMID: 34845186 PMCID: PMC8630201 DOI: 10.1038/s41368-021-00142-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 08/31/2021] [Accepted: 09/05/2021] [Indexed: 11/27/2022] Open
Abstract
The first branchial arch (BA1), which is derived from cranial neural crest (CNC) cells, gives rise to various orofacial tissues. Cre mice are widely used for the determination of CNC and exploration of gene functions in orofacial development. However, there is a lack of Cre mice specifically marked BA1's cells. Pax2-Cre allele was previously generated and has been widely used in the field of inner ear development. Here, by compounding Pax2-Cre and R26R-mTmG mice, we found a specific expression pattern of Pax2+ cells that marked BA1's mesenchymal cells and the BA1-derivatives. Compared to Pax2-Cre; R26R-mTmG allele, GFP+ cells were abundantly found both in BA1 and second branchial arch in Wnt1-Cre;R26R-mTmG mice. As BMP4 signaling is required for orofacial development, we over-activated Bmp4 by using Pax2-Cre; pMes-BMP4 strain. Interestingly, our results showed bilateral hyperplasia between the upper and lower teeth. We also compare the phenotypes of Wnt1-Cre; pMes-BMP4 and Pax2-Cre; pMes-BMP4 strains and found severe deformation of molar buds, palate, and maxilla-mandibular bony structures in Wnt1-Cre; pMes-BMP4 mice; however, the morphology of these orofacial organs were comparable between controls and Pax2-Cre; pMes-BMP4 mice except for bilateral hyperplastic tissues. We further explore the properties of the hyperplastic tissue and found it is not derived from Runx2+ cells but expresses Msx1, and probably caused by abnormal cell proliferation and altered expression pattern of p-Smad1/5/8. In sum, our findings suggest altering BMP4 signaling in BA1-specific cell lineage may lead to unique phenotypes in orofacial regions, further hinting that Pax2-Cre mice could be a new model for genetic manipulation of BA1-derived organogenesis in the orofacial region.
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Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nat Commun 2021; 12:6094. [PMID: 34667153 PMCID: PMC8526749 DOI: 10.1038/s41467-021-26234-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 09/14/2021] [Indexed: 11/09/2022] Open
Abstract
Zygotic genome activation (ZGA) initiates regionalized transcription underlying distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, the direct mechanistic link between the onset of ZGA and the tissue-specific transcription remains unclear. Here, we have addressed the involvement of chromatin organizer Satb2 in orchestrating both processes during zebrafish embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility reveals contrasting molecular activities of maternally deposited and zygotically synthesized Satb2. Maternal Satb2 prevents premature transcription of zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Thus, our comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented highlighting the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant. Activation of the zygotic genome is a critical transition during development, though the link to tissue-specific gene regulation remains unclear. Here the authors demonstrate distinct functions for Satb2 before and after zygotic genome activation, highlighting the temporal coordination of these roles.
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Roffers-Agarwal J, Lidberg KA, Gammill LS. The lysine methyltransferase SETD2 is a dynamically expressed regulator of early neural crest development. Genesis 2021; 59:e23448. [PMID: 34498354 DOI: 10.1002/dvg.23448] [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: 12/22/2020] [Revised: 07/31/2021] [Accepted: 08/13/2021] [Indexed: 11/11/2022]
Abstract
SETD2 is a histone H3 lysine 36 (H3K36) tri-methylase that is upregulated in response to neural crest induction. Because the H3K36 di-methylase NSD3 and cytoplasmic non-histone protein methylation are necessary for neural crest development, we investigated the expression and requirement for SETD2 in the neural crest. SetD2 is expressed throughout the chick blastoderm beginning at gastrulation. Subsequently, SetD2 mRNA becomes restricted to the neural plate, where it is strongly and dynamically expressed as neural tissue is regionalized and cell fate decisions are made. This includes expression in premigratory neural crest cells, which is downregulated prior to migration. Likely due to the early onset of its expression, SETD2 morpholino knockdown does not significantly alter premigratory Sox10 expression or neural crest migration; however, both are disrupted by a methyltransferase mutant SETD2 construct. These results suggest that SETD2 activity is essential for early neural crest development, further demonstrating that lysine methylation is an important mechanism regulating the neural crest.
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Affiliation(s)
- Julaine Roffers-Agarwal
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA.,Developmental Biology Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kevin A Lidberg
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA.,Developmental Biology Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Laura S Gammill
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA.,Developmental Biology Center, University of Minnesota, Minneapolis, Minnesota, USA
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41
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Kanazawa H, Gonda K, Tamura T, Takenoshita S. A case of lipoma, calcification, and brain malformations in the midline of the skull. Radiol Case Rep 2021; 16:2509-2513. [PMID: 34257790 PMCID: PMC8259223 DOI: 10.1016/j.radcr.2021.05.073] [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: 03/11/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 11/19/2022] Open
Abstract
Few cases of pericallosal lipoma with several other lesions, including specific forms of calcification and brain malformations, have been reported. We present the case of an asymptomatic 83-year-old man with a pericallosallipoma with peculiar symmetrical morphology in the midline of the skull. We posit that the lesions began forming in the very early embryonic period and were closely associated with the cranial neural crest cells. We report the neuroradiological findings of this characteristic lesion and discuss several literature reviews on the process of its formation.
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Affiliation(s)
- Hideto Kanazawa
- Department of Neurology, Daido Central Hospital, 1-1-37 Asato, Naha, Okinawa 902-0067, Japan
- Daido Obesity and Metabolism Research Center, Naha, Okinawa, Japan
| | - Kenji Gonda
- Daido Obesity and Metabolism Research Center, Naha, Okinawa, Japan
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University, Fukushima, Japan
- President of Fukushima Medical University, Fukushima, Japan
| | - Takamitsu Tamura
- Department of Neurology, Daido Central Hospital, 1-1-37 Asato, Naha, Okinawa 902-0067, Japan
- Daido Obesity and Metabolism Research Center, Naha, Okinawa, Japan
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Crispatzu G, Rehimi R, Pachano T, Bleckwehl T, Cruz-Molina S, Xiao C, Mahabir E, Bazzi H, Rada-Iglesias A. The chromatin, topological and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo. Nat Commun 2021; 12:4344. [PMID: 34272393 PMCID: PMC8285398 DOI: 10.1038/s41467-021-24641-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 06/21/2021] [Indexed: 12/16/2022] Open
Abstract
Poised enhancers (PEs) represent a genetically distinct set of distal regulatory elements that control the expression of major developmental genes. Before becoming activated in differentiating cells, PEs are already bookmarked in pluripotent cells with unique chromatin and topological features that could contribute to their privileged regulatory properties. However, since PEs were originally characterized in embryonic stem cells (ESC), it is currently unknown whether PEs are functionally conserved in vivo. Here, we show that the chromatin and 3D structural features of PEs are conserved among mouse pluripotent cells both in vitro and in vivo. We also uncovered that the interactions between PEs and their target genes are globally controlled by the combined action of Polycomb, Trithorax and architectural proteins. Moreover, distal regulatory sequences located close to developmental genes and displaying the typical genetic (i.e. CpG islands) and chromatin (i.e. high accessibility and H3K27me3 levels) features of PEs are commonly found across vertebrates. These putative PEs show high sequence conservation within specific vertebrate clades, with only a few being evolutionary conserved across all vertebrates. Lastly, by genetically disrupting PEs in mouse and chicken embryos, we demonstrate that these regulatory elements play essential roles during the induction of major developmental genes in vivo.
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Affiliation(s)
- Giuliano Crispatzu
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
- Department of Internal Medicine II, University Hospital Cologne, Cologne, Germany.
- Cluster of Excellence for Aging Research (CECAD), University of Cologne, Cologne, Germany.
| | - Rizwan Rehimi
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Tomas Pachano
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Tore Bleckwehl
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Sara Cruz-Molina
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - Cally Xiao
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cluster of Excellence for Aging Research (CECAD), University of Cologne, Cologne, Germany
- Department of Dermatology and Venereology, University Hospital Cologne, Cologne, Germany
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Esther Mahabir
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Hisham Bazzi
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cluster of Excellence for Aging Research (CECAD), University of Cologne, Cologne, Germany
- Department of Dermatology and Venereology, University Hospital Cologne, Cologne, Germany
| | - Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
- Cluster of Excellence for Aging Research (CECAD), University of Cologne, Cologne, Germany.
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria-SODERCAN, Santander, Spain.
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Whole-Genome Sequencing Identifies Two Novel Rare Mutations in BMP5 and BMP2 in Monozygotic Twins With Microtia. J Craniofac Surg 2021; 33:e212-e217. [PMID: 34183628 DOI: 10.1097/scs.0000000000007689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
ABSTRACT Microtia is a rare congenital anomaly of the ear; it is regulated by both genetic and environmental factors. However, the mechanisms underlying its pathogenesis are unknown. In this study, the genomes of 2-year-old twin sisters with right microtia were sequenced using human genome-wide sequencing, an approach useful for identifying mutations in genes responsible for congenital microtia. The phenotypes of the twin sisters included congenital microtia on the right side, abnormal auricle shape in the right external ear, a peanut shape for the residual ear, and complete atresia of the right external auditory canal. In the twin sisters, we identified a previously unknown mutation in BMP5(exon4:c.833- 4C>G), as well as a new mutation (exon2:c.G332T:p.S111I) in BMP2, both of which were confirmed using polymerase chain reaction-based amplification of the corresponding genome regions, followed by first-generation sequencing. The exon4:c.833-4C>G mutation in human BMP5 may be the main cause of microtia in the twin sisters. A pathogenic mutation in human BMP2 (exon2:c.G332T:p.S111I) may be responsible for the facial deformity in the twin sisters. Thus, our study demonstrates the potential of genome-wide sequencing for identifying novel mutations associated with microtia on the whole-genome scale and extends the mutation spectrum of BMP5. Additionally, our data suggest that BMP2 is another pathogenic gene associated with microtia.
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Yu J, Xiong C, Zhuo B, Wen Z, Shen J, Liu C, Chang L, Wang K, Wang M, Wu C, Wu X, Xu X, Ruan H, Li G. Analysis of Local Chromatin States Reveals Gene Transcription Potential during Mouse Neural Progenitor Cell Differentiation. Cell Rep 2021; 32:107953. [PMID: 32726618 DOI: 10.1016/j.celrep.2020.107953] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/25/2020] [Accepted: 07/02/2020] [Indexed: 01/23/2023] Open
Abstract
Chromatin dynamics play a critical role in cell fate determination and maintenance by regulating the expression of genes essential for development and differentiation. In mouse embryonic stem cells (mESCs), maintenance of pluripotency coincides with a poised chromatin state containing active and repressive histone modifications. However, the structural features of poised chromatin are largely uncharacterized. By adopting mild time-course MNase-seq with computational analysis, the low-compact chromatin in mESCs is featured in two groups: one in more open regions, corresponding to an active state, and the other enriched with bivalent histone modifications, considered the poised state. A parameter called the chromatin opening potential index (COPI) is also devised to quantify the transcription potential based on the dynamic changes of MNase-seq signals at promoter regions. Use of COPI provides effective prediction of gene activation potential and, more importantly, reveals a few developmental factors essential for mouse neural progenitor cell (NPC) differentiation.
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Affiliation(s)
- Juan Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chaoyang Xiong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Baowen Zhuo
- Baoan Maternal and Child Health Hospital, Jinan University, Shenzhen 518102, China
| | - Zengqi Wen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Shen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Cuifang Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Luyuan Chang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Kehui Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chenyi Wu
- Molecular Biophysics Laboratories, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Xudong Wu
- Department of Cell Biology, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China
| | - Xueqing Xu
- Baoan Maternal and Child Health Hospital, Jinan University, Shenzhen 518102, China.
| | - Haihe Ruan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
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45
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Zhang X, Liu Q, Zhang H, Zhao S, Huang J, Sovannary T, Bunnath L, Aun HS, Samnom H, Su B, Chen H. The distinct morphological phenotypes of Southeast Asian aborigines are shaped by novel mechanisms for adaptation to tropical rainforests. Natl Sci Rev 2021; 9:nwab072. [PMID: 35371514 PMCID: PMC8970429 DOI: 10.1093/nsr/nwab072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 11/13/2022] Open
Abstract
Southeast Asian aborigines, the hunter-gatherer populations living in tropical rainforests, exhibit distinct morphological phenotypes, including short stature, dark skin, curly hair and a wide and snub nose. The underlying genetic architecture and evolutionary mechanism of these phenotypes remain a long-term mystery. We conducted whole genome deep sequencing of 81 Cambodian aborigines from eight ethnic groups. Through a genome-wide scan of selective sweeps, we discovered key genes harboring Cambodian-enriched mutations that may contribute to their phenotypes, including two hair morphogenesis genes (TCHH and TCHHL1), one nasal morphology gene (PAX3) and a set of genes (such as ENTPD1-AS1) associated with short stature. The identified new genes and novel mutations suggest an independent origin of the distinct phenotypes in Cambodian aborigines through parallel evolution, refuting the long-standing argument on the common ancestry of these phenotypes among the worldwide rainforest hunter-gatherers. Notably, our discovery reveals that various types of molecular mechanisms, including antisense transcription and epigenetic regulation, contribute to human morphogenesis, providing novel insights into the genetics of human environmental adaptation.
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Affiliation(s)
- Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Qi Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- School of Future Technology and Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Shilei Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- School of Future Technology and Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiahui Huang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Tuot Sovannary
- Department of Geography and Land Management, Royal University of Phnom Penh, Phnom Penh 12000, Cambodia
| | - Long Bunnath
- Department of Geography and Land Management, Royal University of Phnom Penh, Phnom Penh 12000, Cambodia
| | - Hong Seang Aun
- Department of Geography and Land Management, Royal University of Phnom Penh, Phnom Penh 12000, Cambodia
| | - Ham Samnom
- Capacity Development Facilitator for Handicap International Federation and Freelance Research, Battambang 02358, Cambodia
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Hua Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- School of Future Technology and Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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46
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Cai S, Quan S, Yang G, Chen M, Ye Q, Wang G, Yu H, Wang Y, Qiao S, Zeng X. Nutritional Status Impacts Epigenetic Regulation in Early Embryo Development: A Scoping Review. Adv Nutr 2021; 12:1877-1892. [PMID: 33873200 PMCID: PMC8483970 DOI: 10.1093/advances/nmab038] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 02/03/2021] [Accepted: 03/11/2021] [Indexed: 12/12/2022] Open
Abstract
With the increasing maternal age and the use of assisted reproductive technology in various countries worldwide, the influence of epigenetic modification on embryonic development is increasingly notable and prominent. Epigenetic modification disorders caused by various nutritional imbalance would cause embryonic development abnormalities and even have an indelible impact on health in adulthood. In this scoping review, we summarize the main epigenetic modifications in mammals and the synergies among different epigenetic modifications, especially DNA methylation, histone acetylation, and histone methylation. We performed an in-depth analysis of the regulation of various epigenetic modifications on mammals from zygote formation to cleavage stage and blastocyst stage, and reviewed the modifications of key sites and their potential molecular mechanisms. In addition, we discuss the effects of nutrition (protein, lipids, and one-carbon metabolism) on epigenetic modification in embryos and emphasize the importance of various nutrients in embryonic development and epigenetics during pregnancy. Failures in epigenetic regulation have been implicated in mammalian and human early embryo loss and disease. With the use of reproductive technologies, it is becoming even more important to establish developmentally competent embryos. Therefore, it is essential to evaluate the extent to which embryos are sensitive to these epigenetic modifications and nutrition status. Understanding the epigenetic regulation of early embryo development will help us make better use of reproductive technologies and nutrition regulation to improve reproductive health in mammals.
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Affiliation(s)
- Shuang Cai
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Shuang Quan
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Guangxin Yang
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Meixia Chen
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Qianhong Ye
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Gang Wang
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Haitao Yu
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Yuming Wang
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
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47
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Vincentz JW, Firulli BA, Toolan KP, Osterwalder M, Pennacchio LA, Firulli AB. HAND transcription factors cooperatively specify the aorta and pulmonary trunk. Dev Biol 2021; 476:1-10. [PMID: 33757801 DOI: 10.1016/j.ydbio.2021.03.011] [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: 11/02/2020] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 01/11/2023]
Abstract
Congenital heart defects (CHDs) affecting the cardiac outflow tract (OFT) constitute a significant cause of morbidity and mortality. The OFT develops from migratory cell populations which include the cardiac neural crest cells (cNCCs) and secondary heart field (SHF) derived myocardium and endocardium. The related transcription factors HAND1 and HAND2 have been implicated in human CHDs involving the OFT. Although Hand1 is expressed within the OFT, Hand1 NCC-specific conditional knockout mice (H1CKOs) are viable. Here we show that these H1CKOs present a low penetrance of OFT phenotypes, whereas SHF-specific Hand1 ablation does not reveal any cardiac phenotypes. Further, HAND1 and HAND2 appear functionally redundant within the cNCCs, as a reduction/ablation of Hand2 on an NCC-specific H1CKO background causes pronounced OFT defects. Double conditional Hand1 and Hand2 NCC knockouts exhibit persistent truncus arteriosus (PTA) with 100% penetrance. NCC lineage-tracing and Sema3c in situ mRNA expression reveal that Sema3c-expressing cells are mis-localized, resulting in a malformed septal bridge within the OFTs of H1CKO;H2CKO embryos. Interestingly, Hand1 and Hand2 also genetically interact within the SHF, as SHF H1CKOs on a heterozygous Hand2 background exhibit Ventricular Septal Defects (VSDs) with incomplete penetrance. Previously, we identified a BMP, HAND2, and GATA-dependent Hand1 OFT enhancer sufficient to drive reporter gene expression within the nascent OFT and aorta. Using these transcription inputs as a probe, we identify a novel Hand2 OFT enhancer, suggesting that a conserved BMP-GATA dependent mechanism transcriptionally regulates both HAND factors. These findings support the hypothesis that HAND factors interpret BMP signaling within the cNCCs to cooperatively coordinate OFT morphogenesis.
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Affiliation(s)
- Joshua W Vincentz
- Herman B Wells Center for Pediatric Research Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN, 46202-5225, USA.
| | - Beth A Firulli
- Herman B Wells Center for Pediatric Research Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN, 46202-5225, USA
| | - Kevin P Toolan
- Herman B Wells Center for Pediatric Research Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN, 46202-5225, USA
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Department for BioMedical Research (DBMR), University of Bern, Murtenstrasse 35, 3008, Bern, Switzerland
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA; Comparative Biochemistry Program, University of California, Berkeley, CA, 94720, USA
| | - Anthony B Firulli
- Herman B Wells Center for Pediatric Research Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN, 46202-5225, USA.
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48
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Profiling NSD3-dependent neural crest gene expression reveals known and novel candidate regulatory factors. Dev Biol 2021; 475:118-130. [PMID: 33705737 DOI: 10.1016/j.ydbio.2021.02.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/17/2021] [Accepted: 02/21/2021] [Indexed: 12/17/2022]
Abstract
The lysine methyltransferase NSD3 is required for the expression of key neural crest transcription factors and the migration of neural crest cells. Nevertheless, a complete view of the genes dependent upon NSD3 for expression and the developmental processes impacted by NSD3 in the neural crest was lacking. We used RNA sequencing (RNA-seq) to profile transcripts differentially expressed after NSD3 knockdown in chick premigratory neural crest cells, identifying 674 genes. Gene Ontology and gene set enrichment analyses further support a requirement for NSD3 during neural crest development and show that NSD3 knockdown also upregulates ribosome biogenesis. To validate our results, we selected three genes not previously associated with neural crest development, Astrotactin 1 (Astn1), Dispatched 3 (Disp3), and Tropomyosin 1 (Tpm1). Using whole mount in situ hybridization, we show that premigratory neural crest cells express these genes and that NSD3 knockdown downregulates (Astn1 and Disp3) and upregulates (Tpm1) their expression, consistent with RNA-seq results. Altogether, this study identifies novel putative regulators of neural crest development and provides insight into the transcriptional consequences of NSD3 in the neural crest, with implications for cancer.
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49
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Kitazawa T, Machlab D, Joshi O, Maiorano N, Kohler H, Ducret S, Kessler S, Gezelius H, Soneson C, Papasaikas P, López-Bendito G, Stadler MB, Rijli FM. A unique bipartite Polycomb signature regulates stimulus-response transcription during development. Nat Genet 2021; 53:379-391. [PMID: 33603234 PMCID: PMC7610396 DOI: 10.1038/s41588-021-00789-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/19/2021] [Indexed: 01/31/2023]
Abstract
Rapid cellular responses to environmental stimuli are fundamental for development and maturation. Immediate early genes can be transcriptionally induced within minutes in response to a variety of signals. How their induction levels are regulated and their untimely activation by spurious signals prevented during development is poorly understood. We found that in developing sensory neurons, before perinatal sensory-activity-dependent induction, immediate early genes are embedded into a unique bipartite Polycomb chromatin signature, carrying active H3K27ac on promoters but repressive Ezh2-dependent H3K27me3 on gene bodies. This bipartite signature is widely present in developing cell types, including embryonic stem cells. Polycomb marking of gene bodies inhibits mRNA elongation, dampening productive transcription, while still allowing for fast stimulus-dependent mark removal and bipartite gene induction. We reveal a developmental epigenetic mechanism regulating the rapidity and amplitude of the transcriptional response to relevant stimuli, while preventing inappropriate activation of stimulus-response genes.
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Affiliation(s)
- Taro Kitazawa
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Dania Machlab
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland,Swiss Institute of Bioinformatics, Basel, Switzerland,University of Basel, Basel, Switzerland
| | - Onkar Joshi
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Nicola Maiorano
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Hubertus Kohler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Sebastien Ducret
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Sandra Kessler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Henrik Gezelius
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d’Alacant, Spain
| | - Charlotte Soneson
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Panagiotis Papasaikas
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Guillermina López-Bendito
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d’Alacant, Spain
| | - Michael B. Stadler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Filippo M. Rijli
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland,University of Basel, Basel, Switzerland,Correspondence to:
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50
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Zalc A, Sinha R, Gulati GS, Wesche DJ, Daszczuk P, Swigut T, Weissman IL, Wysocka J. Reactivation of the pluripotency program precedes formation of the cranial neural crest. Science 2021; 371:371/6529/eabb4776. [PMID: 33542111 DOI: 10.1126/science.abb4776] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 11/20/2020] [Indexed: 12/16/2022]
Abstract
During development, cells progress from a pluripotent state to a more restricted fate within a particular germ layer. However, cranial neural crest cells (CNCCs), a transient cell population that generates most of the craniofacial skeleton, have much broader differentiation potential than their ectodermal lineage of origin. Here, we identify a neuroepithelial precursor population characterized by expression of canonical pluripotency transcription factors that gives rise to CNCCs and is essential for craniofacial development. Pluripotency factor Oct4 is transiently reactivated in CNCCs and is required for the subsequent formation of ectomesenchyme. Furthermore, open chromatin landscapes of Oct4+ CNCC precursors resemble those of epiblast stem cells, with additional features suggestive of priming for mesenchymal programs. We propose that CNCCs expand their developmental potential through a transient reacquisition of molecular signatures of pluripotency.
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Affiliation(s)
- Antoine Zalc
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford Medicine, Stanford, CA 94305, USA
| | - Gunsagar S Gulati
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford Medicine, Stanford, CA 94305, USA
| | - Daniel J Wesche
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford Medicine, Stanford, CA 94305, USA
| | - Patrycja Daszczuk
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford Medicine, Stanford, CA 94305, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. .,Institute for Stem Cell Biology and Regenerative Medicine, Stanford Medicine, Stanford, CA 94305, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
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