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Mok CH, Hu D, Losa M, Risolino M, Selleri L, Marcucio RS. PBX1 and PBX3 transcription factors regulate SHH expression in the Frontonasal Ectodermal Zone through complementary mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597450. [PMID: 38895322 PMCID: PMC11185640 DOI: 10.1101/2024.06.04.597450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Sonic hedgehog (SHH) signaling from the frontonasal ectodermal zone (FEZ) is a key regulator of craniofacial morphogenesis. Along with SHH, pre-B-cell leukemia homeobox (PBX) transcription factors regulate midfacial development. PBXs act in the epithelium during fusion of facial primordia, but their specific interactions with SHH have not been fully investigated. We hypothesized that PBX1/3 regulate SHH expression in the FEZ by activating or repressing transcription. The hypothesis was tested by manipulating PBX1/3 expression in chick embryos and profiling epigenomic landscapes at early developmental stages. PBX1/3 expression was perturbed in the chick face beginning at stage 10 (HH10) using RCAS viruses, and the resulting SHH expression was assessed at HH22. Overexpressing PBX1 expanded SHH expression, while overexpressing PBX3 decreased SHH expression. Conversely, reducing PBX1 expression decreased SHH expression, but reducing PBX3 induced ectopic SHH expression. We performed ATAC-seq and mapped binding of PBX1 and PBX3 with ChIP-seq on the FEZ at HH22 to assess direct interactions of PBX1/3 with the SHH locus. These multi-omics approaches uncovered a 400 bp PBX1-enriched element within intron 1 of SHH (chr2:8,173,222-8,173,621). Enhancer activity of this element was demonstrated by electroporation of reporter constructs in ovo and luciferase reporter assays in vitro . When bound by PBX1, this element upregulates transcription, while it downregulates transcription when bound by PBX3. The present study identifies a cis- regulatory element, named SFE1, that interacts with PBX1/3 to modulate SHH expression in the FEZ and establishes that PBX1 and PBX3 play complementary roles in SHH regulation during embryonic development.
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2
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Zhang L, Liang L, Kasimu H, Li W, Liu M, Li H, He S. A 76-base pair duplication within the enhancer region of the HMX1 gene causes sheep microtia. Gene 2024; 909:148307. [PMID: 38395239 DOI: 10.1016/j.gene.2024.148307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/01/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
Sheep congenital microtia is characterized by underdeveloped ears and provides an ideal basis for studying human microtia. This study identified the causal mutation and regulatory mechanisms underlying this disorder. Whole-genome association analysis was conducted using 23 ear tissue samples from sheep with microtia and 28 samples from normal-eared sheep. A significant correlation was found between microtia and a 76-base pair duplication in the enhancer region of the HMX1 gene. Further analysis of offspring phenotypes confirmed an autosomal dominant inheritance pattern. Genotypic analysis showed that individuals that are homozygous for this duplication were earless, heterozygous individuals exhibited shortened ears, and wild-type individuals had normal ears. Moreover, luciferase assays confirmed that this duplication increased HMX1 gene expression, and duplication knock-in mice also exhibited shorter and narrower external ears compared to wild-type mice. Transcriptomic analysis further demonstrated that this duplication enhanced HMX1 gene expression in animal models. This study characterized the causal regulatory mutation underlying sheep microtia.
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Affiliation(s)
- Lihua Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, 830052, China; Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, 830011, China
| | - Long Liang
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, 830011, China
| | - Hailati Kasimu
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, 830011, China
| | - Wenrong Li
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, 830011, China
| | - Mingjun Liu
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, 830011, China
| | - Haiying Li
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, 830052, China.
| | - Sangang He
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, 830011, China.
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3
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Bobola N, Sagerström CG. TALE transcription factors: Cofactors no more. Semin Cell Dev Biol 2024; 152-153:76-84. [PMID: 36509674 DOI: 10.1016/j.semcdb.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/27/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
Exd/PBX, Hth/MEIS and PREP proteins belong to the TALE (three-amino-acid loop extension) superclass of transcription factors (TFs) with an atypical homedomain (HD). Originally discovered as "cofactors" to HOX proteins, revisiting their traditional role in light of genome-wide experiments reveals a strong and reproducible pattern of HOX and TALE co-occupancy across diverse embryonic tissues. While confirming that TALE increases HOX specificity and selectivity in vivo, this wider outlook also reveals novel aspects of HOX:TALE collaboration, namely that HOX TFs generally require pre-bound TALE factors to access their functional binding sites in vivo. In contrast to the restricted expression domains of HOX TFs, TALE factors are largely ubiquitous, and PBX and PREP are expressed at the earliest developmental stages. PBX and MEIS control development of many organs and tissues and their dysregulation is associated with congenital disease and cancer. Accordingly, many instances of TALE cooperation with non HOX TFs have been documented in various systems. The model that emerges from these studies is that TALE TFs create a permissive chromatin platform that is selected by tissue-restricted TFs for binding. In turn, HOX and other tissue-restricted TFs selectively convert a ubiquitous pool of low affinity TALE binding events into high confidence, tissue-restricted binding events associated with transcriptional activation. As a result, TALE:TF complexes are associated with active chromatin and domain/lineage-specific gene activity. TALE ubiquitous expression and broad genomic occupancy, as well as the increasing examples of TALE tissue-specific partners, reveal a universal and obligatory role for TALE in the control of tissue and lineage-specific transcriptional programs, beyond their initial discovery as HOX co-factors.
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Affiliation(s)
- Nicoletta Bobola
- School of Medical Sciences, University of Manchester, Manchester, UK.
| | - Charles G Sagerström
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical School, Aurora, CO, USA.
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4
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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: 5] [Impact Index Per Article: 5.0] [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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5
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Losa M, Barozzi I, Osterwalder M, Hermosilla-Aguayo V, Morabito A, Chacón BH, Zarrineh P, Girdziusaite A, Benazet JD, Zhu J, Mackem S, Capellini TD, Dickel D, Bobola N, Zuniga A, Visel A, Zeller R, Selleri L. A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2. Nat Commun 2023; 14:3993. [PMID: 37414772 PMCID: PMC10325989 DOI: 10.1038/s41467-023-39443-z] [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: 03/17/2022] [Accepted: 06/14/2023] [Indexed: 07/08/2023] Open
Abstract
A lingering question in developmental biology has centered on how transcription factors with widespread distribution in vertebrate embryos can perform tissue-specific functions. Here, using the murine hindlimb as a model, we investigate the elusive mechanisms whereby PBX TALE homeoproteins, viewed primarily as HOX cofactors, attain context-specific developmental roles despite ubiquitous presence in the embryo. We first demonstrate that mesenchymal-specific loss of PBX1/2 or the transcriptional regulator HAND2 generates similar limb phenotypes. By combining tissue-specific and temporally controlled mutagenesis with multi-omics approaches, we reconstruct a gene regulatory network (GRN) at organismal-level resolution that is collaboratively directed by PBX1/2 and HAND2 interactions in subsets of posterior hindlimb mesenchymal cells. Genome-wide profiling of PBX1 binding across multiple embryonic tissues further reveals that HAND2 interacts with subsets of PBX-bound regions to regulate limb-specific GRNs. Our research elucidates fundamental principles by which promiscuous transcription factors cooperate with cofactors that display domain-restricted localization to instruct tissue-specific developmental programs.
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Affiliation(s)
- Marta Losa
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Iros Barozzi
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, Switzerland
| | - Viviana Hermosilla-Aguayo
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Angela Morabito
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Brandon H Chacón
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Peyman Zarrineh
- School of Medical Sciences, University of Manchester, Manchester, UK
| | - Ausra Girdziusaite
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Jean Denis Benazet
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Jianjian Zhu
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Susan Mackem
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Diane Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nicoletta Bobola
- School of Medical Sciences, University of Manchester, Manchester, UK
| | - Aimée Zuniga
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- School of Natural Sciences, University of California, Merced, Merced, CA, 95343, USA
| | - Rolf Zeller
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Licia Selleri
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA.
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6
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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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7
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Marlétaz F, de la Calle-Mustienes E, Acemel RD, Paliou C, Naranjo S, Martínez-García PM, Cases I, Sleight VA, Hirschberger C, Marcet-Houben M, Navon D, Andrescavage A, Skvortsova K, Duckett PE, González-Rajal Á, Bogdanovic O, Gibcus JH, Yang L, Gallardo-Fuentes L, Sospedra I, Lopez-Rios J, Darbellay F, Visel A, Dekker J, Shubin N, Gabaldón T, Nakamura T, Tena JJ, Lupiáñez DG, Rokhsar DS, Gómez-Skarmeta JL. The little skate genome and the evolutionary emergence of wing-like fins. Nature 2023; 616:495-503. [PMID: 37046085 PMCID: PMC10115646 DOI: 10.1038/s41586-023-05868-1] [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: 03/23/2022] [Accepted: 02/21/2023] [Indexed: 04/14/2023]
Abstract
Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins, enabling them to thrive in benthic environments1,2. However, the molecular underpinnings of this unique trait remain unclear. Here we investigate the origin of this phenotypic innovation by developing the little skate Leucoraja erinacea as a genomically enabled model. Analysis of a high-quality chromosome-scale genome sequence for the little skate shows that it preserves many ancestral jawed vertebrate features compared with other sequenced genomes, including numerous ancient microchromosomes. Combining genome comparisons with extensive regulatory datasets in developing fins-including gene expression, chromatin occupancy and three-dimensional conformation-we find skate-specific genomic rearrangements that alter the three-dimensional regulatory landscape of genes that are involved in the planar cell polarity pathway. Functional inhibition of planar cell polarity signalling resulted in a reduction in anterior fin size, confirming that this pathway is a major contributor to batoid fin morphology. We also identified a fin-specific enhancer that interacts with several hoxa genes, consistent with the redeployment of hox gene expression in anterior pectoral fins, and confirmed its potential to activate transcription in the anterior fin using zebrafish reporter assays. Our findings underscore the central role of genome reorganization and regulatory variation in the evolution of phenotypes, shedding light on the molecular origin of an enigmatic trait.
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Affiliation(s)
- Ferdinand Marlétaz
- Centre for Life's Origin and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan.
| | - Elisa de la Calle-Mustienes
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Rafael D Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
- Epigenetics and Sex Development Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Christina Paliou
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Silvia Naranjo
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Pedro Manuel Martínez-García
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Ildefonso Cases
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Victoria A Sleight
- Department of Zoology, University of Cambridge, Cambridge, UK
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | | | - Marina Marcet-Houben
- Barcelona Supercomputing Centre (BCS-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Dina Navon
- Department of Genetics, Rutgers the State University of New Jersey, Piscataway, NJ, USA
| | - Ali Andrescavage
- Department of Genetics, Rutgers the State University of New Jersey, Piscataway, NJ, USA
| | - Ksenia Skvortsova
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Paul Edward Duckett
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Álvaro González-Rajal
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Johan H Gibcus
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Liyan Yang
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Lourdes Gallardo-Fuentes
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Ismael Sospedra
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Fabrice Darbellay
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
- School of Natural Sciences, University of California, Merced, CA, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Neil Shubin
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BCS-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Tetsuya Nakamura
- Department of Genetics, Rutgers the State University of New Jersey, Piscataway, NJ, USA.
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain.
| | - Darío G Lupiáñez
- Epigenetics and Sex Development Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
| | - Daniel S Rokhsar
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
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8
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Abstract
Hox genes encode evolutionarily conserved transcription factors that are essential for the proper development of bilaterian organisms. Hox genes are unique because they are spatially and temporally regulated during development in a manner that is dictated by their tightly linked genomic organization. Although their genetic function during embryonic development has been interrogated, less is known about how these transcription factors regulate downstream genes to direct morphogenetic events. Moreover, the continued expression and function of Hox genes at postnatal and adult stages highlights crucial roles for these genes throughout the life of an organism. Here, we provide an overview of Hox genes, highlighting their evolutionary history, their unique genomic organization and how this impacts the regulation of their expression, what is known about their protein structure, and their deployment in development and beyond.
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Affiliation(s)
- Katharine A. Hubert
- Program in Genetics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Deneen M. Wellik
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
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9
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Leyhr J, Waldmann L, Filipek-Górniok B, Zhang H, Allalou A, Haitina T. A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint. eLife 2022; 11:75749. [PMCID: PMC9665848 DOI: 10.7554/elife.75749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
Abstract
The acquisition of movable jaws was a major event during vertebrate evolution. The role of NK3 homeobox 2 (Nkx3.2) transcription factor in patterning the primary jaw joint of gnathostomes (jawed vertebrates) is well known, however knowledge about its regulatory mechanism is lacking. In this study, we report a proximal enhancer element of Nkx3.2 that is deeply conserved in most gnathostomes but undetectable in the jawless hagfish and lamprey. This enhancer is active in the developing jaw joint region of the zebrafish Danio rerio, and was thus designated as jaw joint regulatory sequence 1 (JRS1). We further show that JRS1 enhancer sequences from a range of gnathostome species, including a chondrichthyan and mammals, have the same activity in the jaw joint as the native zebrafish enhancer, indicating a high degree of functional conservation despite the divergence of cartilaginous and bony fish lineages or the transition of the primary jaw joint into the middle ear of mammals. Finally, we show that deletion of JRS1 from the zebrafish genome using CRISPR/Cas9 results in a significant reduction of early gene expression of nkx3.2 and leads to a transient jaw joint deformation and partial fusion. Emergence of this Nkx3.2 enhancer in early gnathostomes may have contributed to the origin and shaping of the articulating surfaces of vertebrate jaws.
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Affiliation(s)
- Jake Leyhr
- Subdepartment of Evolution and Development, Department of Organismal Biology, Uppsala University
| | - Laura Waldmann
- Subdepartment of Evolution and Development, Department of Organismal Biology, Uppsala University
| | - Beata Filipek-Górniok
- Science for Life Laboratory Genome Engineering Zebrafish Facility, Department of Organismal Biology, Uppsala University
| | - Hanqing Zhang
- Division of Visual Information and Interaction, Department of Information Technology, Uppsala University
- Science for Life Laboratory BioImage Informatics Facility
| | - Amin Allalou
- Division of Visual Information and Interaction, Department of Information Technology, Uppsala University
- Science for Life Laboratory BioImage Informatics Facility
| | - Tatjana Haitina
- Subdepartment of Evolution and Development, Department of Organismal Biology, Uppsala University
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10
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Fabik J, Psutkova V, Machon O. Meis2 controls skeletal formation in the hyoid region. Front Cell Dev Biol 2022; 10:951063. [PMID: 36247013 PMCID: PMC9554219 DOI: 10.3389/fcell.2022.951063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
A vertebrate skull is composed of many skeletal elements which display enormous diversity of shapes. Cranial bone formation embodies a multitude of processes, i.e., epithelial-mesenchymal induction, mesenchymal condensation, and endochondral or intramembranous ossification. Molecular pathways determining complex architecture and growth of the cranial skeleton during embryogenesis are poorly understood. Here, we present a model of the hyoid apparatus development in Wnt1-Cre2-induced Meis2 conditional knock-out (cKO) mice. Meis2 cKO embryos develop an aberrant hyoid apparatus—a complete skeletal chain from the base of the neurocranium to lesser horns of the hyoid, resembling extreme human pathologies of the hyoid-larynx region. We examined key stages of hyoid skeletogenesis to obtain a complex image of the hyoid apparatus formation. Lack of Meis2 resulted in ectopic loci of mesenchymal condensations, ectopic cartilage and bone formation, disinhibition of skeletogenesis, and elevated proliferation of cartilage precursors. We presume that all these mechanisms contribute to formation of the aberrant skeletal chain in the hyoid region. Moreover, Meis2 cKO embryos exhibit severely reduced expression of PBX1 and HAND2 in the hyoid region. Altogether, MEIS2 in conjunction with PBX1 and HAND2 affects mesenchymal condensation, specification and proliferation of cartilage precursors to ensure development of the anatomically correct hyoid apparatus.
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Affiliation(s)
- Jaroslav Fabik
- Department of Developmental Biology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czechia
| | - Viktorie Psutkova
- Department of Developmental Biology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czechia
| | - Ondrej Machon
- Department of Developmental Biology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
- *Correspondence: Ondrej Machon,
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11
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Singh NP, Krumlauf R. Diversification and Functional Evolution of HOX Proteins. Front Cell Dev Biol 2022; 10:798812. [PMID: 35646905 PMCID: PMC9136108 DOI: 10.3389/fcell.2022.798812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/08/2022] [Indexed: 01/07/2023] Open
Abstract
Gene duplication and divergence is a major contributor to the generation of morphological diversity and the emergence of novel features in vertebrates during evolution. The availability of sequenced genomes has facilitated our understanding of the evolution of genes and regulatory elements. However, progress in understanding conservation and divergence in the function of proteins has been slow and mainly assessed by comparing protein sequences in combination with in vitro analyses. These approaches help to classify proteins into different families and sub-families, such as distinct types of transcription factors, but how protein function varies within a gene family is less well understood. Some studies have explored the functional evolution of closely related proteins and important insights have begun to emerge. In this review, we will provide a general overview of gene duplication and functional divergence and then focus on the functional evolution of HOX proteins to illustrate evolutionary changes underlying diversification and their role in animal evolution.
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Affiliation(s)
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, United States
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, United States
- *Correspondence: Robb Krumlauf,
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12
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Leung RF, George AM, Roussel EM, Faux MC, Wigle JT, Eisenstat DD. Genetic Regulation of Vertebrate Forebrain Development by Homeobox Genes. Front Neurosci 2022; 16:843794. [PMID: 35546872 PMCID: PMC9081933 DOI: 10.3389/fnins.2022.843794] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/14/2022] [Indexed: 01/19/2023] Open
Abstract
Forebrain development in vertebrates is regulated by transcription factors encoded by homeobox, bHLH and forkhead gene families throughout the progressive and overlapping stages of neural induction and patterning, regional specification and generation of neurons and glia from central nervous system (CNS) progenitor cells. Moreover, cell fate decisions, differentiation and migration of these committed CNS progenitors are controlled by the gene regulatory networks that are regulated by various homeodomain-containing transcription factors, including but not limited to those of the Pax (paired), Nkx, Otx (orthodenticle), Gsx/Gsh (genetic screened), and Dlx (distal-less) homeobox gene families. This comprehensive review outlines the integral role of key homeobox transcription factors and their target genes on forebrain development, focused primarily on the telencephalon. Furthermore, links of these transcription factors to human diseases, such as neurodevelopmental disorders and brain tumors are provided.
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Affiliation(s)
- Ryan F. Leung
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Ankita M. George
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Enola M. Roussel
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Maree C. Faux
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
| | - Jeffrey T. Wigle
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB, Canada
| | - David D. Eisenstat
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
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13
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Mallen J, Kalsan M, Zarrineh P, Bridoux L, Ahmad S, Bobola N. Molecular Characterization of HOXA2 and HOXA3 Binding Properties. J Dev Biol 2021; 9:jdb9040055. [PMID: 34940502 PMCID: PMC8707757 DOI: 10.3390/jdb9040055] [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: 10/19/2021] [Revised: 11/17/2021] [Accepted: 11/30/2021] [Indexed: 01/06/2023] Open
Abstract
The highly conserved HOX homeodomain (HD) transcription factors (TFs) establish the identity of different body parts along the antero–posterior axis of bilaterian animals. Segment diversification and the morphogenesis of different structures is achieved by generating precise patterns of HOX expression along the antero–posterior axis and by the ability of different HOX TFs to instruct unique and specific transcriptional programs. However, HOX binding properties in vitro, characterised by the recognition of similar AT-rich binding sequences, do not account for the ability of different HOX to instruct segment-specific transcriptional programs. To address this problem, we previously compared HOXA2 and HOXA3 binding in vivo. Here, we explore if sequence motif enrichments observed in vivo are explained by binding affinities in vitro. Unexpectedly, we found that the highest enriched motif in HOXA2 peaks was not recognised by HOXA2 in vitro, highlighting the importance of investigating HOX binding in its physiological context. We also report the ability of HOXA2 and HOXA3 to heterodimerise, which may have functional consequences for the HOX patterning function in vivo.
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Affiliation(s)
- Joshua Mallen
- School of Medical Sciences, University of Manchester, Manchester M13 9PT, UK; (J.M.); (P.Z.)
| | - Manisha Kalsan
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (M.K.); (S.A.)
| | - Peyman Zarrineh
- School of Medical Sciences, University of Manchester, Manchester M13 9PT, UK; (J.M.); (P.Z.)
| | - Laure Bridoux
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 5 (L7.07.10) Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium;
| | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (M.K.); (S.A.)
| | - Nicoletta Bobola
- School of Medical Sciences, University of Manchester, Manchester M13 9PT, UK; (J.M.); (P.Z.)
- Correspondence:
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14
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Parker HJ, De Kumar B, Pushel I, Bronner ME, Krumlauf R. Analysis of lamprey meis genes reveals that conserved inputs from Hox, Meis and Pbx proteins control their expression in the hindbrain and neural tube. Dev Biol 2021; 479:61-76. [PMID: 34310923 DOI: 10.1016/j.ydbio.2021.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/10/2021] [Accepted: 07/22/2021] [Indexed: 11/23/2022]
Abstract
Meis genes are known to play important roles in the hindbrain and neural crest cells of jawed vertebrates. To explore the roles of Meis genes in head development during evolution of vertebrates, we have identified four meis genes in the sea lamprey genome and characterized their patterns of expression and regulation, with a focus on the hindbrain and pharynx. Each of the lamprey meis genes displays temporally and spatially dynamic patterns of expression, some of which are coupled to rhombomeric domains in the developing hindbrain and select pharyngeal arches. Studies of Meis loci in mouse and zebrafish have identified enhancers that are bound by Hox and TALE (Meis and Pbx) proteins, implicating these factors in the direct regulation of Meis expression. We examined the lamprey meis loci and identified a series of cis-elements conserved between lamprey and jawed vertebrate meis genes. In transgenic reporter assays we demonstrated that these elements act as neural enhancers in lamprey embryos, directing reporter expression in appropriate domains when compared to expression of their associated endogenous meis gene. Sequence alignments reveal that these conserved elements are in similar relative positions of the meis loci and contain a series of consensus binding motifs for Hox and TALE proteins. This suggests that ancient Hox and TALE-responsive enhancers regulated expression of ancestral vertebrate meis genes in segmental domains in the hindbrain and have been retained in the meis loci during vertebrate evolution. The presence of conserved Meis, Pbx and Hox binding sites in these lamprey enhancers links Hox and TALE factors to regulation of lamprey meis genes in the developing hindbrain, indicating a deep ancestry for these regulatory interactions prior to the divergence of jawed and jawless vertebrates.
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Affiliation(s)
- Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Irina Pushel
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA; Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, 66160, USA.
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15
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Fabik J, Psutkova V, Machon O. The Mandibular and Hyoid Arches-From Molecular Patterning to Shaping Bone and Cartilage. Int J Mol Sci 2021; 22:7529. [PMID: 34299147 PMCID: PMC8303155 DOI: 10.3390/ijms22147529] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 12/16/2022] Open
Abstract
The mandibular and hyoid arches collectively make up the facial skeleton, also known as the viscerocranium. Although all three germ layers come together to assemble the pharyngeal arches, the majority of tissue within viscerocranial skeletal components differentiates from the neural crest. Since nearly one third of all birth defects in humans affect the craniofacial region, it is important to understand how signalling pathways and transcription factors govern the embryogenesis and skeletogenesis of the viscerocranium. This review focuses on mouse and zebrafish models of craniofacial development. We highlight gene regulatory networks directing the patterning and osteochondrogenesis of the mandibular and hyoid arches that are actually conserved among all gnathostomes. The first part of this review describes the anatomy and development of mandibular and hyoid arches in both species. The second part analyses cell signalling and transcription factors that ensure the specificity of individual structures along the anatomical axes. The third part discusses the genes and molecules that control the formation of bone and cartilage within mandibular and hyoid arches and how dysregulation of molecular signalling influences the development of skeletal components of the viscerocranium. In conclusion, we notice that mandibular malformations in humans and mice often co-occur with hyoid malformations and pinpoint the similar molecular machinery controlling the development of mandibular and hyoid arches.
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Affiliation(s)
- Jaroslav Fabik
- Department of Developmental Biology, Institute of Experimental Medicine of the Czech Academy of Sciences, 14220 Prague, Czech Republic; (J.F.); (V.P.)
- Department of Cell Biology, Faculty of Science, Charles University, 12800 Prague, Czech Republic
| | - Viktorie Psutkova
- Department of Developmental Biology, Institute of Experimental Medicine of the Czech Academy of Sciences, 14220 Prague, Czech Republic; (J.F.); (V.P.)
- Department of Cell Biology, Faculty of Science, Charles University, 12800 Prague, Czech Republic
| | - Ondrej Machon
- Department of Developmental Biology, Institute of Experimental Medicine of the Czech Academy of Sciences, 14220 Prague, Czech Republic; (J.F.); (V.P.)
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16
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Kaiser K, Jang A, Kompanikova P, Lun MP, Prochazka J, Machon O, Dani N, Prochazkova M, Laurent B, Gyllborg D, van Amerongen R, Fame RM, Gupta S, Wu F, Barker RA, Bukova I, Sedlacek R, Kozmik Z, Arenas E, Lehtinen MK, Bryja V. MEIS-WNT5A axis regulates development of fourth ventricle choroid plexus. Development 2021; 148:268365. [PMID: 34032267 DOI: 10.1242/dev.192054] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 04/14/2021] [Indexed: 12/29/2022]
Abstract
The choroid plexus (ChP) produces cerebrospinal fluid and forms an essential brain barrier. ChP tissues form in each brain ventricle, each one adopting a distinct shape, but remarkably little is known about the mechanisms underlying ChP development. Here, we show that epithelial WNT5A is crucial for determining fourth ventricle (4V) ChP morphogenesis and size in mouse. Systemic Wnt5a knockout, or forced Wnt5a overexpression beginning at embryonic day 10.5, profoundly reduced ChP size and development. However, Wnt5a expression was enriched in Foxj1-positive epithelial cells of 4V ChP plexus, and its conditional deletion in these cells affected the branched, villous morphology of the 4V ChP. We found that WNT5A was enriched in epithelial cells localized to the distal tips of 4V ChP villi, where WNT5A acted locally to activate non-canonical WNT signaling via ROR1 and ROR2 receptors. During 4V ChP development, MEIS1 bound to the proximal Wnt5a promoter, and gain- and loss-of-function approaches demonstrated that MEIS1 regulated Wnt5a expression. Collectively, our findings demonstrate a dual function of WNT5A in ChP development and identify MEIS transcription factors as upstream regulators of Wnt5a in the 4V ChP epithelium.
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Affiliation(s)
- Karol Kaiser
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 61137, Czech Republic
| | - Ahram Jang
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Petra Kompanikova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 61137, Czech Republic
| | - Melody P Lun
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jan Prochazka
- Czech Centre for Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, Prague 142 20, Czech Republic
| | - Ondrej Machon
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the CAS, Prague 142 20, Czech Republic
| | - Neil Dani
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Michaela Prochazkova
- Czech Centre for Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, Prague 142 20, Czech Republic
| | - Benoit Laurent
- Research Center on Aging, CIUSSS de l'Estrie - CHUS, Sherbrooke, QC 75361, Canada.,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC 75281, Canada
| | - Daniel Gyllborg
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna SE-106 91, Sweden
| | - Renee van Amerongen
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, Faculty of Science, University of Amsterdam1098 XH, Netherlands
| | - Ryann M Fame
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Suhasini Gupta
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Feizhen Wu
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Roger A Barker
- John van Geest Centre for Brain Repair and WT-MRC Cambridge Stem Cell Centre, University of Cambridge, Cambridge CB2 0PY, UK
| | - Ivana Bukova
- Czech Centre for Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, Prague 142 20, Czech Republic
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, Prague 142 20, Czech Republic
| | - Zbynek Kozmik
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the CAS, Prague 142 20, Czech Republic
| | - Ernest Arenas
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Maria K Lehtinen
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Vitezslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 61137, Czech Republic
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17
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Abstract
The vertebrate eye is derived from the neuroepithelium, surface ectoderm, and extracellular mesenchyme. The neuroepithelium forms an optic cup in which the spatial separation of three domains is established, namely, the region of multipotent retinal progenitor cells (RPCs), the ciliary margin zone (CMZ)-which possesses both a neurogenic and nonneurogenic potential-and the optic disk (OD), the interface between the optic stalk and the neuroretina. Here, we show by genetic ablation in the developing optic cup that Meis1 and Meis2 homeobox genes function redundantly to maintain the retinal progenitor pool while they simultaneously suppress the expression of genes characteristic of CMZ and OD fates. Furthermore, we demonstrate that Meis transcription factors bind regulatory regions of RPC-, CMZ-, and OD-specific genes, thus providing a mechanistic insight into the Meis-dependent gene regulatory network. Our work uncovers the essential role of Meis1 and Meis2 as regulators of cell fate competence, which organize spatial territories in the vertebrate eye.
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18
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López-Delgado AC, Delgado I, Cadenas V, Sánchez-Cabo F, Torres M. Axial skeleton anterior-posterior patterning is regulated through feedback regulation between Meis transcription factors and retinoic acid. Development 2021; 148:dev.193813. [PMID: 33298461 DOI: 10.1242/dev.193813] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/20/2020] [Indexed: 11/20/2022]
Abstract
Vertebrate axial skeletal patterning is controlled by co-linear expression of Hox genes and axial level-dependent activity of HOX protein combinations. MEIS transcription factors act as co-factors of HOX proteins and profusely bind to Hox complex DNA; however, their roles in mammalian axial patterning remain unknown. Retinoic acid (RA) is known to regulate axial skeletal element identity through the transcriptional activity of its receptors; however, whether this role is related to MEIS/HOX activity remains unknown. Here, we study the role of Meis in axial skeleton formation and its relationship to the RA pathway in mice. Meis elimination in the paraxial mesoderm produces anterior homeotic transformations and rib mis-patterning associated to alterations of the hypaxial myotome. Although Raldh2 and Meis positively regulate each other, Raldh2 elimination largely recapitulates the defects associated with Meis deficiency, and Meis overexpression rescues the axial skeletal defects in Raldh2 mutants. We propose a Meis-RA-positive feedback loop, the output of which is Meis levels, that is essential to establish anterior-posterior identities and patterning of the vertebrate axial skeleton.
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Affiliation(s)
- Alejandra C López-Delgado
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28003, Spain
| | - Irene Delgado
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28003, Spain
| | - Vanessa Cadenas
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28003, Spain
| | - Fátima Sánchez-Cabo
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28003, Spain
| | - Miguel Torres
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28003, Spain
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19
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Bridoux L, Zarrineh P, Mallen J, Phuycharoen M, Latorre V, Ladam F, Losa M, Baker SM, Sagerstrom C, Mace KA, Rattray M, Bobola N. HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation. PLoS Genet 2020; 16:e1009162. [PMID: 33315856 PMCID: PMC7769617 DOI: 10.1371/journal.pgen.1009162] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 12/28/2020] [Accepted: 09/28/2020] [Indexed: 11/18/2022] Open
Abstract
Gene expression programs determine cell fate in embryonic development and their dysregulation results in disease. Transcription factors (TFs) control gene expression by binding to enhancers, but how TFs select and activate their target enhancers is still unclear. HOX TFs share conserved homeodomains with highly similar sequence recognition properties, yet they impart the identity of different animal body parts. To understand how HOX TFs control their specific transcriptional programs in vivo, we compared HOXA2 and HOXA3 binding profiles in the mouse embryo. HOXA2 and HOXA3 directly cooperate with TALE TFs and selectively target different subsets of a broad TALE chromatin platform. Binding of HOX and tissue-specific TFs convert low affinity TALE binding into high confidence, tissue-specific binding events, which bear the mark of active enhancers. We propose that HOX paralogs, alone and in combination with tissue-specific TFs, generate tissue-specific transcriptional outputs by modulating the activity of TALE TFs at selected enhancers.
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Affiliation(s)
- Laure Bridoux
- School of Medical Sciences, University of Manchester, Manchester, United Kingdom
| | - Peyman Zarrineh
- School of Health Sciences, University of Manchester, Manchester, United Kingdom
| | - Joshua Mallen
- School of Medical Sciences, University of Manchester, Manchester, United Kingdom
| | - Mike Phuycharoen
- Department of Computer Science, University of Manchester, Manchester, United Kingdom
| | - Victor Latorre
- School of Medical Sciences, University of Manchester, Manchester, United Kingdom
| | - Frank Ladam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusets, United States of America
| | - Marta Losa
- School of Medical Sciences, University of Manchester, Manchester, United Kingdom
| | - Syed Murtuza Baker
- School of Health Sciences, University of Manchester, Manchester, United Kingdom
- School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Charles Sagerstrom
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusets, United States of America
| | - Kimberly A. Mace
- School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Magnus Rattray
- School of Health Sciences, University of Manchester, Manchester, United Kingdom
| | - Nicoletta Bobola
- School of Medical Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
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20
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Wang L, Tang Q, Xu J, Li H, Yang T, Li L, Machon O, Hu T, Chen Y. The transcriptional regulator MEIS2 sets up the ground state for palatal osteogenesis in mice. J Biol Chem 2020; 295:5449-5460. [PMID: 32169905 PMCID: PMC7170518 DOI: 10.1074/jbc.ra120.012684] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 03/10/2020] [Indexed: 02/05/2023] Open
Abstract
Haploinsufficiency of Meis homeobox 2 (MEIS2), encoding a transcriptional regulator, is associated with human cleft palate, and Meis2 inactivation leads to abnormal palate development in mice, implicating MEIS2 functions in palate development. However, its functional mechanisms remain unknown. Here we observed widespread MEIS2 expression in the developing palate in mice. Wnt1Cre -mediated Meis2 inactivation in cranial neural crest cells led to a secondary palate cleft. Importantly, about half of the Wnt1Cre ;Meis2f/f mice exhibited a submucous cleft, providing a model for studying palatal bone formation and patterning. Consistent with complete absence of palatal bones, the results from integrative analyses of MEIS2 by ChIP sequencing, RNA-Seq, and an assay for transposase-accessible chromatin sequencing identified key osteogenic genes regulated directly by MEIS2, indicating that it plays a fundamental role in palatal osteogenesis. De novo motif analysis uncovered that the MEIS2-bound regions are highly enriched in binding motifs for several key osteogenic transcription factors, particularly short stature homeobox 2 (SHOX2). Comparative ChIP sequencing analyses revealed genome-wide co-occupancy of MEIS2 and SHOX2 in addition to their colocalization in the developing palate and physical interaction, suggesting that SHOX2 and MEIS2 functionally interact. However, although SHOX2 was required for proper palatal bone formation and was a direct downstream target of MEIS2, Shox2 overexpression failed to rescue the palatal bone defects in a Meis2-mutant background. These results, together with the fact that Meis2 expression is associated with high osteogenic potential and required for chromatin accessibility of osteogenic genes, support a vital function of MEIS2 in setting up a ground state for palatal osteogenesis.
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Affiliation(s)
- Linyan Wang
- State Key Laboratory of Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China; Department of Cell and Molecular Biology, Tulane University, New Orleans, Louisiana 70118
| | - Qinghuang Tang
- Department of Cell and Molecular Biology, Tulane University, New Orleans, Louisiana 70118
| | - Jue Xu
- Department of Cell and Molecular Biology, Tulane University, New Orleans, Louisiana 70118; West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Hua Li
- Department of Cell and Molecular Biology, Tulane University, New Orleans, Louisiana 70118
| | - Tianfang Yang
- Department of Cell and Molecular Biology, Tulane University, New Orleans, Louisiana 70118
| | - Liwen Li
- Department of Cell and Molecular Biology, Tulane University, New Orleans, Louisiana 70118
| | - Ondrej Machon
- Department of Developmental Biology, Institute of Experimental Medicine of the Czech Academy of Sciences, 14200 Praha, Czech Republic
| | - Tao Hu
- State Key Laboratory of Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - YiPing Chen
- Department of Cell and Molecular Biology, Tulane University, New Orleans, Louisiana 70118.
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21
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Phuycharoen M, Zarrineh P, Bridoux L, Amin S, Losa M, Chen K, Bobola N, Rattray M. Uncovering tissue-specific binding features from differential deep learning. Nucleic Acids Res 2020; 48:e27. [PMID: 31974574 PMCID: PMC7049686 DOI: 10.1093/nar/gkaa009] [Citation(s) in RCA: 8] [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: 04/29/2019] [Revised: 11/04/2019] [Accepted: 01/07/2020] [Indexed: 01/24/2023] Open
Abstract
Transcription factors (TFs) can bind DNA in a cooperative manner, enabling a mutual increase in occupancy. Through this type of interaction, alternative binding sites can be preferentially bound in different tissues to regulate tissue-specific expression programmes. Recently, deep learning models have become state-of-the-art in various pattern analysis tasks, including applications in the field of genomics. We therefore investigate the application of convolutional neural network (CNN) models to the discovery of sequence features determining cooperative and differential TF binding across tissues. We analyse ChIP-seq data from MEIS, TFs which are broadly expressed across mouse branchial arches, and HOXA2, which is expressed in the second and more posterior branchial arches. By developing models predictive of MEIS differential binding in all three tissues, we are able to accurately predict HOXA2 co-binding sites. We evaluate transfer-like and multitask approaches to regularizing the high-dimensional classification task with a larger regression dataset, allowing for the creation of deeper and more accurate models. We test the performance of perturbation and gradient-based attribution methods in identifying the HOXA2 sites from differential MEIS data. Our results show that deep regularized models significantly outperform shallow CNNs as well as k-mer methods in the discovery of tissue-specific sites bound in vivo.
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Affiliation(s)
- Mike Phuycharoen
- Department of Computer Science, The University of Manchester, Oxford Rd, Manchester M13 9PL, UK
| | - Peyman Zarrineh
- School of Health Sciences, The University of Manchester, Oxford Rd, Manchester M13 9PL, UK
| | - Laure Bridoux
- School of Medical Sciences, The University of Manchester, Oxford Rd, Manchester M13 9PL, UK
| | - Shilu Amin
- School of Medical Sciences, The University of Manchester, Oxford Rd, Manchester M13 9PL, UK
| | - Marta Losa
- Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, 513 Parnassus Avenue, HSW 740, San Francisco, CA 94143, USA
| | - Ke Chen
- Department of Computer Science, The University of Manchester, Oxford Rd, Manchester M13 9PL, UK
| | - Nicoletta Bobola
- School of Medical Sciences, The University of Manchester, Oxford Rd, Manchester M13 9PL, UK
| | - Magnus Rattray
- School of Health Sciences, The University of Manchester, Oxford Rd, Manchester M13 9PL, UK
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22
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Parker HJ, Krumlauf R. A Hox gene regulatory network for hindbrain segmentation. Curr Top Dev Biol 2020; 139:169-203. [DOI: 10.1016/bs.ctdb.2020.03.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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23
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Stanney W, Ladam F, Donaldson IJ, Parsons TJ, Maehr R, Bobola N, Sagerström CG. Combinatorial action of NF-Y and TALE at embryonic enhancers defines distinct gene expression programs during zygotic genome activation in zebrafish. Dev Biol 2019; 459:161-180. [PMID: 31862379 DOI: 10.1016/j.ydbio.2019.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/05/2019] [Accepted: 12/05/2019] [Indexed: 01/20/2023]
Abstract
Animal embryogenesis is initiated by maternal factors, but zygotic genome activation (ZGA) shifts regulatory control to the embryo during blastula stages. ZGA is thought to be mediated by maternally provided transcription factors (TFs), but few such TFs have been identified in vertebrates. Here we report that NF-Y and TALE TFs bind zebrafish genomic elements associated with developmental control genes already at ZGA. In particular, co-regulation by NF-Y and TALE is associated with broadly acting genes involved in transcriptional control, while regulation by either NF-Y or TALE defines genes in specific developmental processes, such that NF-Y controls a cilia gene expression program while TALE controls expression of hox genes. We also demonstrate that NF-Y and TALE-occupied genomic elements function as enhancers during embryogenesis. We conclude that combinatorial use of NF-Y and TALE at developmental enhancers permits the establishment of distinct gene expression programs at zebrafish ZGA.
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Affiliation(s)
- William Stanney
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Franck Ladam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Ian J Donaldson
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Teagan J Parsons
- Program in Molecular Medicine and Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - René Maehr
- Program in Molecular Medicine and Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Nicoletta Bobola
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Charles G Sagerström
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
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24
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Tapia-Carrillo D, Tovar H, Velazquez-Caldelas TE, Hernandez-Lemus E. Master Regulators of Signaling Pathways: An Application to the Analysis of Gene Regulation in Breast Cancer. Front Genet 2019; 10:1180. [PMID: 31850059 PMCID: PMC6902642 DOI: 10.3389/fgene.2019.01180] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 10/24/2019] [Indexed: 12/13/2022] Open
Abstract
Analysis of gene regulatory networks allows the identification of master transcriptional factors that control specific groups of genes. In this work, we inferred a gene regulatory network from a large dataset of breast cancer samples to identify the master transcriptional factors that control the genes within signal transduction pathways. The focus in a particular subset of relevant genes constitutes an extension of the original Master Regulator Inference Algorithm (MARINa) analysis. This modified version of MARINa utilizes a restricted molecular signature containing genes from the 25 human pathways in KEGG's signal transduction category. Our breast cancer RNAseq expression dataset consists of 881 samples comprising tumors and normal mammary gland tissue. The top 10 master transcriptional factors found to regulate signal transduction pathways in breast cancer we identified are: TSHZ2, HOXA2, MEIS2, HOXA3, HAND2, HOXA5, TBX18, PEG3, GLI2, and CLOCK. The functional enrichment of the regulons of these master transcriptional factors showed an important proportion of processes related to morphogenesis. Our results suggest that, as part of the aberrant regulation of signaling pathways in breast cancer, pathways similar to the regulation of cell differentiation, cardiovascular system development, and vasculature development may be dysregulated and co-opted in favor of tumor development through the action of these transcription factors.
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Affiliation(s)
- Diana Tapia-Carrillo
- Computational Genomics Department, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico.,Graduate Program in Biological Sciences, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Hugo Tovar
- Computational Genomics Department, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | | | - Enrique Hernandez-Lemus
- Computational Genomics Department, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico.,Center for Complexity Sciences, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
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25
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Schulte D, Geerts D. MEIS transcription factors in development and disease. Development 2019; 146:146/16/dev174706. [PMID: 31416930 DOI: 10.1242/dev.174706] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 06/28/2019] [Indexed: 12/12/2022]
Abstract
MEIS transcription factors are key regulators of embryonic development and cancer. Research on MEIS genes in the embryo and in stem cell systems has revealed novel and surprising mechanisms by which these proteins control gene expression. This Primer summarizes recent findings about MEIS protein activity and regulation in development, and discusses new insights into the role of MEIS genes in disease, focusing on the pathogenesis of solid cancers.
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Affiliation(s)
- Dorothea Schulte
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, 60528 Frankfurt, Germany
| | - Dirk Geerts
- Department of Medical Biology L2-109, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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26
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HOXA2 activity regulation by cytoplasmic relocation, protein stabilization and post-translational modification. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194404. [PMID: 31323436 DOI: 10.1016/j.bbagrm.2019.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/19/2019] [Accepted: 07/07/2019] [Indexed: 11/22/2022]
Abstract
HOX proteins are homeodomain transcription factors critically involved in patterning animal embryos and controlling organogenesis. While the functions of HOX proteins and the processes under their control begin to be well documented, the modalities of HOX protein activity regulation remain poorly understood. Here we show that HOXA2 interacts with PPP1CB, a catalytic subunit of the Ser/Thr PP1 phosphatase complex. This interaction co-localizes in the cytoplasm with a previously described HOXA2 interactor, KPC2, which belongs to the KPC E3 ubiquitin ligase complex. We provide evidence that HOXA2, PPP1CB and KPC2 define a molecularly and functionally interacting complex. Collectively, our experiments support that PPP1CB and KPC2 together inhibit the activity of HOXA2 by activating its nuclear export, but favored HOXA2 de-ubiquitination and stabilization thereby establishing a store of HOXA2 in the cytoplasm.
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27
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Ranganathan S, Cheung J, Cassidy M, Ginter C, Pata JD, McDonough KA. Novel structural features drive DNA binding properties of Cmr, a CRP family protein in TB complex mycobacteria. Nucleic Acids Res 2019; 46:403-420. [PMID: 29165665 PMCID: PMC5758884 DOI: 10.1093/nar/gkx1148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 11/13/2017] [Indexed: 11/16/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) encodes two CRP/FNR family transcription factors (TF) that contribute to virulence, Cmr (Rv1675c) and CRPMt (Rv3676). Prior studies identified distinct chromosomal binding profiles for each TF despite their recognizing overlapping DNA motifs. The present study shows that Cmr binding specificity is determined by discriminator nucleotides at motif positions 4 and 13. X-ray crystallography and targeted mutational analyses identified an arginine-rich loop that expands Cmr’s DNA interactions beyond the classical helix-turn-helix contacts common to all CRP/FNR family members and facilitates binding to imperfect DNA sequences. Cmr binding to DNA results in a pronounced asymmetric bending of the DNA and its high level of cooperativity is consistent with DNA-facilitated dimerization. A unique N-terminal extension inserts between the DNA binding and dimerization domains, partially occluding the site where the canonical cAMP binding pocket is found. However, an unstructured region of this N-terminus may help modulate Cmr activity in response to cellular signals. Cmr’s multiple levels of DNA interaction likely enhance its ability to integrate diverse gene regulatory signals, while its novel structural features establish Cmr as an atypical CRP/FNR family member.
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Affiliation(s)
- Sridevi Ranganathan
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA
| | - Jonah Cheung
- New York Structural Biology Center, New York, NY 10027, USA
| | | | | | - Janice D Pata
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA.,Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA
| | - Kathleen A McDonough
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, NY 12201, USA.,Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, PO Box 22002, Albany, NY 12201-2002, USA
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28
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Porcelli D, Fischer B, Russell S, White R. Chromatin accessibility plays a key role in selective targeting of Hox proteins. Genome Biol 2019; 20:115. [PMID: 31159833 PMCID: PMC6547607 DOI: 10.1186/s13059-019-1721-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 05/21/2019] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Hox transcription factors specify segmental diversity along the anterior-posterior body axis in metazoans. While the different Hox family members show clear functional specificity in vivo, they all show similar binding specificity in vitro and a satisfactory understanding of in vivo Hox target selectivity is still lacking. RESULTS Using transient transfection in Kc167 cells, we systematically analyze the binding of all eight Drosophila Hox proteins. We find that Hox proteins show considerable binding selectivity in vivo even in the absence of canonical Hox cofactors Extradenticle and Homothorax. Hox binding selectivity is strongly associated with chromatin accessibility, being highest in less accessible chromatin. Individual Hox proteins exhibit different propensities to bind less accessible chromatin, and high binding selectivity is associated with high-affinity binding regions, leading to a model where Hox proteins derive binding selectivity through affinity-based competition with nucleosomes. Extradenticle/Homothorax cofactors generally facilitate Hox binding, promoting binding to regions in less accessible chromatin but with little effect on the overall selectivity of Hox targeting. These cofactors collaborate with Hox proteins in opening chromatin, in contrast to the pioneer factor, Glial cells missing, which facilitates Hox binding by independently generating accessible chromatin regions. CONCLUSIONS These studies indicate that chromatin accessibility plays a key role in Hox selectivity. We propose that relative chromatin accessibility provides a basis for subtle differences in binding specificity and affinity to generate significantly different sets of in vivo genomic targets for different Hox proteins.
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Affiliation(s)
- Damiano Porcelli
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY UK
| | - Bettina Fischer
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, CB2 1QR UK
| | - Steven Russell
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, CB2 1QR UK
| | - Robert White
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY UK
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29
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The human HOXA9 protein uses paralog-specific residues of the homeodomain to interact with TALE-class cofactors. Sci Rep 2019; 9:5664. [PMID: 30952900 PMCID: PMC6450960 DOI: 10.1038/s41598-019-42096-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 03/22/2019] [Indexed: 12/15/2022] Open
Abstract
HOX proteins interact with PBX and MEIS cofactors, which belong to the TALE-class of homeodomain (HD)-containing transcription factors. Although the formation of HOX-PBX complexes depends on a unique conserved HOX motif called hexapeptide (HX), the additional presence of MEIS induces a remodeling of the interaction, leading to a global dispensability of the HX motif for trimeric complex formation in the large majority of HOX proteins. In addition, it was shown that the anterior HOXB3 and central HOXA7 and HOXC8 proteins could use different alternative TALE interaction motifs, with or without the HX motif, depending on the DNA-binding site and cell context. Here we dissected the molecular interaction properties of the human posterior HOXA9 protein with its TALE cofactors, PBX1 and MEIS1. Analysis was performed on different DNA-binding sites in vitro and by doing Bimolecular Fluorescence Complementation (BiFC) in different cell lines. Notably, we observed that the HOXA9-TALE interaction relies consistently on the redundant activity of the HX motif and two paralog-specific residues of the HOXA9 HD. Together with previous work, our results show that HOX proteins interact with their generic TALE cofactors through various modalities, ranging from unique and context-independent to versatile and context-dependent TALE binding interfaces.
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30
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Selleri L, Zappavigna V, Ferretti E. 'Building a perfect body': control of vertebrate organogenesis by PBX-dependent regulatory networks. Genes Dev 2019; 33:258-275. [PMID: 30824532 PMCID: PMC6411007 DOI: 10.1101/gad.318774.118] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pbx genes encode transcription factors that belong to the TALE (three-amino-acid loop extension) superclass of homeodomain proteins. We have witnessed a surge in information about the roles of this gene family as leading actors in the transcriptional control of development. PBX proteins represent a clear example of how transcription factors can regulate developmental processes by combinatorial properties, acting within multimeric complexes to implement activation or repression of transcription depending on their interaction partners. Here, we revisit long-emphasized functions of PBX transcription factors as cofactors for HOX proteins, major architects of the body plan. We further discuss new knowledge on roles of PBX proteins in different developmental contexts as upstream regulators of Hox genes-as factors that interact with non-HOX proteins and can work independently of HOX-as well as potential pioneer factors. Committed to building a perfect body, PBX proteins govern regulatory networks that direct essential morphogenetic processes and organogenesis in vertebrate development. Perturbations of PBX-dependent networks can cause human congenital disease and cancer.
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Affiliation(s)
- Licia Selleri
- Program in Craniofacial Biology, University of California at San Francisco, San Francisco, California 94143, USA.,Institute of Human Genetics, University of California at San Francisco, San Francisco, California 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, California 94143, USA.,Department of Orofacial Sciences, University of California at San Francisco, San Francisco, California 94143, USA.,Department of Anatomy, University of California at San Francisco, San Francisco, California 94143, USA
| | - Vincenzo Zappavigna
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Elisabetta Ferretti
- The Novo Nordisk Foundation Center for Stem Cell Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
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31
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A Hox-TALE regulatory circuit for neural crest patterning is conserved across vertebrates. Nat Commun 2019; 10:1189. [PMID: 30867425 PMCID: PMC6416258 DOI: 10.1038/s41467-019-09197-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 02/26/2019] [Indexed: 12/13/2022] Open
Abstract
In jawed vertebrates (gnathostomes), Hox genes play an important role in patterning head and jaw formation, but mechanisms coupling Hox genes to neural crest (NC) are unknown. Here we use cross-species regulatory comparisons between gnathostomes and lamprey, a jawless extant vertebrate, to investigate conserved ancestral mechanisms regulating Hox2 genes in NC. Gnathostome Hoxa2 and Hoxb2 NC enhancers mediate equivalent NC expression in lamprey and gnathostomes, revealing ancient conservation of Hox upstream regulatory components in NC. In characterizing a lamprey hoxα2 NC/hindbrain enhancer, we identify essential Meis, Pbx, and Hox binding sites that are functionally conserved within Hoxa2/Hoxb2 NC enhancers. This suggests that the lamprey hoxα2 enhancer retains ancestral activity and that Hoxa2/Hoxb2 NC enhancers are ancient paralogues, which diverged in hindbrain and NC activities. This identifies an ancestral mechanism for Hox2 NC regulation involving a Hox-TALE regulatory circuit, potentiated by inputs from Meis and Pbx proteins and Hox auto-/cross-regulatory interactions.
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32
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Luo Z, Rhie SK, Farnham PJ. The Enigmatic HOX Genes: Can We Crack Their Code? Cancers (Basel) 2019; 11:cancers11030323. [PMID: 30866492 PMCID: PMC6468460 DOI: 10.3390/cancers11030323] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/01/2019] [Accepted: 03/01/2019] [Indexed: 02/06/2023] Open
Abstract
Homeobox genes (HOX) are a large family of transcription factors that direct the formation of many body structures during early embryonic development. There are 39 genes in the subgroup of homeobox genes that constitute the human HOX gene family. Correct embryonic development of flies and vertebrates is, in part, mediated by the unique and highly regulated expression pattern of the HOX genes. Disruptions in these fine-tuned regulatory mechanisms can lead to developmental problems and to human diseases such as cancer. Unfortunately, the molecular mechanisms of action of the HOX family of transcription factors are severely under-studied, likely due to idiosyncratic details of their structure, expression, and function. We suggest that a concerted and collaborative effort to identify interacting protein partners, produce genome-wide binding profiles, and develop HOX network inhibitors in a variety of human cell types will lead to a deeper understanding of human development and disease. Within, we review the technological challenges and possible approaches needed to achieve this goal.
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Affiliation(s)
- Zhifei Luo
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
| | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
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33
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Caratti G, Iqbal M, Hunter L, Kim D, Wang P, Vonslow RM, Begley N, Tetley AJ, Woodburn JL, Pariollaud M, Maidstone R, Donaldson IJ, Zhang Z, Ince LM, Kitchen G, Baxter M, Poolman TM, Daniels DA, Stirling DR, Brocker C, Gonzalez F, Loudon AS, Bechtold DA, Rattray M, Matthews LC, Ray DW. REVERBa couples the circadian clock to hepatic glucocorticoid action. J Clin Invest 2018; 128:4454-4471. [PMID: 30179226 PMCID: PMC6160001 DOI: 10.1172/jci96138] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 07/18/2018] [Indexed: 01/15/2023] Open
Abstract
The glucocorticoid receptor (GR) is a major drug target in inflammatory disease. However, chronic glucocorticoid (GC) treatment leads to disordered energy metabolism, including increased weight gain, adiposity, and hepatosteatosis — all programs modulated by the circadian clock. We demonstrated that while antiinflammatory GC actions were maintained irrespective of dosing time, the liver was significantly more GC sensitive during the day. Temporal segregation of GC action was underpinned by a physical interaction of GR with the circadian transcription factor REVERBa and co-binding with liver-specific hepatocyte nuclear transcription factors (HNFs) on chromatin. REVERBa promoted efficient GR recruitment to chromatin during the day, acting in part by maintaining histone acetylation, with REVERBa-dependent GC responses providing segregation of carbohydrate and lipid metabolism. Importantly, deletion of Reverba inverted circadian liver GC sensitivity and protected mice from hepatosteatosis induced by chronic GC administration. Our results reveal a mechanism by which the circadian clock acts through REVERBa in liver on elements bound by HNF4A/HNF6 to direct GR action on energy metabolism.
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Affiliation(s)
- Giorgio Caratti
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Mudassar Iqbal
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Louise Hunter
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Donghwan Kim
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Ping Wang
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Ryan M Vonslow
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Nicola Begley
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Abigail J Tetley
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Joanna L Woodburn
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Marie Pariollaud
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Robert Maidstone
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Ian J Donaldson
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Zhenguang Zhang
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Louise M Ince
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Gareth Kitchen
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Matthew Baxter
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Toryn M Poolman
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Dion A Daniels
- Biopharmaceutical Molecular Discovery, GlaxoSmithKline, Medicines Research Centre, Stevenage, United Kingdom
| | - David R Stirling
- Biopharmaceutical Molecular Discovery, GlaxoSmithKline, Medicines Research Centre, Stevenage, United Kingdom
| | - Chad Brocker
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Frank Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Andrew Si Loudon
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - David A Bechtold
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Magnus Rattray
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Laura C Matthews
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom.,Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, Leeds, United Kingdom
| | - David W Ray
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, and Specialist Medicine, Central Manchester Foundation Trust, Manchester, United Kingdom.,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom
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34
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Targeting EZH2 reactivates a breast cancer subtype-specific anti-metastatic transcriptional program. Nat Commun 2018; 9:2547. [PMID: 29959321 PMCID: PMC6026192 DOI: 10.1038/s41467-018-04864-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/21/2018] [Indexed: 02/06/2023] Open
Abstract
Emerging evidence has illustrated the importance of epigenomic reprogramming in cancer, with altered post-translational modifications of histones contributing to pathogenesis. However, the contributions of histone modifiers to breast cancer progression are unclear, and how these processes vary between molecular subtypes has yet to be adequately addressed. Here we report that genetic or pharmacological targeting of the epigenetic modifier Ezh2 dramatically hinders metastatic behaviour in both a mouse model of breast cancer and patient-derived xenografts reflective of the Luminal B subtype. We further define a subtype-specific molecular mechanism whereby EZH2 maintains H3K27me3-mediated repression of the FOXC1 gene, thereby inactivating a FOXC1-driven, anti-invasive transcriptional program. We demonstrate that higher FOXC1 is predictive of favourable outcome specifically in Luminal B breast cancer patients and establish the use of EZH2 methyltransferase inhibitors as a viable strategy to block metastasis in Luminal B breast cancer, where options for targeted therapy are limited. Histone modifications in cancer can contribute to pathogenesis. Here, the authors demonstrate that targeting epigenetic modifier Ezh2 hinders metastatic behaviour in Luminal B breast cancer models, and highlight a mechanism where Ezh2 contributes to metastatic behaviour by repression of FOXC1.
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35
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Ladam F, Stanney W, Donaldson IJ, Yildiz O, Bobola N, Sagerström CG. TALE factors use two distinct functional modes to control an essential zebrafish gene expression program. eLife 2018; 7:36144. [PMID: 29911973 PMCID: PMC6023610 DOI: 10.7554/elife.36144] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/08/2018] [Indexed: 12/21/2022] Open
Abstract
TALE factors are broadly expressed embryonically and known to function in complexes with transcription factors (TFs) like Hox proteins at gastrula/segmentation stages, but it is unclear if such generally expressed factors act by the same mechanism throughout embryogenesis. We identify a TALE-dependent gene regulatory network (GRN) required for anterior development and detect TALE occupancy associated with this GRN throughout embryogenesis. At blastula stages, we uncover a novel functional mode for TALE factors, where they occupy genomic DECA motifs with nearby NF-Y sites. We demonstrate that TALE and NF-Y form complexes and regulate chromatin state at genes of this GRN. At segmentation stages, GRN-associated TALE occupancy expands to include HEXA motifs near PBX:HOX sites. Hence, TALE factors control a key GRN, but utilize distinct DNA motifs and protein partners at different stages – a strategy that may also explain their oncogenic potential and may be employed by other broadly expressed TFs.
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Affiliation(s)
- Franck Ladam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - William Stanney
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Ian J Donaldson
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Ozge Yildiz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Nicoletta Bobola
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Charles G Sagerström
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
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36
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Jain D, Nemec S, Luxey M, Gauthier Y, Bemmo A, Balsalobre A, Drouin J. Regulatory integration of Hox factor activity with T-box factors in limb development. Development 2018; 145:dev.159830. [PMID: 29490982 DOI: 10.1242/dev.159830] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/16/2018] [Indexed: 01/26/2023]
Abstract
In tetrapods, Tbx4, Tbx5 and Hox cluster genes are crucial for forelimb and hindlimb development and mutations in these genes are responsible for congenital limb defects. The molecular basis of their integrated mechanisms of action in the context of limb development remains poorly understood. We studied Tbx4 and Hoxc10 owing to their overlapping loss-of-function phenotypes and colocalized expression in mouse hindlimb buds. We report an extensive overlap between Tbx4 and Hoxc10 genome occupancy and their putative target genes. Tbx4 and Hoxc10 interact directly with each other, have the ability to bind to a previously unrecognized T-box-Hox composite DNA motif and show synergistic activity when acting on reporter genes. Pitx1, the master regulator for hindlimb specification, also shows extensive genomic colocalization with Tbx4 and Hoxc10. Genome occupancy by Tbx4 in hindlimb buds is similar to Tbx5 occupancy in forelimbs. By contrast, another Hox factor, Hoxd13, also interacts with Tbx4/Tbx5 but antagonizes Tbx4/Tbx5-dependent transcriptional activity. Collectively, the modulation of Tbx-dependent activity by Hox factors acting on common DNA targets may integrate different developmental processes for the balanced formation of proportionate limbs.
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Affiliation(s)
- Deepak Jain
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada.,Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6 Canada
| | - Stephen Nemec
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada.,Department of Experimental Medicine, McGill University, Montreal, QC, H4A 3J1 Canada
| | - Maëva Luxey
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada
| | - Yves Gauthier
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada
| | - Amandine Bemmo
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada
| | - Aurelio Balsalobre
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada
| | - Jacques Drouin
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada .,Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6 Canada.,Department of Experimental Medicine, McGill University, Montreal, QC, H4A 3J1 Canada.,Departement de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, QC, H3J 3J7 Canada
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37
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Coupling the roles of Hox genes to regulatory networks patterning cranial neural crest. Dev Biol 2018; 444 Suppl 1:S67-S78. [PMID: 29571614 DOI: 10.1016/j.ydbio.2018.03.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/17/2018] [Accepted: 03/17/2018] [Indexed: 11/20/2022]
Abstract
The neural crest is a transient population of cells that forms within the developing central nervous system and migrates away to generate a wide range of derivatives throughout the body during vertebrate embryogenesis. These cells are of evolutionary and clinical interest, constituting a key defining trait in the evolution of vertebrates and alterations in their development are implicated in a high proportion of birth defects and craniofacial abnormalities. In the hindbrain and the adjacent cranial neural crest cells (cNCCs), nested domains of Hox gene expression provide a combinatorial'Hox-code' for specifying regional properties in the developing head. Hox genes have been shown to play important roles at multiple stages in cNCC development, including specification, migration, and differentiation. However, relatively little is known about the underlying gene-regulatory mechanisms involved, both upstream and downstream of Hox genes. Furthermore, it is still an open question as to how the genes of the neural crest GRN are linked to Hox-dependent pathways. In this review, we describe Hox gene expression, function and regulation in cNCCs with a view to integrating these genes within the emerging gene regulatory network for cNCC development. We highlight early roles for Hox1 genes in cNCC specification, proposing that this may be achieved, in part, by regulation of the balance between pluripotency and differentiation in precursor cells within the neuro-epithelium. We then describe what is known about the regulation of Hox gene expression in cNCCs and discuss this from the perspective of early vertebrate evolution.
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38
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Losa M, Risolino M, Li B, Hart J, Quintana L, Grishina I, Yang H, Choi IF, Lewicki P, Khan S, Aho R, Feenstra J, Vincent CT, Brown AMC, Ferretti E, Williams T, Selleri L. Face morphogenesis is promoted by Pbx-dependent EMT via regulation of Snail1 during frontonasal prominence fusion. Development 2018; 145:dev157628. [PMID: 29437830 PMCID: PMC5868993 DOI: 10.1242/dev.157628] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 01/24/2018] [Indexed: 12/17/2022]
Abstract
Human cleft lip with or without cleft palate (CL/P) is a common craniofacial abnormality caused by impaired fusion of the facial prominences. We have previously reported that, in the mouse embryo, epithelial apoptosis mediates fusion at the seam where the prominences coalesce. Here, we show that apoptosis alone is not sufficient to remove the epithelial layers. We observed morphological changes in the seam epithelia, intermingling of cells of epithelial descent into the mesenchyme and molecular signatures of epithelial-mesenchymal transition (EMT). Utilizing mouse lines with cephalic epithelium-specific Pbx loss exhibiting CL/P, we demonstrate that these cellular behaviors are Pbx dependent, as is the transcriptional regulation of the EMT driver Snail1. Furthermore, in the embryo, the majority of epithelial cells expressing high levels of Snail1 do not undergo apoptosis. Pbx1 loss- and gain-of-function in a tractable epithelial culture system revealed that Pbx1 is both necessary and sufficient for EMT induction. This study establishes that Pbx-dependent EMT programs mediate murine upper lip/primary palate morphogenesis and fusion via regulation of Snail1. Of note, the EMT signatures observed in the embryo are mirrored in the epithelial culture system.
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Affiliation(s)
- Marta Losa
- Program in Craniofacial Biology, Institute of Human Genetics, Eli and Edyth Broad Center of Regeneration Medicine & Stem Cell Research, Departments of Orofacial Sciences and Anatomy, University of California, San Francisco, 513 Parnassus Avenue, HSW 710, San Francisco, CA 94143, USA
| | - Maurizio Risolino
- Program in Craniofacial Biology, Institute of Human Genetics, Eli and Edyth Broad Center of Regeneration Medicine & Stem Cell Research, Departments of Orofacial Sciences and Anatomy, University of California, San Francisco, 513 Parnassus Avenue, HSW 710, San Francisco, CA 94143, USA
| | - Bingsi Li
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - James Hart
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Laura Quintana
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Irina Grishina
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Hui Yang
- Departments of Craniofacial Biology and Cell and Developmental Biology, University of Colorado at Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Irene F Choi
- Departments of Craniofacial Biology and Cell and Developmental Biology, University of Colorado at Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Patrick Lewicki
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Sameer Khan
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Robert Aho
- Program in Craniofacial Biology, Institute of Human Genetics, Eli and Edyth Broad Center of Regeneration Medicine & Stem Cell Research, Departments of Orofacial Sciences and Anatomy, University of California, San Francisco, 513 Parnassus Avenue, HSW 710, San Francisco, CA 94143, USA
| | - Jennifer Feenstra
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
- Karolinska Institute, Department of Physiology and Pharmacology, Nanna svartz väg 2, 17177 Stockholm, Sweden
| | - C Theresa Vincent
- Karolinska Institute, Department of Physiology and Pharmacology, Nanna svartz väg 2, 17177 Stockholm, Sweden
- Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Anthony M C Brown
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Elisabetta Ferretti
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Trevor Williams
- Departments of Craniofacial Biology and Cell and Developmental Biology, University of Colorado at Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Licia Selleri
- Program in Craniofacial Biology, Institute of Human Genetics, Eli and Edyth Broad Center of Regeneration Medicine & Stem Cell Research, Departments of Orofacial Sciences and Anatomy, University of California, San Francisco, 513 Parnassus Avenue, HSW 710, San Francisco, CA 94143, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
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39
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Dard A, Reboulet J, Jia Y, Bleicher F, Duffraisse M, Vanaker JM, Forcet C, Merabet S. Human HOX Proteins Use Diverse and Context-Dependent Motifs to Interact with TALE Class Cofactors. Cell Rep 2018. [DOI: 10.1016/j.celrep.2018.02.070] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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40
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Laser Capture and Deep Sequencing Reveals the Transcriptomic Programmes Regulating the Onset of Pancreas and Liver Differentiation in Human Embryos. Stem Cell Reports 2017; 9:1387-1394. [PMID: 29056335 PMCID: PMC5830993 DOI: 10.1016/j.stemcr.2017.09.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 09/22/2017] [Accepted: 09/25/2017] [Indexed: 01/10/2023] Open
Abstract
To interrogate the alternative fates of pancreas and liver in the earliest stages of human organogenesis, we developed laser capture, RNA amplification, and computational analysis of deep sequencing. Pancreas-enriched gene expression was less conserved between human and mouse than for liver. The dorsal pancreatic bud was enriched for components of Notch, Wnt, BMP, and FGF signaling, almost all genes known to cause pancreatic agenesis or hypoplasia, and over 30 unexplored transcription factors. SOX9 and RORA were imputed as key regulators in pancreas compared with EP300, HNF4A, and FOXA family members in liver. Analyses implied that current in vitro human stem cell differentiation follows a dorsal rather than a ventral pancreatic program and pointed to additional factors for hepatic differentiation. In summary, we provide the transcriptional codes regulating the start of human liver and pancreas development to facilitate stem cell research and clinical interpretation without inter-species extrapolation. Transcriptomic signatures at the inception of human liver and pancreas development Limited conservation of pancreas-enriched gene expression between human and mouse Human PSC protocols imply a dorsal rather than a ventral pancreatic program New pancreatic transcription factors imputed by differential analysis
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41
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Losa M, Latorre V, Andrabi M, Ladam F, Sagerström C, Novoa A, Zarrineh P, Bridoux L, Hanley NA, Mallo M, Bobola N. A tissue-specific, Gata6-driven transcriptional program instructs remodeling of the mature arterial tree. eLife 2017; 6:31362. [PMID: 28952437 PMCID: PMC5630260 DOI: 10.7554/elife.31362] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 09/25/2017] [Indexed: 01/23/2023] Open
Abstract
Connection of the heart to the systemic circulation is a critical developmental event that requires selective preservation of embryonic vessels (aortic arches). However, why some aortic arches regress while others are incorporated into the mature aortic tree remains unclear. By microdissection and deep sequencing in mouse, we find that neural crest (NC) only differentiates into vascular smooth muscle cells (SMCs) around those aortic arches destined for survival and reorganization, and identify the transcription factor Gata6 as a crucial regulator of this process. Gata6 is expressed in SMCs and its target genes activation control SMC differentiation. Furthermore, Gata6 is sufficient to promote SMCs differentiation in vivo, and drive preservation of aortic arches that ought to regress. These findings identify Gata6-directed differentiation of NC to SMCs as an essential mechanism that specifies the aortic tree, and provide a new framework for how mutations in GATA6 lead to congenital heart disorders in humans.
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Affiliation(s)
- Marta Losa
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Victor Latorre
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Munazah Andrabi
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Franck Ladam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Charles Sagerström
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Ana Novoa
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Peyman Zarrineh
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Laure Bridoux
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Neil A Hanley
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom.,Endocrinology Department, Central Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Moises Mallo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Nicoletta Bobola
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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42
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Zouaz A, Auradkar A, Delfini MC, Macchi M, Barthez M, Ela Akoa S, Bastianelli L, Xie G, Deng WM, Levine SS, Graba Y, Saurin AJ. The Hox proteins Ubx and AbdA collaborate with the transcription pausing factor M1BP to regulate gene transcription. EMBO J 2017; 36:2887-2906. [PMID: 28871058 DOI: 10.15252/embj.201695751] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 08/02/2017] [Accepted: 08/07/2017] [Indexed: 11/09/2022] Open
Abstract
In metazoans, the pausing of RNA polymerase II at the promoter (paused Pol II) has emerged as a widespread and conserved mechanism in the regulation of gene transcription. While critical in recruiting Pol II to the promoter, the role transcription factors play in transitioning paused Pol II into productive Pol II is, however, little known. By studying how Drosophila Hox transcription factors control transcription, we uncovered a molecular mechanism that increases productive transcription. We found that the Hox proteins AbdA and Ubx target gene promoters previously bound by the transcription pausing factor M1BP, containing paused Pol II and enriched with promoter-proximal Polycomb Group (PcG) proteins, yet lacking the classical H3K27me3 PcG signature. We found that AbdA binding to M1BP-regulated genes results in reduction in PcG binding, the release of paused Pol II, increases in promoter H3K4me3 histone marks and increased gene transcription. Linking transcription factors, PcG proteins and paused Pol II states, these data identify a two-step mechanism of Hox-driven transcription, with M1BP binding leading to Pol II recruitment followed by AbdA targeting, which results in a change in the chromatin landscape and enhanced transcription.
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Affiliation(s)
- Amel Zouaz
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
| | - Ankush Auradkar
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
| | | | - Meiggie Macchi
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
| | - Marine Barthez
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
| | - Serge Ela Akoa
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
| | - Leila Bastianelli
- MGX-Montpellier GenomiX c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Gengqiang Xie
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Stuart S Levine
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yacine Graba
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
| | - Andrew J Saurin
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
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43
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Abstract
Distinct combinations of transcription factors are necessary to elicit cell fate changes in embryonic development. Yet within each group of fate-changing transcription factors, a subset called 'pioneer factors' are dominant in their ability to engage silent, unmarked chromatin and initiate the recruitment of other factors, thereby imparting new function to regulatory DNA sequences. Recent studies have shown that pioneer factors are also crucial for cellular reprogramming and that they are implicated in the marked changes in gene regulatory networks that occur in various cancers. Here, we provide an overview of the contexts in which pioneer factors function, how they can target silent genes, and their limitations at regions of heterochromatin. Understanding how pioneer factors regulate gene expression greatly enhances our understanding of how specific developmental lineages are established as well as how cell fates can be manipulated.
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Affiliation(s)
- Makiko Iwafuchi-Doi
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 9-131 SCTR, 3400 Civic Center Blvd., Philadelphia, PA 19104-5157, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 9-131 SCTR, 3400 Civic Center Blvd., Philadelphia, PA 19104-5157, USA
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44
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Abstract
Bobola previews work from the Schulte laboratory showing that the atypical homeodomain protein MEIS2 facilitates chromatin accessibility of transcriptionally inactive genes in neuronal differentiation. How transcription factors (TFs) control enhancer and promoter functions to effect changes in gene expression is an important question. In this issue, Hau et al. (2017. J. Cell Biol.https://doi.org/10.1083/jcb.201701154) show that the TALE TF MEIS recruits the histone modifier PARP1/ARTD1 at promoters to decompact chromatin and activate transcription.
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Affiliation(s)
- Nicoletta Bobola
- Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, England, UK
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45
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Hau AC, Grebbin BM, Agoston Z, Anders-Maurer M, Müller T, Groß A, Kolb J, Langer JD, Döring C, Schulte D. MEIS homeodomain proteins facilitate PARP1/ARTD1-mediated eviction of histone H1. J Cell Biol 2017; 216:2715-2729. [PMID: 28739678 PMCID: PMC5584172 DOI: 10.1083/jcb.201701154] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 05/08/2017] [Accepted: 06/14/2017] [Indexed: 11/22/2022] Open
Abstract
PARP1/ARTD1 induces chromatin opening by posttranslational modification of the linker histone H1, but how PARP1 is targeted to physiologically correct gene loci is poorly understood. Hau et al. show that in differentiating neurons, PARP1 is rapidly and specifically recruited to a neuron-specific promoter by the atypical homeodomain protein MEIS2. Pre–B-cell leukemia homeobox (PBX) and myeloid ecotropic viral integration site (MEIS) proteins control cell fate decisions in many physiological and pathophysiological contexts, but how these proteins function mechanistically remains poorly defined. Focusing on the first hours of neuronal differentiation of adult subventricular zone–derived stem/progenitor cells, we describe a sequence of events by which PBX-MEIS facilitates chromatin accessibility of transcriptionally inactive genes: In undifferentiated cells, PBX1 is bound to the H1-compacted promoter/proximal enhancer of the neuron-specific gene doublecortin (Dcx). Once differentiation is induced, MEIS associates with chromatin-bound PBX1, recruits PARP1/ARTD1, and initiates PARP1-mediated eviction of H1 from the chromatin fiber. These results for the first time link MEIS proteins to PARP-regulated chromatin dynamics and provide a mechanistic basis to explain the profound cellular changes elicited by these proteins.
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Affiliation(s)
- Ann-Christin Hau
- Institute of Neurology, Edinger Institute, University Hospital Frankfurt, J.W. Goethe University, Frankfurt, Germany
| | - Britta Moyo Grebbin
- Institute of Neurology, Edinger Institute, University Hospital Frankfurt, J.W. Goethe University, Frankfurt, Germany
| | - Zsuzsa Agoston
- Institute of Neurology, Edinger Institute, University Hospital Frankfurt, J.W. Goethe University, Frankfurt, Germany
| | - Marie Anders-Maurer
- Institute of Neurology, Edinger Institute, University Hospital Frankfurt, J.W. Goethe University, Frankfurt, Germany
| | - Tamara Müller
- Institute of Neurology, Edinger Institute, University Hospital Frankfurt, J.W. Goethe University, Frankfurt, Germany
| | - Anja Groß
- Institute of Neurology, Edinger Institute, University Hospital Frankfurt, J.W. Goethe University, Frankfurt, Germany
| | - Jasmine Kolb
- Institute of Neurology, Edinger Institute, University Hospital Frankfurt, J.W. Goethe University, Frankfurt, Germany
| | - Julian D Langer
- Department of Molecular Membrane Biology, Max Planck Institute for Biophysics, Frankfurt, Germany
| | - Claudia Döring
- Senckenberg Institute of Pathology, University Hospital Frankfurt, J.W. Goethe University, Frankfurt, Germany
| | - Dorothea Schulte
- Institute of Neurology, Edinger Institute, University Hospital Frankfurt, J.W. Goethe University, Frankfurt, Germany
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46
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Bobola N, Merabet S. Homeodomain proteins in action: similar DNA binding preferences, highly variable connectivity. Curr Opin Genet Dev 2016; 43:1-8. [PMID: 27768937 DOI: 10.1016/j.gde.2016.09.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 09/28/2016] [Indexed: 12/18/2022]
Abstract
Homeodomain proteins are evolutionary conserved proteins present in the entire eukaryote kingdom. They execute functions that are essential for life, both in developing and adult organisms. Most homeodomain proteins act as transcription factors and bind DNA to control the activity of other genes. In contrast to their similar DNA binding specificity, homeodomain proteins execute highly diverse and context-dependent functions. Several factors, including genome accessibility, DNA shape, combinatorial binding and the ability to interact with many transcriptional partners, diversify the activity of homeodomain proteins and culminate in the activation of highly dynamic, context-specific transcriptional programs. Clarifying how homeodomain transcription factors work is central to our understanding of development, disease and evolution.
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Affiliation(s)
- Nicoletta Bobola
- School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.
| | - Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon, Centre National de Recherche Scientifique, Ecole Normale Supérieure de Lyon, France.
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47
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Spatiotemporal regulation of enhancers during cardiogenesis. Cell Mol Life Sci 2016; 74:257-265. [PMID: 27497925 PMCID: PMC5219004 DOI: 10.1007/s00018-016-2322-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 07/20/2016] [Accepted: 08/02/2016] [Indexed: 01/02/2023]
Abstract
With the advance in chromatin immunoprecipitation followed by high-throughput sequencing, there has been a dramatic increase in our understanding of distal enhancer function. In the developing heart, the identification and characterisation of such enhancers have deepened our knowledge of the mechanisms of transcriptional regulation that drives cardiac differentiation. With next-generation sequencing techniques becoming widely accessible, the quantity of data describing the genome-wide distribution of cardiac-specific transcription factor and chromatin modifiers has rapidly increased and it is now becoming clear that the usage of enhancers is highly dynamic and complex, both during the development and in the adult. The identification of those enhancers has revealed new insights into the transcriptional mechanisms of how tissue-specific gene expression patterns are established, maintained, and change dynamically during development and upon physiological stress.
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Ye W, Song Y, Huang Z, Osterwalder M, Ljubojevic A, Xu J, Bobick B, Abassah-Oppong S, Ruan N, Shamby R, Yu D, Zhang L, Cai CL, Visel A, Zhang Y, Cobb J, Chen Y. A unique stylopod patterning mechanism by Shox2-controlled osteogenesis. Development 2016; 143:2548-60. [PMID: 27287812 PMCID: PMC4958343 DOI: 10.1242/dev.138750] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 05/31/2016] [Indexed: 02/05/2023]
Abstract
Vertebrate appendage patterning is programmed by Hox-TALE factor-bound regulatory elements. However, it remains unclear which cell lineages are commissioned by Hox-TALE factors to generate regional specific patterns and whether other Hox-TALE co-factors exist. In this study, we investigated the transcriptional mechanisms controlled by the Shox2 transcriptional regulator in limb patterning. Harnessing an osteogenic lineage-specific Shox2 inactivation approach we show that despite widespread Shox2 expression in multiple cell lineages, lack of the stylopod observed upon Shox2 deficiency is a specific result of Shox2 loss of function in the osteogenic lineage. ChIP-Seq revealed robust interaction of Shox2 with cis-regulatory enhancers clustering around skeletogenic genes that are also bound by Hox-TALE factors, supporting a lineage autonomous function of Shox2 in osteogenic lineage fate determination and skeleton patterning. Pbx ChIP-Seq further allowed the genome-wide identification of cis-regulatory modules exhibiting co-occupancy of Pbx, Meis and Shox2 transcriptional regulators. Integrative analysis of ChIP-Seq and RNA-Seq data and transgenic enhancer assays indicate that Shox2 patterns the stylopod as a repressor via interaction with enhancers active in the proximal limb mesenchyme and antagonizes the repressive function of TALE factors in osteogenesis.
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Affiliation(s)
- Wenduo Ye
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA
| | - Yingnan Song
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA Southern Center for Biomedical Research and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350108, People's Republic of China
| | - Zhen Huang
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA Southern Center for Biomedical Research and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350108, People's Republic of China
| | | | - Anja Ljubojevic
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Jue Xu
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Brent Bobick
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Samuel Abassah-Oppong
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Ningsheng Ruan
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA Southern Center for Biomedical Research and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350108, People's Republic of China
| | - Ross Shamby
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA
| | - Diankun Yu
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA
| | - Lu Zhang
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chen-Leng Cai
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA School of Natural Sciences, University of California at Merced, Merced, CA 95343, USA
| | - Yanding Zhang
- Southern Center for Biomedical Research and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350108, People's Republic of China
| | - John Cobb
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - YiPing Chen
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA Southern Center for Biomedical Research and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350108, People's Republic of China
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49
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Rosin JM, Li W, Cox LL, Rolfe SM, Latorre V, Akiyama JA, Visel A, Kuramoto T, Bobola N, Turner EE, Cox TC. A distal 594 bp ECR specifies Hmx1 expression in pinna and lateral facial morphogenesis and is regulated by the Hox-Pbx-Meis complex. Development 2016; 143:2582-92. [PMID: 27287804 DOI: 10.1242/dev.133736] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 05/23/2016] [Indexed: 11/20/2022]
Abstract
Hmx1 encodes a homeodomain transcription factor expressed in the developing lateral craniofacial mesenchyme, retina and sensory ganglia. Mutation or mis-regulation of Hmx1 underlies malformations of the eye and external ear in multiple species. Deletion or insertional duplication of an evolutionarily conserved region (ECR) downstream of Hmx1 has recently been described in rat and cow, respectively. Here, we demonstrate that the impact of Hmx1 loss is greater than previously appreciated, with a variety of lateral cranioskeletal defects, auriculofacial nerve deficits, and duplication of the caudal region of the external ear. Using a transgenic approach, we demonstrate that a 594 bp sequence encompassing the ECR recapitulates specific aspects of the endogenous Hmx1 lateral facial expression pattern. Moreover, we show that Hoxa2, Meis and Pbx proteins act cooperatively on the ECR, via a core 32 bp sequence, to regulate Hmx1 expression. These studies highlight the conserved role for Hmx1 in BA2-derived tissues and provide an entry point for improved understanding of the causes of the frequent lateral facial birth defects in humans.
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Affiliation(s)
- Jessica M Rosin
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Wenjie Li
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA Department of Oral Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Liza L Cox
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA Department of Pediatrics (Craniofacial Medicine), University of Washington, Seattle, WA 98195, USA
| | - Sara M Rolfe
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Victor Latorre
- School of Dentistry, Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Jennifer A Akiyama
- Functional Genomics Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Axel Visel
- Functional Genomics Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA DOE Joint Genome Institute, Walnut Creek, CA 94598, USA School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Takashi Kuramoto
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Nicoletta Bobola
- School of Dentistry, Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Eric E Turner
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Timothy C Cox
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA Department of Oral Health Sciences, University of Washington, Seattle, WA 98195, USA Department of Pediatrics (Craniofacial Medicine), University of Washington, Seattle, WA 98195, USA Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
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50
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Abstract
Hox proteins are a deeply conserved group of transcription factors originally defined for their critical roles in governing segmental identity along the antero-posterior (AP) axis in
Drosophila. Over the last 30 years, numerous data generated in evolutionarily diverse taxa have clearly shown that changes in the expression patterns of these genes are closely associated with the regionalization of the AP axis, suggesting that
Hox genes have played a critical role in the evolution of novel body plans within Bilateria. Despite this deep functional conservation and the importance of these genes in AP patterning, key questions remain regarding many aspects of
Hox biology. In this commentary, we highlight recent reports that have provided novel insight into the origins of the mammalian
Hox cluster, the role of
Hox genes in the generation of a limbless body plan, and a novel putative mechanism in which
Hox genes may encode specificity along the AP axis. Although the data discussed here offer a fresh perspective, it is clear that there is still much to learn about
Hox biology and the roles it has played in the evolution of the Bilaterian body plan.
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Affiliation(s)
- Steven M Hrycaj
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, 48109-2200, USA
| | - Deneen M Wellik
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, 48109-2200, USA; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, 48109-2200, USA
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