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Konuma J, Fujisawa T, Nishiyama T, Kasahara M, Shibata TF, Nozawa M, Shigenobu S, Toyoda A, Hasebe M, Sota T. Odd-Paired is Involved in Morphological Divergence of Snail-Feeding Beetles. Mol Biol Evol 2024; 41:msae110. [PMID: 38857185 PMCID: PMC11214159 DOI: 10.1093/molbev/msae110] [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: 12/12/2023] [Revised: 04/15/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024] Open
Abstract
Body shape and size diversity and their evolutionary rates correlate with species richness at the macroevolutionary scale. However, the molecular genetic mechanisms underlying the morphological diversification across related species are poorly understood. In beetles, which account for one-fourth of the known species, adaptation to different trophic niches through morphological diversification appears to have contributed to species radiation. Here, we explored the key genes for the morphological divergence of the slender to stout body shape related to divergent feeding methods on large to small snails within the genus Carabus. We show that the zinc-finger transcription factor encoded by odd-paired (opa) controls morphological variation in the snail-feeding ground beetle Carabus blaptoides. Specifically, opa was identified as the gene underlying the slender to stout morphological difference between subspecies through genetic mapping and functional analysis via gene knockdown. Further analyses revealed that changes in opa cis-regulatory sequences likely contributed to the differences in body shape and size between C. blaptoides subspecies. Among opa cis-regulatory sequences, single nucleotide polymorphisms on the transcription factor binding sites may be associated with the morphological differences between C. blaptoides subspecies. opa was highly conserved in a wide range of taxa, especially in beetles. Therefore, opa may play an important role in adaptive morphological divergence in beetles.
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Affiliation(s)
- Junji Konuma
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Tomochika Fujisawa
- Center for Data Science Education and Research, Shiga University, Hikone, Shiga, Japan
| | - Tomoaki Nishiyama
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Ishikawa, Japan
| | - Masahiro Kasahara
- Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba, Japan
| | | | - Masafumi Nozawa
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
- Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | | | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, The Graduate School for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
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Koromila T, Gao F, Iwasaki Y, He P, Pachter L, Gergen JP, Stathopoulos A. Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos. eLife 2020; 9:e59610. [PMID: 32701060 PMCID: PMC7417190 DOI: 10.7554/elife.59610] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 07/22/2020] [Indexed: 01/29/2023] Open
Abstract
Pioneer factors such as Zelda (Zld) help initiate zygotic transcription in Drosophila early embryos, but whether other factors support this dynamic process is unclear. Odd-paired (Opa), a zinc-finger transcription factor expressed at cellularization, controls the transition of genes from pair-rule to segmental patterns along the anterior-posterior axis. Finding that Opa also regulates expression through enhancer sog_Distal along the dorso-ventral axis, we hypothesized Opa's role is more general. Chromatin-immunoprecipitation (ChIP-seq) confirmed its in vivo binding to sog_Distal but also identified widespread binding throughout the genome, comparable to Zld. Furthermore, chromatin assays (ATAC-seq) demonstrate that Opa, like Zld, influences chromatin accessibility genome-wide at cellularization, suggesting both are pioneer factors with common as well as distinct targets. Lastly, embryos lacking opa exhibit widespread, late patterning defects spanning both axes. Collectively, these data suggest Opa is a general timing factor and likely late-acting pioneer factor that drives a secondary wave of zygotic gene expression.
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Affiliation(s)
- Theodora Koromila
- California Institute of Technology, Division of Biology and Biological EngineeringPasadenaUnited States
| | - Fan Gao
- California Institute of Technology, Division of Biology and Biological EngineeringPasadenaUnited States
| | - Yasuno Iwasaki
- Stony Brook University, Department of Biochemistry and Cell Biology and Center for Developmental GeneticsStony BrookUnited States
| | - Peng He
- California Institute of Technology, Division of Biology and Biological EngineeringPasadenaUnited States
| | - Lior Pachter
- California Institute of Technology, Division of Biology and Biological EngineeringPasadenaUnited States
| | - J Peter Gergen
- Stony Brook University, Department of Biochemistry and Cell Biology and Center for Developmental GeneticsStony BrookUnited States
| | - Angelike Stathopoulos
- California Institute of Technology, Division of Biology and Biological EngineeringPasadenaUnited States
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Soluri IV, Zumerling LM, Payan Parra OA, Clark EG, Blythe SA. Zygotic pioneer factor activity of Odd-paired/Zic is necessary for late function of the Drosophila segmentation network. eLife 2020; 9:e53916. [PMID: 32347792 PMCID: PMC7190358 DOI: 10.7554/elife.53916] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/29/2020] [Indexed: 12/20/2022] Open
Abstract
Because chromatin determines whether information encoded in DNA is accessible to transcription factors, dynamic chromatin states in development may constrain how gene regulatory networks impart embryonic pattern. To determine the interplay between chromatin states and regulatory network function, we performed ATAC-seq on Drosophila embryos during the establishment of the segmentation network, comparing wild-type and mutant embryos in which all graded maternal patterning inputs are eliminated. While during the period between zygotic genome activation and gastrulation many regions maintain stable accessibility, cis-regulatory modules (CRMs) within the network undergo extensive patterning-dependent changes in accessibility. A component of the network, Odd-paired (opa), is necessary for pioneering accessibility of late segmentation network CRMs. opa-driven changes in accessibility are accompanied by equivalent changes in gene expression. Interfering with the timing of opa activity impacts the proper patterning of expression. These results indicate that dynamic systems for chromatin regulation directly impact the reading of embryonic patterning information.
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Affiliation(s)
- Isabella V Soluri
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Lauren M Zumerling
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Omar A Payan Parra
- Program in Interdisciplinary Biological Sciences, Northwestern UniversityEvanstonUnited States
- Department of Neurobiology, Northwestern UniversityEvanstonUnited States
| | - Eleanor G Clark
- Program in Interdisciplinary Biological Sciences, Northwestern UniversityEvanstonUnited States
| | - Shelby A Blythe
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
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Tohmonda T, Kamiya A, Ishiguro A, Iwaki T, Fujimi TJ, Hatayama M, Aruga J. Identification and Characterization of Novel Conserved Domains in Metazoan Zic Proteins. Mol Biol Evol 2018; 35:2205-2229. [DOI: 10.1093/molbev/msy122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Takahide Tohmonda
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
| | - Akiko Kamiya
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
| | - Akira Ishiguro
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
| | - Takashi Iwaki
- Meguro Parasitological Museum, Meguro-Ku, Tokyo, Japan
| | - Takahiko J Fujimi
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
| | - Minoru Hatayama
- Department of Medical Pharmacology, Nagasaki University Institute of Biomedical Sciences, Nagasaki, Japan
| | - Jun Aruga
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-Shi, Saitama, Japan
- Department of Medical Pharmacology, Nagasaki University Institute of Biomedical Sciences, Nagasaki, Japan
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Role of Zic Family Proteins in Transcriptional Regulation and Chromatin Remodeling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1046:353-380. [DOI: 10.1007/978-981-10-7311-3_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Link between the causative genes of holoprosencephaly: Zic2 directly regulates Tgif1 expression. Sci Rep 2018; 8:2140. [PMID: 29391420 PMCID: PMC5794963 DOI: 10.1038/s41598-018-20242-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/15/2018] [Indexed: 02/07/2023] Open
Abstract
One of the causal genes for holoprosencephaly (HPE) is ZIC2 (HPE5). It belongs to the zinc finger protein of the cerebellum (Zic) family of genes that share a C2H2-type zinc finger domain, similar to the GLI family of genes. In order to clarify the role of Zic2 in gene regulation, we searched for its direct target genes using chromatin immunoprecipitation (ChIP). We identified TGIF1 (HPE4), another holoprosencephaly-causative gene in humans. We identified Zic2-binding sites (ZBS) on the 5′ flanking region of Tgif1 by in vitro DNA binding assays. ZBS were essential for Zic2-dependent transcriptional activation in reporter gene assays. Zic2 showed a higher affinity to ZBS than GLI-binding sequences. Zic2-binding to the cis-regulatory element near the Tgif1 promoter may be involved in the mechanism underlying forebrain development and incidences of HPE.
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Hursh DA, Stultz BG. Odd-Paired: The Drosophila Zic Gene. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1046:41-58. [PMID: 29442316 DOI: 10.1007/978-981-10-7311-3_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Zinc finger in the cerebellum (Zic) proteins are a family of transcription factors with multiple roles during development, particularly in neural tissues. The founding member of the Zic family is the Drosophila odd-paired (opa) gene. The Opa protein has a DNA binding domain containing five Cys2His2-type zinc fingers and has been shown to act as a sequence-specific DNA binding protein. Opa has significant homology to mammalian Zic1, Zic2, and Zic3 within the zinc finger domain and in two other conserved regions outside that domain. opa was initially identified as a pair-rule gene, part of the hierarchy of genes that establish the segmental body plan of the early Drosophila embryo. However, its wide expression pattern during embryogenesis indicates it plays additional roles. Embryos deficient in opa die before hatching with aberrant segmentation but also with defects in larval midgut formation. Post-embryonically, opa plays important roles in adult head development and circadian rhythm. Based on extensive neural expression, opa is predicted to be involved in many aspects of neural development and behavior, like other proteins of the Zic family. Consensus DNA binding sites have been identified for Opa and have been shown to activate transcription in vivo. However, there is evidence Opa may serve as a transcriptional regulator in the absence of direct DNA binding, as has been seen for other Zic proteins.
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Affiliation(s)
- Deborah A Hursh
- Division of Cell and Gene Therapy, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
| | - Brian G Stultz
- Division of Cell and Gene Therapy, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
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Mendoza-García P, Hugosson F, Fallah M, Higgins ML, Iwasaki Y, Pfeifer K, Wolfstetter G, Varshney G, Popichenko D, Gergen JP, Hens K, Deplancke B, Palmer RH. The Zic family homologue Odd-paired regulates Alk expression in Drosophila. PLoS Genet 2017; 13:e1006617. [PMID: 28369060 PMCID: PMC5393633 DOI: 10.1371/journal.pgen.1006617] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 04/17/2017] [Accepted: 02/07/2017] [Indexed: 01/30/2023] Open
Abstract
The Anaplastic Lymphoma Kinase (Alk) receptor tyrosine kinase (RTK) plays a critical role in the specification of founder cells (FCs) in the Drosophila visceral mesoderm (VM) during embryogenesis. Reporter gene and CRISPR/Cas9 deletion analysis reveals enhancer regions in and upstream of the Alk locus that influence tissue-specific expression in the amnioserosa (AS), the VM and the epidermis. By performing high throughput yeast one-hybrid screens (Y1H) with a library of Drosophila transcription factors (TFs) we identify Odd-paired (Opa), the Drosophila homologue of the vertebrate Zic family of TFs, as a novel regulator of embryonic Alk expression. Further characterization identifies evolutionarily conserved Opa-binding cis-regulatory motifs in one of the Alk associated enhancer elements. Employing Alk reporter lines as well as CRISPR/Cas9-mediated removal of regulatory elements in the Alk locus, we show modulation of Alk expression by Opa in the embryonic AS, epidermis and VM. In addition, we identify enhancer elements that integrate input from additional TFs, such as Binou (Bin) and Bagpipe (Bap), to regulate VM expression of Alk in a combinatorial manner. Taken together, our data show that the Opa zinc finger TF is a novel regulator of embryonic Alk expression. The Alk receptor tyrosine kinase is employed repeatedly during Drosophila development to drive signaling events in a variety of tissues. The spatial and temporal expression pattern of the Alk gene is tightly regulated. Identifying factors that influence the expression of Alk is important to better understand how Alk signaling is controlled. In this paper we characterize cis-regulatory sequences in the Alk locus and the transcription factors that bind them to govern Alk expression in the Drosophila embryo. Using a robotic protein-DNA interaction assay, we identified the Zic family transcription factor Odd-paired as a factor that binds to regulatory elements in the Alk locus. Binding of Odd-paired to Alkcis-regulatory elements varies spatially, revealing a requirement for additional transcription factors such as the NK3 and FoxF orthologues Bagpipe and Biniou in a subset of Alk-expressing tissues. Our findings provide new insight into the dynamics underlying temporal and spatial regulation of the Alk receptor during embryogenesis.
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Affiliation(s)
- Patricia Mendoza-García
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Fredrik Hugosson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Mahsa Fallah
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Michael L. Higgins
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Yasuno Iwasaki
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Kathrin Pfeifer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Georg Wolfstetter
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Gaurav Varshney
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | | | - J. Peter Gergen
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Korneel Hens
- Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, United Kingdom
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Lausanne, Switzerland
| | - Ruth H. Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- * E-mail:
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Clark E, Akam M. Odd-paired controls frequency doubling in Drosophila segmentation by altering the pair-rule gene regulatory network. eLife 2016; 5:e18215. [PMID: 27525481 PMCID: PMC5035143 DOI: 10.7554/elife.18215] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/14/2016] [Indexed: 01/08/2023] Open
Abstract
The Drosophila embryo transiently exhibits a double-segment periodicity, defined by the expression of seven 'pair-rule' genes, each in a pattern of seven stripes. At gastrulation, interactions between the pair-rule genes lead to frequency doubling and the patterning of 14 parasegment boundaries. In contrast to earlier stages of Drosophila anteroposterior patterning, this transition is not well understood. By carefully analysing the spatiotemporal dynamics of pair-rule gene expression, we demonstrate that frequency-doubling is precipitated by multiple coordinated changes to the network of regulatory interactions between the pair-rule genes. We identify the broadly expressed but temporally patterned transcription factor, Odd-paired (Opa/Zic), as the cause of these changes, and show that the patterning of the even-numbered parasegment boundaries relies on Opa-dependent regulatory interactions. Our findings indicate that the pair-rule gene regulatory network has a temporally modulated topology, permitting the pair-rule genes to play stage-specific patterning roles.
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Affiliation(s)
- Erik Clark
- Laboratory for Development and Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Michael Akam
- Laboratory for Development and Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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Abstract
decapentaplegic (dpp), the Drosophila ortholog of BMP 2/4, directs ventral adult head morphogenesis through expression in the peripodial epithelium of the eye-antennal disc. This dpp expressing domain exerts effects both on the peripodial epithelium, and the underlying disc proper epithelium. We have uncovered a role for the Jun N-terminal kinase (JNK) pathway in dpp-mediated ventral head development. JNK activity is required for dpp's action on the disc proper, but in the absence of dpp expression, excessive JNK activity is produced, leading to specific loss of maxillary palps. In this review we outline our hypotheses on how dpp acts by both short range and longer range mechanisms to direct head morphogenesis and speculate on the dual role of JNK signaling in this process. Finally, we describe the regulatory control of dpp expression in the eye-antennal disc, and pose the problem of how the various expression domains of a secreted protein can be targeted to their specific functions.
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Affiliation(s)
- Deborah A Hursh
- a Division of Cell and Gene Therapies , Center for Biologics Evaluation and Research, Food and Drug Administration , Silver Spring , MD , USA
| | - Brian G Stultz
- a Division of Cell and Gene Therapies , Center for Biologics Evaluation and Research, Food and Drug Administration , Silver Spring , MD , USA
| | - Sung Yeon Park
- b Ischemic/Hypoxic Disease Institute , Department of Physiology , Seoul National University College of Medicine , Seoul , Republic of Korea
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Slattery M, Ma L, Spokony RF, Arthur RK, Kheradpour P, Kundaje A, Nègre N, Crofts A, Ptashkin R, Zieba J, Ostapenko A, Suchy S, Victorsen A, Jameel N, Grundstad AJ, Gao W, Moran JR, Rehm EJ, Grossman RL, Kellis M, White KP. Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster. Genome Res 2015; 24:1224-35. [PMID: 24985916 PMCID: PMC4079976 DOI: 10.1101/gr.168807.113] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Annotation of regulatory elements and identification of the transcription-related factors (TRFs) targeting these elements are key steps in understanding how cells interpret their genetic blueprint and their environment during development, and how that process goes awry in the case of disease. One goal of the modENCODE (model organism ENCyclopedia of DNA Elements) Project is to survey a diverse sampling of TRFs, both DNA-binding and non-DNA-binding factors, to provide a framework for the subsequent study of the mechanisms by which transcriptional regulators target the genome. Here we provide an updated map of the Drosophila melanogaster regulatory genome based on the location of 84 TRFs at various stages of development. This regulatory map reveals a variety of genomic targeting patterns, including factors with strong preferences toward proximal promoter binding, factors that target intergenic and intronic DNA, and factors with distinct chromatin state preferences. The data also highlight the stringency of the Polycomb regulatory network, and show association of the Trithorax-like (Trl) protein with hotspots of DNA binding throughout development. Furthermore, the data identify more than 5800 instances in which TRFs target DNA regions with demonstrated enhancer activity. Regions of high TRF co-occupancy are more likely to be associated with open enhancers used across cell types, while lower TRF occupancy regions are associated with complex enhancers that are also regulated at the epigenetic level. Together these data serve as a resource for the research community in the continued effort to dissect transcriptional regulatory mechanisms directing Drosophila development.
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Affiliation(s)
- Matthew Slattery
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Lijia Ma
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Rebecca F Spokony
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Robert K Arthur
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Pouya Kheradpour
- Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Anshul Kundaje
- Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Nicolas Nègre
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA; Université de Montpellier II and INRA, UMR1333 DGIMI, F-34095 Montpellier, France
| | - Alex Crofts
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Ryan Ptashkin
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jennifer Zieba
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Alexander Ostapenko
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Sarah Suchy
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Alec Victorsen
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Nader Jameel
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - A Jason Grundstad
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Wenxuan Gao
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jennifer R Moran
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - E Jay Rehm
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Robert L Grossman
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA; Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kevin P White
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
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Slattery M, Voutev R, Ma L, Nègre N, White KP, Mann RS. Divergent transcriptional regulatory logic at the intersection of tissue growth and developmental patterning. PLoS Genet 2013; 9:e1003753. [PMID: 24039600 PMCID: PMC3764184 DOI: 10.1371/journal.pgen.1003753] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 07/10/2013] [Indexed: 12/19/2022] Open
Abstract
The Yorkie/Yap transcriptional coactivator is a well-known regulator of cellular proliferation in both invertebrates and mammals. As a coactivator, Yorkie (Yki) lacks a DNA binding domain and must partner with sequence-specific DNA binding proteins in the nucleus to regulate gene expression; in Drosophila, the developmental regulators Scalloped (Sd) and Homothorax (Hth) are two such partners. To determine the range of target genes regulated by these three transcription factors, we performed genome-wide chromatin immunoprecipitation experiments for each factor in both the wing and eye-antenna imaginal discs. Strong, tissue-specific binding patterns are observed for Sd and Hth, while Yki binding is remarkably similar across both tissues. Binding events common to the eye and wing are also present for Sd and Hth; these are associated with genes regulating cell proliferation and “housekeeping” functions, and account for the majority of Yki binding. In contrast, tissue-specific binding events for Sd and Hth significantly overlap enhancers that are active in the given tissue, are enriched in Sd and Hth DNA binding sites, respectively, and are associated with genes that are consistent with each factor's previously established tissue-specific functions. Tissue-specific binding events are also significantly associated with Polycomb targeted chromatin domains. To provide mechanistic insights into tissue-specific regulation, we identify and characterize eye and wing enhancers of the Yki-targeted bantam microRNA gene and demonstrate that they are dependent on direct binding by Hth and Sd, respectively. Overall these results suggest that both Sd and Hth use distinct strategies – one shared between tissues and associated with Yki, the other tissue-specific, generally Yki-independent and associated with developmental patterning – to regulate distinct gene sets during development. The Hippo tumor suppressor pathway controls proliferation in a tissue-nonspecific fashion in Drosophila epithelial progenitor tissues via the transcriptional coactivator Yorkie (Yki). However, despite the tissue-nonspecific role that Yki plays in tissue growth, the transcription factors that recruit Yki to DNA, most notably Scalloped (Sd) and Homothorax (Hth), are important regulators of developmental patterning with many tissue-specific functions. Thus, these three transcriptional regulators – Yki, Sd, and Hth – provide a model for exploring the properties of protein-DNA interactions that regulate both tissue-shared and tissue-specific functions. With this goal in mind, we identified the positions in the fly genome that are bound by Yki, Sd, and Hth in the progenitors of the wing and eye-antenna structures of the fly. These data not only provide a global view of the Yki gene regulatory network, they reveal an unusual amount of tissue specificity in the genomic regions targeted by Sd and Hth, but not Yki. The data also reveal that tissue-specific binding is very likely to overlap tissue-specific enhancer regions, provide important clues for how tissue-specific Sd and Hth binding occurs, and support the idea that gene regulatory networks are plastic, with spatial differences in binding significantly impacting network structures.
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Affiliation(s)
- Matthew Slattery
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Roumen Voutev
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
| | - Lijia Ma
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Nicolas Nègre
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Université de Montpellier 2 and INRA, UMR1333 DGIMI, Montpellier, France
| | - Kevin P. White
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Richard S. Mann
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
- * E-mail:
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Stultz BG, Park SY, Mortin MA, Kennison JA, Hursh DA. Hox proteins coordinate peripodial decapentaplegic expression to direct adult head morphogenesis in Drosophila. Dev Biol 2012; 369:362-76. [PMID: 22824425 DOI: 10.1016/j.ydbio.2012.07.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 06/29/2012] [Accepted: 07/12/2012] [Indexed: 02/04/2023]
Abstract
The Drosophila BMP, decapentaplegic (dpp), controls morphogenesis of the ventral adult head through expression limited to the lateral peripodial epithelium of the eye-antennal disc by a 3.5 kb enhancer in the 5' end of the gene. We recovered a 15 bp deletion mutation within this enhancer that identified a homeotic (Hox) response element that is a direct target of labial and the homeotic cofactors homothorax and extradenticle. Expression of labial and homothorax are required for dpp expression in the peripodial epithelium, while the Hox gene Deformed represses labial in this location, thus limiting its expression and indirectly that of dpp to the lateral side of the disc. The expression of these homeodomain genes is in turn regulated by the dpp pathway, as dpp signalling is required for labial expression but represses homothorax. This Hox-BMP regulatory network is limited to the peripodial epithelium of the eye-antennal disc, yet is crucial to the morphogenesis of the head, which fate maps suggest arises primarily from the disc proper, not the peripodial epithelium. Thus Hox/BMP interactions in the peripodial epithelium of the eye-antennal disc contribute inductively to the shape of the external form of the adult Drosophila head.
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Affiliation(s)
- Brian G Stultz
- Division of Cell and Gene Therapy, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892, USA
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Fujioka M, Jaynes JB. Regulation of a duplicated locus: Drosophila sloppy paired is replete with functionally overlapping enhancers. Dev Biol 2011; 362:309-19. [PMID: 22178246 DOI: 10.1016/j.ydbio.2011.12.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 11/16/2011] [Accepted: 12/01/2011] [Indexed: 11/28/2022]
Abstract
In order to investigate regulation and redundancy within the sloppy paired (slp) locus, we analyzed 30 kilobases of DNA encompassing the tandem, coordinately regulated slp1 and slp2 transcription units. We found a remarkable array of stripe enhancers with overlapping activities surrounding the slp1 transcription unit, and, unexpectedly, glial cell enhancers surrounding slp2. The slp stripe regulatory region generates 7 stripes at blastoderm, and later 14 stripes that persist throughout embryogenesis. Phylogenetic analysis among drosophilids suggests that the multiplicity of stripe enhancers did not evolve through recent duplication. Most of the direct integration among cis-regulatory modules appears to be simply additive, with one notable exception. Despite the apparent redundancy among stripe enhancers, transgenic rescue suggests that most are required for full function, to maintain wingless expression and parasegment boundaries throughout embryogenesis. Transgenic rescue also reveals indirect positive autoregulation by the 7 early stripes, without which alternate stripes within the 14-stripe pattern are lost, leading to embryos with a pair-rule phenotype.
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Affiliation(s)
- Miki Fujioka
- Dept. of Biochemistry and Molecular Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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Pourebrahim R, Houtmeyers R, Ghogomu S, Janssens S, Thelie A, Tran HT, Langenberg T, Vleminckx K, Bellefroid E, Cassiman JJ, Tejpar S. Transcription factor Zic2 inhibits Wnt/β-catenin protein signaling. J Biol Chem 2011; 286:37732-40. [PMID: 21908606 DOI: 10.1074/jbc.m111.242826] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Zic transcription factors play critical roles during embryonic development. Mutations in the ZIC2 gene are associated with human holoprosencephaly, but the etiology is still unclear. Here, we report a novel function for ZIC2 as a regulator of β-catenin·TCF4-mediated transcription. We show that ZIC2 can bind directly to the DNA-binding high mobility group box of TCF4 via its zinc finger domain and inhibit the transcriptional activity of the β-catenin·TCF4 complex. However, the binding of TCF4 to DNA was not affected by ZIC2. Zic2 RNA injection completely inhibited β-catenin-induced axis duplication in Xenopus embryos and strongly blocked the ability of β-catenin to induce expression of known Wnt targets in animal caps. Moreover, Zic2 knockdown in transgenic Xenopus Wnt reporter embryos led to ectopic Wnt signaling activity mainly at the midbrain-hindbrain boundary. Together, our results demonstrate a previously unknown role for ZIC2 as a transcriptional regulator of the β-catenin·TCF4 complex.
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Affiliation(s)
- Rasoul Pourebrahim
- Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
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