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Mukherjee A, Fallacaro S, Ratchasanmuang P, Zinski J, Boka A, Shankta K, Mir M. A fine kinetic balance of interactions directs transcription factor hubs to genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589811. [PMID: 38659757 PMCID: PMC11042322 DOI: 10.1101/2024.04.16.589811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Eukaryotic gene regulation relies on the binding of sequence-specific transcription factors (TFs). TFs bind chromatin transiently yet occupy their target sites by forming high-local concentration microenvironments (hubs and condensates) that increase the frequency of binding events. Despite their ubiquity, such microenvironments have been difficult to study in endogenous contexts due to technical limitations. Here, we overcome these limitations and investigate how hubs drive TF occupancy at their targets. Using a DNA binding perturbation to a hub-forming TF, Zelda, in Drosophila embryos, we find that hub properties, including the stability and frequencies of associations to targets, are key determinants of TF occupancy. Our data suggest that the targeting of these hubs is driven not just by specific DNA motif recognition, but also by a fine-tuned kinetic balance of interactions between TFs and their co-binding partners.
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Affiliation(s)
- Apratim Mukherjee
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Samantha Fallacaro
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Developmental, Stem Cell, and Regenerative Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Puttachai Ratchasanmuang
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Howard Hughes Medical Institute, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Joseph Zinski
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Alan Boka
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kareena Shankta
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Roy and Diana Vagelos Program in Life Sciences and Management, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mustafa Mir
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Howard Hughes Medical Institute, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
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2
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O'Haren T, Aoki T, Rieder LE. Zelda is dispensable for Drosophila melanogaster histone gene regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572383. [PMID: 38187550 PMCID: PMC10769256 DOI: 10.1101/2023.12.19.572383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
To ensure that the embryo can package exponentially increasing amounts of DNA, replication-dependent histones are some of the earliest transcribed genes from the zygotic genome. However, how the histone genes are identified is not known. The pioneer factors Zelda and CLAMP collaborate at a subset of genes to regulate zygotic genome activation in Drosophila melanogaster and target early activated genes to induce transcription. CLAMP also regulates the embryonic histone genes and helps establish the histone locus body, a suite of factors that controls histone mRNA biosynthesis. The relationship between Zelda and CLAMP led us to hypothesize that Zelda helps identify histone genes for early embryonic expression. We found that Zelda targets the histone locus early during embryogenesis, prior to histone gene expression. However, depletion of zelda in the early embryo does not affect histone mRNA levels or histone locus body formation. While surprising, these results concur with other investigations into Zelda's role in the early embryo, suggesting the earliest factors responsible for specifying the zygotic histone genes remain undiscovered.
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Affiliation(s)
- Tommy O'Haren
- Emory University Department of Biology, Atlanta, GA 30322, USA
| | - Tsutomu Aoki
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540 USA
| | - Leila E Rieder
- Emory University Department of Biology, Atlanta, GA 30322, USA
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3
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Harrison MM, Marsh AJ, Rushlow CA. Setting the stage for development: the maternal-to-zygotic transition in Drosophila. Genetics 2023; 225:iyad142. [PMID: 37616526 PMCID: PMC10550319 DOI: 10.1093/genetics/iyad142] [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: 05/18/2023] [Accepted: 07/18/2023] [Indexed: 08/26/2023] Open
Abstract
The zygote has a daunting task ahead of itself; it must develop from a single cell (fertilized egg) into a fully functioning adult with a multitude of different cell types. In the beginning, the zygote has help from its mother, in the form of gene products deposited into the egg, but eventually, it must rely on its own resources to proceed through development. The transfer of developmental control from the mother to the embryo is called the maternal-to-zygotic transition (MZT). All animals undergo this transition, which is defined by two main processes-the degradation of maternal RNAs and the synthesis of new RNAs from the zygote's own genome. Here, we review the regulation of the MZT in Drosophila, but given the broad conservation of this essential process, much of the regulation is shared among metazoans.
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Affiliation(s)
- Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706USA
| | - Audrey J Marsh
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706USA
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4
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Gaskill MM, Soluri IV, Branks AE, Boka AP, Stadler MR, Vietor K, Huang HYS, Gibson TJ, Mukherjee A, Mir M, Blythe SA, Harrison MM. Localization of the Drosophila pioneer factor GAF to subnuclear foci is driven by DNA binding and required to silence satellite repeat expression. Dev Cell 2023; 58:1610-1624.e8. [PMID: 37478844 PMCID: PMC10528433 DOI: 10.1016/j.devcel.2023.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/19/2023] [Accepted: 06/29/2023] [Indexed: 07/23/2023]
Abstract
The eukaryotic genome is organized to enable the precise regulation of gene expression. This organization is established as the embryo transitions from a fertilized gamete to a totipotent zygote. To understand the factors and processes that drive genomic organization, we focused on the pioneer factor GAGA factor (GAF) that is required for early development in Drosophila. GAF transcriptionally activates the zygotic genome and is localized to subnuclear foci. This non-uniform distribution is driven by binding to highly abundant GA repeats. At GA repeats, GAF is necessary to form heterochromatin and silence transcription. Thus, GAF is required to establish both active and silent regions. We propose that foci formation enables GAF to have opposing transcriptional roles within a single nucleus. Our data support a model in which the subnuclear concentration of transcription factors acts to organize the nucleus into functionally distinct domains essential for the robust regulation of gene expression.
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Affiliation(s)
- Marissa M Gaskill
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Isabella V Soluri
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Annemarie E Branks
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Alan P Boka
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Michael R Stadler
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Katherine Vietor
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hao-Yu S Huang
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tyler J Gibson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Apratim Mukherjee
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mustafa Mir
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Regenerative, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shelby A Blythe
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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5
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Cho CY, O'Farrell PH. Stepwise modifications of transcriptional hubs link pioneer factor activity to a burst of transcription. Nat Commun 2023; 14:4848. [PMID: 37563108 PMCID: PMC10415302 DOI: 10.1038/s41467-023-40485-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/29/2023] [Indexed: 08/12/2023] Open
Abstract
Binding of transcription factors (TFs) promotes the subsequent recruitment of coactivators and preinitiation complexes to initiate eukaryotic transcription, but this time course is usually not visualized. It is commonly assumed that recruited factors eventually co-reside in a higher-order structure, allowing distantly bound TFs to activate transcription at core promoters. We use live imaging of endogenously tagged proteins, including the pioneer TF Zelda, the coactivator dBrd4, and RNA polymerase II (RNAPII), to define a cascade of events upstream of transcriptional initiation in early Drosophila embryos. These factors are sequentially and transiently recruited to discrete clusters during activation of non-histone genes. Zelda and the acetyltransferase dCBP nucleate dBrd4 clusters, which then trigger pre-transcriptional clustering of RNAPII. Subsequent transcriptional elongation disperses clusters of dBrd4 and RNAPII. Our results suggest that activation of transcription by eukaryotic TFs involves a succession of distinct biomolecular condensates that culminates in a self-limiting burst of transcription.
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Affiliation(s)
- Chun-Yi Cho
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Patrick H O'Farrell
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA.
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6
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Colonnetta MM, Schedl P, Deshpande G. Germline/soma distinction in Drosophila embryos requires regulators of zygotic genome activation. eLife 2023; 12:78188. [PMID: 36598809 PMCID: PMC9812407 DOI: 10.7554/elife.78188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 12/23/2022] [Indexed: 01/05/2023] Open
Abstract
In Drosophila melanogaster embryos, somatic versus germline identity is the first cell fate decision. Zygotic genome activation (ZGA) orchestrates regionalized gene expression, imparting specific identity on somatic cells. ZGA begins with a minor wave that commences at nuclear cycle (NC)8 under the guidance of chromatin accessibility factors (Zelda, CLAMP, GAF), followed by the major wave during NC14. By contrast, primordial germ cell (PGC) specification requires maternally deposited and posteriorly anchored germline determinants. This is accomplished by a centrosome coordinated release and sequestration of germ plasm during the precocious cellularization of PGCs in NC10. Here, we report a novel requirement for Zelda and CLAMP during the establishment of the germline/soma distinction. When their activity is compromised, PGC determinants are not properly sequestered, and specification is disrupted. Conversely, the spreading of PGC determinants from the posterior pole adversely influences transcription in the neighboring somatic nuclei. These reciprocal aberrations can be correlated with defects in centrosome duplication/separation that are known to induce inappropriate transmission of the germ plasm. Interestingly, consistent with the ability of bone morphogenetic protein (BMP) signaling to influence specification of embryonic PGCs, reduction in the transcript levels of a BMP family ligand, decapentaplegic (dpp), is exacerbated at the posterior pole.
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Affiliation(s)
- Megan M Colonnetta
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Paul Schedl
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Girish Deshpande
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
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7
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Larson ED, Komori H, Fitzpatrick ZA, Krabbenhoft SD, Lee CY, Harrison M. Premature translation of the Drosophila zygotic genome activator Zelda is not sufficient to precociously activate gene expression. G3 (BETHESDA, MD.) 2022; 12:6649735. [PMID: 35876878 PMCID: PMC9434156 DOI: 10.1093/g3journal/jkac159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/15/2022] [Indexed: 05/22/2023]
Abstract
Following fertilization, the unified germ cells rapidly transition to a totipotent embryo. Maternally deposited mRNAs encode the proteins necessary for this reprogramming as the zygotic genome remains transcriptionally quiescent during the initial stages of development. The transcription factors required to activate the zygotic genome are among these maternally deposited mRNAs and are robustly translated following fertilization. In Drosophila, the mRNA encoding Zelda, the major activator of the zygotic genome, is not translated until 1 h after fertilization. Here we demonstrate that zelda translation is repressed in the early embryo by the TRIM-NHL protein Brain tumor (BRAT). BRAT also regulates Zelda levels in the larval neuroblast lineage. In the embryo, BRAT-mediated translational repression is regulated by the Pan Gu kinase, which is triggered by egg activation. The Pan Gu kinase phosphorylates translational regulators, suggesting that Pan Gu kinase activity alleviates translational repression of zelda by BRAT and coupling translation of zelda with that of other regulators of early embryonic development. Using the premature translation of zelda in embryos lacking BRAT activity, we showed that early translation of a zygotic genome activator is not sufficient to drive precocious gene expression. Instead, Zelda-target genes showed increased expression at the time they are normally activated. We propose that transition through early development requires the integration of multiple processes, including the slowing of the nuclear division cycle and activation of the zygotic genome. These processes are coordinately controlled by Pan Gu kinase-mediated regulation of translation.
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Affiliation(s)
- Elizabeth D Larson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hideyuki Komori
- Department of Cell and Developmental Biology and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zoe A Fitzpatrick
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Samuel D Krabbenhoft
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Cheng-Yu Lee
- Department of Cell and Developmental Biology and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Melissa Harrison
- Corresponding author: Department of Biomolecular Chemistry, University of Wisconsin-Madison, 440 Henry Mall, 6204B Biochemical Sciences Building, Madison, WI 53706, USA.
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8
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Larson ED, Komori H, Gibson TJ, Ostgaard CM, Hamm DC, Schnell JM, Lee CY, Harrison MM. Cell-type-specific chromatin occupancy by the pioneer factor Zelda drives key developmental transitions in Drosophila. Nat Commun 2021; 12:7153. [PMID: 34887421 PMCID: PMC8660810 DOI: 10.1038/s41467-021-27506-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 11/24/2021] [Indexed: 12/14/2022] Open
Abstract
During Drosophila embryogenesis, the essential pioneer factor Zelda defines hundreds of cis-regulatory regions and in doing so reprograms the zygotic transcriptome. While Zelda is essential later in development, it is unclear how the ability of Zelda to define cis-regulatory regions is shaped by cell-type-specific chromatin architecture. Asymmetric division of neural stem cells (neuroblasts) in the fly brain provide an excellent paradigm for investigating the cell-type-specific functions of this pioneer factor. We show that Zelda synergistically functions with Notch to maintain neuroblasts in an undifferentiated state. Zelda misexpression reprograms progenitor cells to neuroblasts, but this capacity is limited by transcriptional repressors critical for progenitor commitment. Zelda genomic occupancy in neuroblasts is reorganized as compared to the embryo, and this reorganization is correlated with differences in chromatin accessibility and cofactor availability. We propose that Zelda regulates essential transitions in the neuroblasts and embryo through a shared gene-regulatory network driven by cell-type-specific enhancers.
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Affiliation(s)
- Elizabeth D Larson
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Hideyuki Komori
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Tyler J Gibson
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Cyrina M Ostgaard
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Danielle C Hamm
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jack M Schnell
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Stem Cell and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Cheng-Yu Lee
- Division of Genetic Medicine, Department of Internal Medicine and Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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9
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Colonnetta MM, Abrahante JE, Schedl P, Gohl DM, Deshpande G. CLAMP regulates zygotic genome activation in Drosophila embryos. Genetics 2021; 219:iyab107. [PMID: 34849887 PMCID: PMC8633140 DOI: 10.1093/genetics/iyab107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/15/2020] [Indexed: 11/13/2022] Open
Abstract
Embryonic patterning is critically dependent on zygotic genome activation (ZGA). In Drosophila melanogaster embryos, the pioneer factor Zelda directs ZGA, possibly in conjunction with other factors. Here, we have explored the novel involvement of Chromatin-Linked Adapter for MSL Proteins (CLAMP) during ZGA. CLAMP binds thousands of sites genome-wide throughout early embryogenesis. Interestingly, CLAMP relocates to target promoter sequences across the genome when ZGA is initiated. Although there is a considerable overlap between CLAMP and Zelda binding sites, the proteins display distinct temporal dynamics. To assess whether CLAMP occupancy affects gene expression, we analyzed transcriptomes of embryos zygotically compromised for either clamp or zelda and found that transcript levels of many zygotically activated genes are similarly affected. Importantly, compromising either clamp or zelda disrupted the expression of critical segmentation and sex determination genes bound by CLAMP (and Zelda). Furthermore, clamp knockdown embryos recapitulate other phenotypes observed in Zelda-depleted embryos, including nuclear division defects, centrosome aberrations, and a disorganized actomyosin network. Based on these data, we propose that CLAMP acts in concert with Zelda to regulate early zygotic transcription.
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Affiliation(s)
- Megan M Colonnetta
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, Minneapolis, MN 55455, USA
| | - Paul Schedl
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Daryl M Gohl
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA
| | - Girish Deshpande
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
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10
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Duan J, Rieder L, Colonnetta MM, Huang A, Mckenney M, Watters S, Deshpande G, Jordan W, Fawzi N, Larschan E. CLAMP and Zelda function together to promote Drosophila zygotic genome activation. eLife 2021; 10:e69937. [PMID: 34342574 PMCID: PMC8367384 DOI: 10.7554/elife.69937] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/02/2021] [Indexed: 12/22/2022] Open
Abstract
During the essential and conserved process of zygotic genome activation (ZGA), chromatin accessibility must increase to promote transcription. Drosophila is a well-established model for defining mechanisms that drive ZGA. Zelda (ZLD) is a key pioneer transcription factor (TF) that promotes ZGA in the Drosophila embryo. However, many genomic loci that contain GA-rich motifs become accessible during ZGA independent of ZLD. Therefore, we hypothesized that other early TFs that function with ZLD have not yet been identified, especially those that are capable of binding to GA-rich motifs such as chromatin-linked adaptor for male-specific lethal (MSL) proteins (CLAMP). Here, we demonstrate that Drosophila embryonic development requires maternal CLAMP to (1) activate zygotic transcription; (2) increase chromatin accessibility at promoters of specific genes that often encode other essential TFs; and (3) enhance chromatin accessibility and facilitate ZLD occupancy at a subset of key embryonic promoters. Thus, CLAMP functions as a pioneer factor that plays a targeted yet essential role in ZGA.
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Affiliation(s)
- Jingyue Duan
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown UniversityProvidenceUnited States
| | - Leila Rieder
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Megan M Colonnetta
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Annie Huang
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown UniversityProvidenceUnited States
| | - Mary Mckenney
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown UniversityProvidenceUnited States
| | - Scott Watters
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown UniversityProvidenceUnited States
| | - Girish Deshpande
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown UniversityProvidenceUnited States
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - William Jordan
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown UniversityProvidenceUnited States
| | - Nicolas Fawzi
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown UniversityProvidenceUnited States
| | - Erica Larschan
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown UniversityProvidenceUnited States
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11
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Espinola SM, Götz M, Bellec M, Messina O, Fiche JB, Houbron C, Dejean M, Reim I, Cardozo Gizzi AM, Lagha M, Nollmann M. Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development. Nat Genet 2021; 53:477-486. [PMID: 33795867 DOI: 10.1038/s41588-021-00816-z] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 02/09/2021] [Indexed: 12/15/2022]
Abstract
Acquisition of cell fate is thought to rely on the specific interaction of remote cis-regulatory modules (CRMs), for example, enhancers and target promoters. However, the precise interplay between chromatin structure and gene expression is still unclear, particularly within multicellular developing organisms. In the present study, we employ Hi-M, a single-cell spatial genomics approach, to detect CRM-promoter looping interactions within topologically associating domains (TADs) during early Drosophila development. By comparing cis-regulatory loops in alternate cell types, we show that physical proximity does not necessarily instruct transcriptional states. Moreover, multi-way analyses reveal that multiple CRMs spatially coalesce to form hubs. Loops and CRM hubs are established early during development, before the emergence of TADs. Moreover, CRM hubs are formed, in part, via the action of the pioneer transcription factor Zelda and precede transcriptional activation. Our approach provides insight into the role of CRM-promoter interactions in defining transcriptional states, as well as distinct cell types.
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Affiliation(s)
- Sergio Martin Espinola
- Centre de Biologie Structurale, CNRS UMR 5048, INSERM U1054, Univ Montpellier, Montpellier, France
| | - Markus Götz
- Centre de Biologie Structurale, CNRS UMR 5048, INSERM U1054, Univ Montpellier, Montpellier, France
| | | | - Olivier Messina
- Centre de Biologie Structurale, CNRS UMR 5048, INSERM U1054, Univ Montpellier, Montpellier, France.,IGMM, CNRS, Univ Montpellier, Montpellier, France
| | - Jean-Bernard Fiche
- Centre de Biologie Structurale, CNRS UMR 5048, INSERM U1054, Univ Montpellier, Montpellier, France
| | - Christophe Houbron
- Centre de Biologie Structurale, CNRS UMR 5048, INSERM U1054, Univ Montpellier, Montpellier, France
| | | | - Ingolf Reim
- Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Andrés M Cardozo Gizzi
- Centro de Investigación en Medicina Traslacional Severo Amuchastegui, Instituto Universitario de Ciencias Biomédicas de Córdoba, Consejo Nacional de Investigaciones Científicas y Técnicas, Córdoba, Argentina
| | - Mounia Lagha
- IGMM, CNRS, Univ Montpellier, Montpellier, France.
| | - Marcelo Nollmann
- Centre de Biologie Structurale, CNRS UMR 5048, INSERM U1054, Univ Montpellier, Montpellier, France.
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12
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Gaskill MM, Gibson TJ, Larson ED, Harrison MM. GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo. eLife 2021; 10:e66668. [PMID: 33720012 PMCID: PMC8079149 DOI: 10.7554/elife.66668] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/14/2021] [Indexed: 12/11/2022] Open
Abstract
Following fertilization, the genomes of the germ cells are reprogrammed to form the totipotent embryo. Pioneer transcription factors are essential for remodeling the chromatin and driving the initial wave of zygotic gene expression. In Drosophila melanogaster, the pioneer factor Zelda is essential for development through this dramatic period of reprogramming, known as the maternal-to-zygotic transition (MZT). However, it was unknown whether additional pioneer factors were required for this transition. We identified an additional maternally encoded factor required for development through the MZT, GAGA Factor (GAF). GAF is necessary to activate widespread zygotic transcription and to remodel the chromatin accessibility landscape. We demonstrated that Zelda preferentially controls expression of the earliest transcribed genes, while genes expressed during widespread activation are predominantly dependent on GAF. Thus, progression through the MZT requires coordination of multiple pioneer-like factors, and we propose that as development proceeds control is gradually transferred from Zelda to GAF.
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Affiliation(s)
- Marissa M Gaskill
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Tyler J Gibson
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Elizabeth D Larson
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
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13
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DeAngelis MW, Coolon JD, Johnson RI. Comparative transcriptome analyses of the Drosophila pupal eye. G3-GENES GENOMES GENETICS 2021; 11:5995320. [PMID: 33561221 PMCID: PMC8043229 DOI: 10.1093/g3journal/jkaa003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/08/2020] [Indexed: 12/04/2022]
Abstract
Tissue function is dependent on correct cellular organization and behavior. As a result, the identification and study of genes that contribute to tissue morphogenesis is of paramount importance to the fields of cell and developmental biology. Many of the genes required for tissue patterning and organization are highly conserved between phyla. This has led to the emergence of several model organisms and developmental systems that are used to study tissue morphogenesis. One such model is the Drosophila melanogaster pupal eye that has a highly stereotyped arrangement of cells. In addition, the pupal eye is postmitotic that allows for the study of tissue morphogenesis independent from any effects of proliferation. While the changes in cell morphology and organization that occur throughout pupal eye development are well documented, less is known about the corresponding transcriptional changes that choreograph these processes. To identify these transcriptional changes, we dissected wild-type Canton S pupal eyes and performed RNA-sequencing. Our analyses identified differential expression of many loci that are documented regulators of pupal eye morphogenesis and contribute to multiple biological processes including signaling, axon projection, adhesion, and cell survival. We also identified differential expression of genes not previously implicated in pupal eye morphogenesis such as components of the Toll pathway, several non-classical cadherins, and components of the muscle sarcomere, which could suggest these loci function as novel patterning factors.
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Affiliation(s)
- Miles W DeAngelis
- Department of Biology, Wesleyan University, 52 Lawn Avenue, Middletown, CT 06459, USA
| | - Joseph D Coolon
- Department of Biology, Wesleyan University, 52 Lawn Avenue, Middletown, CT 06459, USA
| | - Ruth I Johnson
- Department of Biology, Wesleyan University, 52 Lawn Avenue, Middletown, CT 06459, USA
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14
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Eck E, Liu J, Kazemzadeh-Atoufi M, Ghoreishi S, Blythe SA, Garcia HG. Quantitative dissection of transcription in development yields evidence for transcription-factor-driven chromatin accessibility. eLife 2020; 9:e56429. [PMID: 33074101 PMCID: PMC7738189 DOI: 10.7554/elife.56429] [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: 02/27/2020] [Accepted: 10/16/2020] [Indexed: 12/28/2022] Open
Abstract
Thermodynamic models of gene regulation can predict transcriptional regulation in bacteria, but in eukaryotes, chromatin accessibility and energy expenditure may call for a different framework. Here, we systematically tested the predictive power of models of DNA accessibility based on the Monod-Wyman-Changeux (MWC) model of allostery, which posits that chromatin fluctuates between accessible and inaccessible states. We dissected the regulatory dynamics of hunchback by the activator Bicoid and the pioneer-like transcription factor Zelda in living Drosophila embryos and showed that no thermodynamic or non-equilibrium MWC model can recapitulate hunchback transcription. Therefore, we explored a model where DNA accessibility is not the result of thermal fluctuations but is catalyzed by Bicoid and Zelda, possibly through histone acetylation, and found that this model can predict hunchback dynamics. Thus, our theory-experiment dialogue uncovered potential molecular mechanisms of transcriptional regulatory dynamics, a key step toward reaching a predictive understanding of developmental decision-making.
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Affiliation(s)
- Elizabeth Eck
- Biophysics Graduate Group, University of California at BerkeleyBerkeleyUnited States
| | - Jonathan Liu
- Department of Physics, University of California at BerkeleyBerkeleyUnited States
| | | | - Sydney Ghoreishi
- Department of Molecular and Cell Biology, University of California at BerkeleyBerkeleyUnited States
| | - Shelby A Blythe
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Hernan G Garcia
- Biophysics Graduate Group, University of California at BerkeleyBerkeleyUnited States
- Department of Physics, University of California at BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California at BerkeleyBerkeleyUnited States
- Institute for Quantitative Biosciences-QB3, University of California at BerkeleyBerkeleyUnited States
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15
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Bravo González‐Blas C, Quan X, Duran‐Romaña R, Taskiran II, Koldere D, Davie K, Christiaens V, Makhzami S, Hulselmans G, de Waegeneer M, Mauduit D, Poovathingal S, Aibar S, Aerts S. Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics. Mol Syst Biol 2020; 16:e9438. [PMID: 32431014 PMCID: PMC7237818 DOI: 10.15252/msb.20209438] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 01/02/2023] Open
Abstract
Single-cell technologies allow measuring chromatin accessibility and gene expression in each cell, but jointly utilizing both layers to map bona fide gene regulatory networks and enhancers remains challenging. Here, we generate independent single-cell RNA-seq and single-cell ATAC-seq atlases of the Drosophila eye-antennal disc and spatially integrate the data into a virtual latent space that mimics the organization of the 2D tissue using ScoMAP (Single-Cell Omics Mapping into spatial Axes using Pseudotime ordering). To validate spatially predicted enhancers, we use a large collection of enhancer-reporter lines and identify ~ 85% of enhancers in which chromatin accessibility and enhancer activity are coupled. Next, we infer enhancer-to-gene relationships in the virtual space, finding that genes are mostly regulated by multiple, often redundant, enhancers. Exploiting cell type-specific enhancers, we deconvolute cell type-specific effects of bulk-derived chromatin accessibility QTLs. Finally, we discover that Prospero drives neuronal differentiation through the binding of a GGG motif. In summary, we provide a comprehensive spatial characterization of gene regulation in a 2D tissue.
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Affiliation(s)
| | - Xiao‐Jiang Quan
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | | | - Ibrahim Ihsan Taskiran
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | - Duygu Koldere
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | | | - Valerie Christiaens
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | - Samira Makhzami
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | - Maxime de Waegeneer
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | - David Mauduit
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | | | - Sara Aibar
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | - Stein Aerts
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
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16
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Nystrom SL, Niederhuber MJ, McKay DJ. Expression of E93 provides an instructive cue to control dynamic enhancer activity and chromatin accessibility during development. Development 2020; 147:dev181909. [PMID: 32094114 PMCID: PMC7097197 DOI: 10.1242/dev.181909] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 02/10/2020] [Indexed: 12/14/2022]
Abstract
How temporal cues combine with spatial inputs to control gene expression during development is poorly understood. Here, we test the hypothesis that the Drosophila transcription factor E93 controls temporal gene expression by regulating chromatin accessibility. Precocious expression of E93 early in wing development reveals that it can simultaneously activate and deactivate different target enhancers. Notably, the precocious patterns of enhancer activity resemble the wild-type patterns that occur later in development, suggesting that expression of E93 alters the competence of enhancers to respond to spatial cues. Genomic profiling reveals that precocious E93 expression is sufficient to regulate chromatin accessibility at a subset of its targets. These accessibility changes mimic those that normally occur later in development, indicating that precocious E93 accelerates the wild-type developmental program. Further, we find that target enhancers that do not respond to precocious E93 in early wings become responsive after a developmental transition, suggesting that parallel temporal pathways work alongside E93. These findings support a model wherein E93 expression functions as an instructive cue that defines a broad window of developmental time through control of chromatin accessibility.
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Affiliation(s)
- Spencer L Nystrom
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew J Niederhuber
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daniel J McKay
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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17
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Nevil M, Gibson TJ, Bartolutti C, Iyengar A, Harrison MM. Establishment of chromatin accessibility by the conserved transcription factor Grainy head is developmentally regulated. Development 2020; 147:dev185009. [PMID: 32098765 PMCID: PMC10624965 DOI: 10.1242/dev.185009] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/07/2020] [Indexed: 12/18/2022]
Abstract
The dramatic changes in gene expression required for development necessitate the establishment of cis-regulatory modules defined by regions of accessible chromatin. Pioneer transcription factors have the unique property of binding closed chromatin and facilitating the establishment of these accessible regions. Nonetheless, much of how pioneer transcription factors coordinate changes in chromatin accessibility during development remains unknown. To determine whether pioneer-factor function is intrinsic to the protein or whether pioneering activity is developmentally modulated, we studied the highly conserved, essential transcription factor Grainy head (Grh). Prior work established that Grh is expressed throughout Drosophila development and is a pioneer factor in the larva. We demonstrated that Grh remains bound to mitotic chromosomes, a property shared with other pioneer factors. By assaying chromatin accessibility in embryos lacking maternal and/or zygotic Grh at three stages of development, we discovered that Grh is not required for chromatin accessibility in early embryogenesis, in contrast to its essential functions later in development. Our data reveal that the pioneering activity of Grh is temporally regulated and likely influenced by additional factors expressed at a given developmental stage.
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Affiliation(s)
- Markus Nevil
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tyler J Gibson
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Constantine Bartolutti
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Anusha Iyengar
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
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18
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McDaniel SL, Hollatz AJ, Branstad AM, Gaskill MM, Fox CA, Harrison MM. Tissue-Specific DNA Replication Defects in Drosophila melanogaster Caused by a Meier-Gorlin Syndrome Mutation in Orc4. Genetics 2020; 214:355-367. [PMID: 31818869 PMCID: PMC7017028 DOI: 10.1534/genetics.119.302938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
Meier-Gorlin syndrome is a rare recessive disorder characterized by a number of distinct tissue-specific developmental defects. Genes encoding members of the origin recognition complex (ORC) and additional proteins essential for DNA replication (CDC6, CDT1, GMNN, CDC45, MCM5, and DONSON) are mutated in individuals diagnosed with MGS. The essential role of ORC is to license origins during the G1 phase of the cell cycle, but ORC has also been implicated in several nonreplicative functions. Because of its essential role in DNA replication, ORC is required for every cell division during development. Thus, it is unclear how the Meier-Gorlin syndrome mutations in genes encoding ORC lead to the tissue-specific defects associated with the disease. To begin to address these issues, we used Cas9-mediated genome engineering to generate a Drosophila melanogaster model of individuals carrying a specific Meier-Gorlin syndrome mutation in ORC4 along with control strains. Together these strains provide the first metazoan model for an MGS mutation in which the mutation was engineered at the endogenous locus along with precisely defined control strains. Flies homozygous for the engineered MGS allele reach adulthood, but with several tissue-specific defects. Genetic analysis revealed that this Orc4 allele was a hypomorph. Mutant females were sterile, and phenotypic analyses suggested that defects in DNA replication was an underlying cause. By leveraging the well-studied Drosophila system, we provide evidence that a disease-causing mutation in Orc4 disrupts DNA replication, and we propose that in individuals with MGS defects arise preferentially in tissues with a high-replication demand.
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Affiliation(s)
- Stephen L McDaniel
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Allison J Hollatz
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Anna M Branstad
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Marissa M Gaskill
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Catherine A Fox
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
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19
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Abstract
Following fertilization, the two specified gametes must unite to create an entirely new organism. The genome is initially transcriptionally quiescent, allowing the zygote to be reprogrammed into a totipotent state. Gradually, the genome is activated through a process known as the maternal-to-zygotic transition, which enables zygotic gene products to replace the maternal supply that initiated development. This essential transition has been broadly characterized through decades of research in several model organisms. However, we still lack a full mechanistic understanding of how genome activation is executed and how this activation relates to the reprogramming of the zygotic chromatin architecture. Recent work highlights the central role of transcriptional activators and suggests that these factors may coordinate transcriptional activation with other developmental changes.
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20
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McDaniel SL, Harrison MM. Optogenetic Inactivation of Transcription Factors in the Early Embryo of Drosophila. Bio Protoc 2019; 9:e3296. [PMID: 33654809 DOI: 10.21769/bioprotoc.3296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/11/2019] [Accepted: 06/19/2019] [Indexed: 11/02/2022] Open
Abstract
The early embryo of Drosophila melanogaster exists as a rapidly dividing syncytium of nuclei that are transcriptionally silent. Maternally deposited factors are required to awaken the genome and assist in the transition from maternal to zygotic control of development. Because many of these essential factors are maternally deposited and the early nuclear divisions are so rapid, it has been difficult to assess the functional role of transcription factors at discrete points in early embryonic development. To address this issue, we have developed an optogenetic system that can rapidly and reversibly inactivate transcription factors with nuclear-cycle resolution. The temporal precision enabled by this technique will allow a mechanistic understanding of how transcription factors function together to control genome activation and patterning in the early embryo and is likely broadly applicable to factors throughout embryogenesis.
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Affiliation(s)
- Stephen L McDaniel
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
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21
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Ventos-Alfonso A, Ylla G, Belles X. Zelda and the maternal-to-zygotic transition in cockroaches. FEBS J 2019; 286:3206-3221. [PMID: 30993896 DOI: 10.1111/febs.14856] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 03/22/2019] [Accepted: 04/15/2019] [Indexed: 12/22/2022]
Abstract
In the endopterygote Drosophila melanogaster, Zelda is an activator of the zygotic genome during the maternal-to-zygotic transition (MZT). Zelda binds cis-regulatory elements (TAGteam heptamers), making chromatin accessible for gene transcription. Zelda has been studied in other endopterygotes: Apis mellifera and Tribolium castaneum, and the paraneopteran Rhodnius prolixus. We studied Zelda in the cockroach Blattella germanica, a hemimetabolan, short germ-band, and polyneopteran species. B. germanica Zelda has the complete set of functional domains, which is typical of species displaying ancestral features concerning embryogenesis. Interestingly, we found D. melanogaster TAGteam heptamers in the B. germanica genome. The canonical one, CAGGTAG, is present at a similar proportion in the genome of these two species and in the genome of other insects, suggesting that the genome admits as many CAGGTAG motifs as its length allows. Zelda-depleted embryos of B. germanica show defects involving blastoderm formation and abdomen development, and genes contributing to these processes are down-regulated. We conclude that in B. germanica, Zelda strictly activates the zygotic genome, within the MZT, a role conserved in more derived endopterygote insects. In B. germanica, zelda is expressed during MZT, whereas in D. melanogaster and T. castaneum it is expressed beyond this transition. In these species and A. mellifera, Zelda has functions even in postembryonic development. The expansion of zelda expression beyond the MZT in endopterygotes might be related with the evolutionary innovation of holometabolan metamorphosis. DATABASES: The RNA-seq datasets of B. germanica, D. melanogaster, and T. castaneum are accessible at the GEO databases GSE99785, GSE18068, GSE63770, and GSE84253. In addition, the RNA-seq library from T. castaneum adult females is available at SRA: SRX021963. The B. germanica reference genome is available as BioProject PRJNA203136.
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Affiliation(s)
- Alba Ventos-Alfonso
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Guillem Ylla
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Xavier Belles
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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22
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McDaniel SL, Gibson TJ, Schulz KN, Fernandez Garcia M, Nevil M, Jain SU, Lewis PW, Zaret KS, Harrison MM. Continued Activity of the Pioneer Factor Zelda Is Required to Drive Zygotic Genome Activation. Mol Cell 2019; 74:185-195.e4. [PMID: 30797686 DOI: 10.1016/j.molcel.2019.01.014] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/10/2018] [Accepted: 01/08/2019] [Indexed: 02/08/2023]
Abstract
Reprogramming cell fate during the first stages of embryogenesis requires that transcriptional activators gain access to the genome and remodel the zygotic transcriptome. Nonetheless, it is not clear whether the continued activity of these pioneering factors is required throughout zygotic genome activation or whether they are only required early to establish cis-regulatory regions. To address this question, we developed an optogenetic strategy to rapidly and reversibly inactivate the master regulator of genome activation in Drosophila, Zelda. Using this strategy, we demonstrate that continued Zelda activity is required throughout genome activation. We show that Zelda binds DNA in the context of nucleosomes and suggest that this allows Zelda to occupy the genome despite the rapid division cycles in the early embryo. These data identify a powerful strategy to inactivate transcription factor function during development and suggest that reprogramming in the embryo may require specific, continuous pioneering functions to activate the genome.
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Affiliation(s)
- Stephen L McDaniel
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison WI 53706, USA
| | - Tyler J Gibson
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison WI 53706, USA
| | - Katharine N Schulz
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison WI 53706, USA
| | - Meilin Fernandez Garcia
- Institute for Regenerative Medicine and Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Markus Nevil
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison WI 53706, USA
| | - Siddhant U Jain
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison WI 53706, USA
| | - Peter W Lewis
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison WI 53706, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine and Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison WI 53706, USA.
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23
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Mir M, Stadler MR, Ortiz SA, Hannon CE, Harrison MM, Darzacq X, Eisen MB. Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos. eLife 2018; 7:e40497. [PMID: 30589412 PMCID: PMC6307861 DOI: 10.7554/elife.40497] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/30/2018] [Indexed: 12/12/2022] Open
Abstract
The regulation of transcription requires the coordination of numerous activities on DNA, yet how transcription factors mediate these activities remains poorly understood. Here, we use lattice light-sheet microscopy to integrate single-molecule and high-speed 4D imaging in developing Drosophila embryos to study the nuclear organization and interactions of the key transcription factors Zelda and Bicoid. In contrast to previous studies suggesting stable, cooperative binding, we show that both factors interact with DNA with surprisingly high off-rates. We find that both factors form dynamic subnuclear hubs, and that Bicoid binding is enriched within Zelda hubs. Remarkably, these hubs are both short lived and interact only transiently with sites of active Bicoid-dependent transcription. Based on our observations, we hypothesize that, beyond simply forming bridges between DNA and the transcription machinery, transcription factors can organize other proteins into hubs that transiently drive multiple activities at their gene targets. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Mustafa Mir
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Michael R Stadler
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Stephan A Ortiz
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Colleen E Hannon
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Melissa M Harrison
- Department of Biomolecular ChemistryUniversity of Wisconsin–MadisonMadisonUnited States
| | - Xavier Darzacq
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Michael B Eisen
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyUnited States
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24
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Temporal control of gene expression by the pioneer factor Zelda through transient interactions in hubs. Nat Commun 2018; 9:5194. [PMID: 30518940 PMCID: PMC6281682 DOI: 10.1038/s41467-018-07613-z] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 11/09/2018] [Indexed: 12/31/2022] Open
Abstract
Pioneer transcription factors can engage nucleosomal DNA, which leads to local chromatin remodeling and to the establishment of transcriptional competence. However, the impact of enhancer priming by pioneer factors on the temporal control of gene expression and on mitotic memory remains unclear. Here we employ quantitative live imaging methods and mathematical modeling to test the effect of the pioneer factor Zelda on transcriptional dynamics and memory in Drosophila embryos. We demonstrate that increasing the number of Zelda binding sites accelerates the kinetics of nuclei transcriptional activation regardless of their transcriptional past. Despite its known pioneering activities, we show that Zelda does not remain detectably associated with mitotic chromosomes and is neither necessary nor sufficient to foster memory. We further reveal that Zelda forms sub-nuclear dynamic hubs where Zelda binding events are transient. We propose that Zelda facilitates transcriptional activation by accumulating in microenvironments where it could accelerate the duration of multiple pre-initiation steps.
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25
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Hamm DC, Harrison MM. Regulatory principles governing the maternal-to-zygotic transition: insights from Drosophila melanogaster. Open Biol 2018; 8:180183. [PMID: 30977698 PMCID: PMC6303782 DOI: 10.1098/rsob.180183] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/09/2018] [Indexed: 12/19/2022] Open
Abstract
The onset of metazoan development requires that two terminally differentiated germ cells, a sperm and an oocyte, become reprogrammed to the totipotent embryo, which can subsequently give rise to all the cell types of the adult organism. In nearly all animals, maternal gene products regulate the initial events of embryogenesis while the zygotic genome remains transcriptionally silent. Developmental control is then passed from mother to zygote through a process known as the maternal-to-zygotic transition (MZT). The MZT comprises an intimately connected set of molecular events that mediate degradation of maternally deposited mRNAs and transcriptional activation of the zygotic genome. This essential developmental transition is conserved among metazoans but is perhaps best understood in the fruit fly, Drosophila melanogaster. In this article, we will review our understanding of the events that drive the MZT in Drosophila embryos and highlight parallel mechanisms driving this transition in other animals.
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Affiliation(s)
| | - Melissa M. Harrison
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
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26
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Nunes da Fonseca R, Venancio TM. Maternal or zygotic: Unveiling the secrets of the Pancrustacea transcription factor zelda. PLoS Genet 2018; 14:e1007201. [PMID: 29494591 PMCID: PMC5832190 DOI: 10.1371/journal.pgen.1007201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Rodrigo Nunes da Fonseca
- Laboratório Integrado de Bioquímica Hatisaburo Masuda, Núcleo em Ecologia e Desenvolvimento SócioAmbiental de Macaé (NUPEM), Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular—INCT-EM, Brazil
- * E-mail: (RNdF); (TMV)
| | - Thiago M. Venancio
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular—INCT-EM, Brazil
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro, Brazil
- * E-mail: (RNdF); (TMV)
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