1
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Freund MM, Harrison MM, Torres-Zelada EF. Exploring the reciprocity between pioneer factors and development. Development 2024; 151:dev201921. [PMID: 38958075 PMCID: PMC11266817 DOI: 10.1242/dev.201921] [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] [Indexed: 07/04/2024]
Abstract
Development is regulated by coordinated changes in gene expression. Control of these changes in expression is largely governed by the binding of transcription factors to specific regulatory elements. However, the packaging of DNA into chromatin prevents the binding of many transcription factors. Pioneer factors overcome this barrier owing to unique properties that enable them to bind closed chromatin, promote accessibility and, in so doing, mediate binding of additional factors that activate gene expression. Because of these properties, pioneer factors act at the top of gene-regulatory networks and drive developmental transitions. Despite the ability to bind target motifs in closed chromatin, pioneer factors have cell type-specific chromatin occupancy and activity. Thus, developmental context clearly shapes pioneer-factor function. Here, we discuss this reciprocal interplay between pioneer factors and development: how pioneer factors control changes in cell fate and how cellular environment influences pioneer-factor binding and activity.
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Affiliation(s)
- Meghan M. Freund
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
| | - Melissa M. Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
| | - Eliana F. Torres-Zelada
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
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2
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Dachani S, Kaleem M, Mujtaba MA, Mahajan N, Ali SA, Almutairy AF, Mahmood D, Anwer MK, Ali MD, Kumar S. A Comprehensive Review of Various Therapeutic Strategies for the Management of Skin Cancer. ACS OMEGA 2024; 9:10030-10048. [PMID: 38463249 PMCID: PMC10918819 DOI: 10.1021/acsomega.3c09780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/02/2024] [Accepted: 02/08/2024] [Indexed: 03/12/2024]
Abstract
Skin cancer (SC) poses a global threat to the healthcare system and is expected to increase significantly over the next two decades if not diagnosed at an early stage. Early diagnosis is crucial for successful treatment, as the disease becomes more challenging to cure as it progresses. However, identifying new drugs, achieving clinical success, and overcoming drug resistance remain significant challenges. To overcome these obstacles and provide effective treatment, it is crucial to understand the causes of skin cancer, how cells grow and divide, factors that affect cell growth, and how drug resistance occurs. In this review, we have explained various therapeutic approaches for SC treatment via ligands, targeted photosensitizers, natural and synthetic drugs for the treatment of SC, an epigenetic approach for management of melanoma, photodynamic therapy, and targeted therapy for BRAF-mutated melanoma. This article also provides a detailed summary of the various natural drugs that are effective in managing melanoma and reducing the occurrence of skin cancer at early stages and focuses on the current status and future prospects of various therapies available for the management of skin cancer.
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Affiliation(s)
- Sudharshan
Reddy Dachani
- Department
of Pharmacy Practice, College of Pharmacy, Shaqra University, Al-Dawadmi Campus, Al-Dawadmi 11961, Saudi Arabia
| | - Mohammed Kaleem
- Department
of Pharmacology, Babasaheb Balpande College of Pharmacy, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440037, Maharashtra, India
| | - Md. Ali Mujtaba
- Department
of Pharmaceutics, Faculty of Pharmacy, Northern
Border University, Arar 91911, Saudi Arabia
| | - Nilesh Mahajan
- Department
of Pharmaceutics, Dabasaheb Balpande College of Pharmacy, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440037, Maharashtra, India
| | - Sayyed A. Ali
- Department
of Pharmaceutics, Dabasaheb Balpande College of Pharmacy, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440037, Maharashtra, India
| | - Ali F Almutairy
- Department
of Pharmacology and Toxicology, College of Pharmacy, Qassim University, Buraydah 51452, Saudi Arabia
| | - Danish Mahmood
- Department
of Pharmacology and Toxicology, College of Pharmacy, Qassim University, Buraydah 51452, Saudi Arabia
| | - Md. Khalid Anwer
- Department
of Pharmaceutics, College of Pharmacy, Prince
Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia
| | - Mohammad Daud Ali
- Department
of Pharmacy, Mohammed Al-Mana College for
Medical Sciences, Abdulrazaq Bin Hammam Street, Al Safa 34222, Dammam, Saudi Arabia
| | - Sanjay Kumar
- Department
of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Uttar Pradesh 201306, India
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3
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Hunt G, Vaid R, Pirogov S, Pfab A, Ziegenhain C, Sandberg R, Reimegård J, Mannervik M. Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network. Genome Biol 2024; 25:2. [PMID: 38166964 PMCID: PMC10763363 DOI: 10.1186/s13059-023-03135-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Formation of tissue-specific transcriptional programs underlies multicellular development, including dorsoventral (DV) patterning of the Drosophila embryo. This involves interactions between transcriptional enhancers and promoters in a chromatin context, but how the chromatin landscape influences transcription is not fully understood. RESULTS Here we comprehensively resolve differential transcriptional and chromatin states during Drosophila DV patterning. We find that RNA Polymerase II pausing is established at DV promoters prior to zygotic genome activation (ZGA), that pausing persists irrespective of cell fate, but that release into productive elongation is tightly regulated and accompanied by tissue-specific P-TEFb recruitment. DV enhancers acquire distinct tissue-specific chromatin states through CBP-mediated histone acetylation that predict the transcriptional output of target genes, whereas promoter states are more tissue-invariant. Transcriptome-wide inference of burst kinetics in different cell types revealed that while DV genes are generally characterized by a high burst size, either burst size or frequency can differ between tissues. CONCLUSIONS The data suggest that pausing is established by pioneer transcription factors prior to ZGA and that release from pausing is imparted by enhancer chromatin state to regulate bursting in a tissue-specific manner in the early embryo. Our results uncover how developmental patterning is orchestrated by tissue-specific bursts of transcription from Pol II primed promoters in response to enhancer regulatory cues.
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Affiliation(s)
- George Hunt
- Department Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Roshan Vaid
- Department Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Sergei Pirogov
- Department Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Alexander Pfab
- Department Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | | | - Rickard Sandberg
- Department Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Johan Reimegård
- Department Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mattias Mannervik
- Department Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
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4
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Sun J, Zhang C, Gao F, Stathopoulos A. Single-cell transcriptomics illuminates regulatory steps driving anterior-posterior patterning of Drosophila embryonic mesoderm. Cell Rep 2023; 42:113289. [PMID: 37858470 DOI: 10.1016/j.celrep.2023.113289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/29/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023] Open
Abstract
Single-cell technologies promise to uncover how transcriptional programs orchestrate complex processes during embryogenesis. Here, we apply a combination of single-cell technology and genetic analysis to investigate the dynamic transcriptional changes associated with Drosophila embryo morphogenesis at gastrulation. Our dataset encompassing the blastoderm-to-gastrula transition provides a comprehensive single-cell map of gene expression across cell lineages validated by genetic analysis. Subclustering and trajectory analyses revealed a surprising stepwise progression in patterning to transition zygotic gene expression and specify germ layers as well as uncovered an early role for ecdysone signaling in epithelial-to-mesenchymal transition in the mesoderm. We also show multipotent progenitors arise prior to gastrulation by analyzing the transcription trajectory of caudal mesoderm cells, including a derivative that ultimately incorporates into visceral muscles of the midgut and hindgut. This study provides a rich resource of gastrulation and elucidates spatially regulated temporal transitions of transcription states during the process.
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Affiliation(s)
- Jingjing Sun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Chen Zhang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Fan Gao
- Bioinformatics Resource Center, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Angelike Stathopoulos
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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5
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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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6
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Zhao J, Perkins ML, Norstad M, Garcia HG. A bistable autoregulatory module in the developing embryo commits cells to binary expression fates. Curr Biol 2023; 33:2851-2864.e11. [PMID: 37453424 PMCID: PMC10428078 DOI: 10.1016/j.cub.2023.06.060] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 04/13/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023]
Abstract
Bistable autoactivation has been proposed as a mechanism for cells to adopt binary fates during embryonic development. However, it is unclear whether the autoactivating modules found within developmental gene regulatory networks are bistable, unless their parameters are quantitatively determined. Here, we combine in vivo live imaging with mathematical modeling to dissect the binary cell fate dynamics of the fruit fly pair-rule gene fushi tarazu (ftz), which is regulated by two known enhancers: the early (non-autoregulating) element and the autoregulatory element. Live imaging of transcription and protein concentration in the blastoderm revealed that binary Ftz fates are achieved as Ftz expression rapidly transitions from being dictated by the early element to the autoregulatory element. Moreover, we discovered that Ftz concentration alone is insufficient to activate the autoregulatory element, and that this element only becomes responsive to Ftz at a prescribed developmental time. Based on these observations, we developed a dynamical systems model and quantitated its kinetic parameters directly from experimental measurements. Our model demonstrated that the ftz autoregulatory module is indeed bistable and that the early element transiently establishes the content of the binary cell fate decision to which the autoregulatory module then commits. Further in silico analysis revealed that the autoregulatory element locks the Ftz fate quickly, within 35 min of exposure to the transient signal of the early element. Overall, our work confirms the widely held hypothesis that autoregulation can establish developmental fates through bistability and, most importantly, provides a framework for the quantitative dissection of cellular decision-making.
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Affiliation(s)
- Jiaxi Zhao
- Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mindy Liu Perkins
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Matthew Norstad
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hernan G Garcia
- Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA; Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub - San Francisco, San Francisco, CA 94158, USA.
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7
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Birnie A, Plat A, Korkmaz C, Bothma JP. Precisely timed regulation of enhancer activity defines the binary expression pattern of Fushi tarazu in the Drosophila embryo. Curr Biol 2023:S0960-9822(23)00453-0. [PMID: 37116484 PMCID: PMC10373528 DOI: 10.1016/j.cub.2023.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 03/13/2023] [Accepted: 04/05/2023] [Indexed: 04/30/2023]
Abstract
The genes that drive development each typically have many different enhancers. Properly coordinating the action of these different enhancers is crucial to correctly specifying cell-fate decisions, yet it remains poorly understood how their activity is choregraphed in time. To shed light on this question, we used recently developed single-cell live imaging tools to dissect the regulation of Fushi tarazu (Ftz) in Drosophila melanogaster embryos. Ftz is a transcription factor that is expressed in asymmetric stripes by two distinct enhancers: autoregulatory and zebra. The anterior edge of each stripe needs to be sharply defined to specify essential lineage boundaries. Here, we tracked how boundary cells commit to either a high-Ftz or low-Ftz fate by measuring Ftz protein traces in real time and simultaneously quantifying transcription from the endogenous locus and individual enhancers. This revealed that the autoregulatory enhancer does not establish this fate choice. Instead, it perpetuates the decision defined by zebra. This is contrary to the prevailing view that autoregulation drives the fate decision by causing bi-stable Ftz expression. Furthermore, we showed that the autoregulatory enhancer is not activated based on a Ftz-concentration threshold but through a timing-based mechanism. We hypothesize that this is regulated by several ubiquitously expressed pioneer-like transcription factors, which have recently been shown to act as timers in the embryo. Our work provides new insight into how precisely timed enhancer activity can directly regulate the dynamics of gene regulatory networks, which may be a general mechanism for ensuring that embryogenesis runs like clockwork.
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Affiliation(s)
- Anthony Birnie
- Hubrecht Institute-KNAW, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Audrey Plat
- Hubrecht Institute-KNAW, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Cemil Korkmaz
- Hubrecht Institute-KNAW, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Jacques P Bothma
- Hubrecht Institute-KNAW, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
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8
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Fenelon KD, Gao F, Borad P, Abbasi S, Pachter L, Koromila T. Cell-specific occupancy dynamics between the pioneer-like factor Opa/ZIC and Ocelliless/OTX regulate early head development in embryos. Front Cell Dev Biol 2023; 11:1126507. [PMID: 37051467 PMCID: PMC10083704 DOI: 10.3389/fcell.2023.1126507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
During development, embryonic patterning systems direct a set of initially uncommitted pluripotent cells to differentiate into a variety of cell types and tissues. A core network of transcription factors, such as Zelda/POU5F1, Odd-paired (Opa)/ZIC3 and Ocelliless (Oc)/OTX2, are conserved across animals. While Opa is essential for a second wave of zygotic activation after Zelda, it is unclear whether Opa drives head cell specification, in the Drosophila embryo. Our hypothesis is that Opa and Oc are interacting with distinct cis-regulatory regions for shaping cell fates in the embryonic head. Super-resolution microscopy and meta-analysis of single-cell RNAseq datasets show that opa’s and oc’s overlapping expression domains are dynamic in the head region, with both factors being simultaneously transcribed at the blastula stage. Additionally, analysis of single-embryo RNAseq data reveals a subgroup of Opa-bound genes to be Opa-independent in the cellularized embryo. Interrogation of these genes against Oc ChIPseq combined with in situ data, suggests that Opa is competing with Oc for the regulation of a subgroup of genes later in gastrulation. Specifically, we find that Oc binds to late, head-specific enhancers independently and activates them in a head-specific wave of zygotic transcription, suggesting distinct roles for Oc in the blastula and gastrula stages.
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Affiliation(s)
- Kelli D. Fenelon
- Department of Biology, UT Arlington, Arlington, TX, United States
| | - Fan Gao
- Caltech Bioinformatics Resource Center (CBRC), Caltech, Pasadena, CA, United States
| | - Priyanshi Borad
- Department of Biology, UT Arlington, Arlington, TX, United States
| | - Shiva Abbasi
- Department of Biology, UT Arlington, Arlington, TX, United States
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
- Department of Computational Biology and Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Theodora Koromila
- Department of Biology, UT Arlington, Arlington, TX, United States
- *Correspondence: Theodora Koromila,
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9
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Cheatle Jarvela AM, Trelstad CS, Pick L. Anterior-posterior patterning of segments in Anopheles stephensi offers insights into the transition from sequential to simultaneous segmentation in holometabolous insects. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:116-130. [PMID: 34734470 PMCID: PMC9061899 DOI: 10.1002/jez.b.23102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 10/13/2021] [Accepted: 10/16/2021] [Indexed: 11/10/2022]
Abstract
The gene regulatory network for segmentation in arthropods offers valuable insights into how networks evolve owing to the breadth of species examined and the extremely detailed knowledge gained in the model organism Drosophila melanogaster. These studies have shown that Drosophila's network represents a derived state that acquired changes to accelerate segment patterning, whereas most insects specify segments gradually as the embryo elongates. Such heterochronic shifts in segmentation have potentially emerged multiple times within holometabolous insects, resulting in many mechanistic variants and difficulties in isolating underlying commonalities that permit such shifts. Recent studies identified regulatory genes that work as timing factors, coordinating gene expression transitions during segmentation. These studies predict that changes in timing factor deployment explain shifts in segment patterning relative to other developmental events. Here, we test this hypothesis by characterizing the temporal and spatial expression of the pair-rule patterning genes in the malaria vector mosquito, Anopheles stephensi. This insect is a Dipteran (fly), like Drosophila, but represents an ancient divergence within this clade, offering a useful counterpart for evo-devo studies. In mosquito embryos, we observe anterior to posterior sequential addition of stripes for many pair-rule genes and a wave of broad timer gene expression across this axis. Segment polarity gene stripes are added sequentially in the wake of the timer gene wave and the full pattern is not complete until the embryo is fully elongated. This "progressive segmentation" mode in Anopheles displays commonalities with both Drosophila's rapid segmentation mechanism and sequential modes used by more distantly related insects.
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Affiliation(s)
- Alys M. Cheatle Jarvela
- Department of Entomology, University of Maryland, College Park, 4291 Fieldhouse Drive, College Park, MD 20742, U.S.A
| | - Catherine S. Trelstad
- Department of Entomology, University of Maryland, College Park, 4291 Fieldhouse Drive, College Park, MD 20742, U.S.A
| | - Leslie Pick
- Department of Entomology, University of Maryland, College Park, 4291 Fieldhouse Drive, College Park, MD 20742, U.S.A
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10
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Abstract
The control of gene expression in eukaryotes relies on how transcription factors and RNA polymerases manipulate the structure of chromatin. These interactions are especially important in development as gene expression programs change. Chromatin generally limits the accessibility of DNA, and thus exposing sequences at regulatory elements is critical for gene expression. However, it is challenging to understand how transcription factors manipulate chromatin structure and the sequence of regulatory events. The Drosophila embryo has provided a powerful setting to directly observe the establishment and elaboration of chromatin features and experimentally test the causality of transcriptional events that are shared among many metazoans. The large embryo is tractable by live imaging, and a variety of well-developed tools allow the manipulation of factors during early development. The early embryo develops as a syncytium with rapid nuclear divisions and no zygotic transcription, with largely featureless chromatin. Thus, studies in this system have revealed the progression of genome activation triggered by pioneer factors that initiate DNA exposure at regulatory elements and the establishment of chromatin domains, including heterochromatin, the nucleolus, and nuclear bodies. The de novo emergence of nuclear structures in the early embryo reveals features of chromatin dynamics that are likely to be central to transcriptional regulation in all cells.
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Affiliation(s)
- Kami Ahmad
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N., P.O. Box 19024, Seattle, WA 98109-1024, USA
| | - Steven Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N., P.O. Box 19024, Seattle, WA 98109-1024, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road Chevy Chase, MD 20815-6789, USA
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11
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Clark E, Battistara M, Benton MA. A timer gene network is spatially regulated by the terminal system in the Drosophila embryo. eLife 2022; 11:e78902. [PMID: 36524728 PMCID: PMC10065802 DOI: 10.7554/elife.78902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
In insect embryos, anteroposterior patterning is coordinated by the sequential expression of the 'timer' genes caudal, Dichaete, and odd-paired, whose expression dynamics correlate with the mode of segmentation. In Drosophila, the timer genes are expressed broadly across much of the blastoderm, which segments simultaneously, but their expression is delayed in a small 'tail' region, just anterior to the hindgut, which segments during germband extension. Specification of the tail and the hindgut depends on the terminal gap gene tailless, but beyond this the regulation of the timer genes is poorly understood. We used a combination of multiplexed imaging, mutant analysis, and gene network modelling to resolve the regulation of the timer genes, identifying 11 new regulatory interactions and clarifying the mechanism of posterior terminal patterning. We propose that a dynamic Tailless expression gradient modulates the intrinsic dynamics of a timer gene cross-regulatory module, delineating the tail region and delaying its developmental maturation.
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Affiliation(s)
- Erik Clark
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Margherita Battistara
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
- Department of Physiology, Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
| | - Matthew A Benton
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
- Developmental Biology Unit, EMBLHeidelbergGermany
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12
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REDfly: An Integrated Knowledgebase for Insect Regulatory Genomics. INSECTS 2022; 13:insects13070618. [PMID: 35886794 PMCID: PMC9323752 DOI: 10.3390/insects13070618] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/29/2022]
Abstract
Simple Summary Understanding how genes are regulated is a vital area of current biological research and a crucial adjunct to ongoing efforts to sequence entire genomes. Knowing the DNA sequences responsible for gene regulation—transcriptional cis-regulatory modules (CRMs, e.g., “enhancers”) and transcription factor binding sites (TFBSs)—is important for many areas of research including interpretation and validation of data developed by large-scale genomics projects, providing training data for machine-learning CRM-discovery methods, genome annotation, modeling gene-regulatory networks, studying the evolution of gene regulation, and numerous aspects of the basic biology of transcriptional regulation. Knowledge of insect CRMs is also an important step in developing biotechnology methods for control of insect disease vectors and for eliminating pathogen transmission. The REDfly (Regulatory Element Database for Fly) database integrates all of the available insect cis-regulatory information from multiple sources to provide a comprehensive collection of known regulatory elements. In this paper, we describe REDfly’s basic contents and data model, emphasizing recently added features, and provide illustrated walk-throughs of some common search scenarios. Abstract We provide here an updated description of the REDfly (Regulatory Element Database for Fly) database of transcriptional regulatory elements, a unique resource that provides regulatory annotation for the genome of Drosophila and other insects. The genomic sequences regulating insect gene expression—transcriptional cis-regulatory modules (CRMs, e.g., “enhancers”) and transcription factor binding sites (TFBSs)—are not currently curated by any other major database resources. However, knowledge of such sequences is important, as CRMs play critical roles with respect to disease as well as normal development, phenotypic variation, and evolution. Characterized CRMs also provide useful tools for both basic and applied research, including developing methods for insect control. REDfly, which is the most detailed existing platform for metazoan regulatory-element annotation, includes over 40,000 experimentally verified CRMs and TFBSs along with their DNA sequences, their associated genes, and the expression patterns they direct. Here, we briefly describe REDfly’s contents and data model, with an emphasis on the new features implemented since 2020. We then provide an illustrated walk-through of several common REDfly search use cases.
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13
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Schmidt-Ott U, Yoon Y. Evolution and loss of ß-catenin and TCF-dependent axis specification in insects. CURRENT OPINION IN INSECT SCIENCE 2022; 50:100877. [PMID: 35104659 PMCID: PMC9133022 DOI: 10.1016/j.cois.2022.100877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Mechanisms and evolution of primary axis specification in insects are discussed in the context of the roles of ß-catenin and TCF in polarizing metazoan embryos. Three hypotheses are presented. First, insects with sequential segmentation and posterior growth use cell-autonomous mechanisms for establishing embryo polarity via the nuclear ratio of ß-catenin and TCF. Second, TCF homologs establish competence for anterior specification. Third, the evolution of simultaneous segmentation mechanisms, also known as long-germ development, resulted in primary axis specification mechanisms that are independent of ß-catenin but reliant on TCF, a condition that preceded the frequent replacement of anterior determinants in long germ insects.
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Affiliation(s)
- Urs Schmidt-Ott
- University of Chicago, Dept. of Organismal Biology and Anatomy, 1027 East 57th Street, Chicago, IL 60637, USA.
| | - Yoseop Yoon
- University of California, Irvine, Dept. of Microbiology and Molecular Genetics, School of Medicine, 811 Health Sciences Rd., Med Sci B262, CA 92617, USA
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14
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Zhu H, Zhao SD, Ray A, Zhang Y, Li X. A comprehensive temporal patterning gene network in Drosophila medulla neuroblasts revealed by single-cell RNA sequencing. Nat Commun 2022; 13:1247. [PMID: 35273186 PMCID: PMC8913700 DOI: 10.1038/s41467-022-28915-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 02/12/2022] [Indexed: 12/24/2022] Open
Abstract
During development, neural progenitors are temporally patterned to sequentially generate a variety of neural types. In Drosophila neural progenitors called neuroblasts, temporal patterning is regulated by cascades of Temporal Transcription Factors (TTFs). However, known TTFs were mostly identified through candidate approaches and may not be complete. In addition, many fundamental questions remain concerning the TTF cascade initiation, progression, and termination. In this work, we use single-cell RNA sequencing of Drosophila medulla neuroblasts of all ages to identify a list of previously unknown TTFs, and experimentally characterize their roles in temporal patterning and neuronal specification. Our study reveals a comprehensive temporal gene network that patterns medulla neuroblasts from start to end. Furthermore, the speed of the cascade progression is regulated by Lola transcription factors expressed in all medulla neuroblasts. Our comprehensive study of the medulla neuroblast temporal cascade illustrates mechanisms that may be conserved in the temporal patterning of neural progenitors. During development, neural progenitors generate a variety of neural types sequentially. Here the authors examine gene expression patterns in Drosophila neural progenitors at single-cell level, and identify a gene regulatory network controlling the sequential generation of different neural types.
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Affiliation(s)
- Hailun Zhu
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sihai Dave Zhao
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Alokananda Ray
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yu Zhang
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Xin Li
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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15
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Balsalobre A, Drouin J. Pioneer factors as master regulators of the epigenome and cell fate. Nat Rev Mol Cell Biol 2022; 23:449-464. [PMID: 35264768 DOI: 10.1038/s41580-022-00464-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2022] [Indexed: 12/23/2022]
Abstract
Pioneer factors are transcription factors with the unique ability to initiate opening of closed chromatin. The stability of cell identity relies on robust mechanisms that maintain the epigenome and chromatin accessibility to transcription factors. Pioneer factors counter these mechanisms to implement new cell fates through binding of DNA target sites in closed chromatin and introduction of active-chromatin histone modifications, primarily at enhancers. As master regulators of enhancer activation, pioneers are thus crucial for the implementation of correct cell fate decisions in development, and as such, they hold tremendous potential for therapy through cellular reprogramming. The power of pioneer factors to reshape the epigenome also presents an Achilles heel, as their misexpression has major pathological consequences, such as in cancer. In this Review, we discuss the emerging mechanisms of pioneer factor functions and their roles in cell fate specification, cellular reprogramming and cancer.
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Affiliation(s)
- Aurelio Balsalobre
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal, Montreal, QC, Canada
| | - Jacques Drouin
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal, Montreal, QC, Canada.
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16
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Taylor SE, Dearden PK. The Nasonia pair-rule gene regulatory network retains its function over 300 million years of evolution. Development 2022; 149:274657. [PMID: 35142336 PMCID: PMC8959145 DOI: 10.1242/dev.199632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 01/28/2022] [Indexed: 11/20/2022]
Abstract
Insect segmentation is a well-studied and tractable system with which to investigate the genetic regulation of development. Though insects segment their germband using a variety of methods, modelling work implies that a single gene regulatory network can underpin the two main types of insect segmentation. This means limited genetic changes are required to explain significant differences in segmentation mode between different insects. This idea needs to be tested in a wider variety of species, and the nature of the gene regulatory network (GRN) underlying this model has not been tested. Some insects, e.g. Nasonia vitripennis and Apis mellifera segment progressively, a pattern not examined in previous studies of this segmentation model, producing stripes at different times progressively through the embryo, but not from a segment addition zone. Here, we aim to understand the GRNs patterning Nasonia using a simulation-based approach. We found that an existing model of Drosophila segmentation (
Clark, 2017) can be used to recapitulate the progressive segmentation of Nasonia, if provided with altered inputs in the form of expression of the timer genes Nv-caudal and Nv-odd paired. We predict limited topological changes to the pair-rule network and show, by RNAi knockdown, that Nv-odd paired is required for morphological segmentation. Together this implies that very limited changes to the Drosophila network are required to simulate Nasonia segmentation, despite significant differences in segmentation modes, implying that Nasonia use a very similar version of an ancestral GRN used by Drosophila, which must therefore have been conserved for at least 300 million years. Summary: The gene regulatory network that controls segmentation in the wasp Nasonia is functionally similar to that of Drosophila, despite different modes of segmentation and 300 million years of divergence.
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Affiliation(s)
- Shannon E. Taylor
- Genomics Aotearoa and Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9016, Aotearoa-New Zealand
| | - Peter K. Dearden
- Genomics Aotearoa and Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9016, Aotearoa-New Zealand
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17
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The embryonic transcriptome of Parhyale hawaiensis reveals different dynamics of microRNAs and mRNAs during the maternal-zygotic transition. Sci Rep 2022; 12:174. [PMID: 34996916 PMCID: PMC8741983 DOI: 10.1038/s41598-021-03642-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/09/2021] [Indexed: 11/18/2022] Open
Abstract
Parhyale hawaiensis has emerged as the crustacean model of choice due to its tractability, ease of imaging, sequenced genome, and development of CRISPR/Cas9 genome editing tools. However, transcriptomic datasets spanning embryonic development are lacking, and there is almost no annotation of non-protein-coding RNAs, including microRNAs. We have sequenced microRNAs, together with mRNAs and long non-coding RNAs, in Parhyale using paired size-selected RNA-seq libraries at seven time-points covering important transitions in embryonic development. Focussing on microRNAs, we annotate 175 loci in Parhyale, 88 of which have no known homologs. We use these data to annotate the microRNAome of 37 crustacean genomes, and suggest a core crustacean microRNA set of around 61 sequence families. We examine the dynamic expression of microRNAs and mRNAs during the maternal-zygotic transition. Our data suggest that zygotic genome activation occurs in two waves in Parhyale with microRNAs transcribed almost exclusively in the second wave. Contrary to findings in other arthropods, we do not predict a general role for microRNAs in clearing maternal transcripts. These data significantly expand the available transcriptomics resources for Parhyale, and facilitate its use as a model organism for the study of small RNAs in processes ranging from embryonic development to regeneration.
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18
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Lepeta K, Bauer M, Aguilar G, Vigano MA, Matsuda S, Affolter M. Studying Protein Function Using Nanobodies and Other Protein Binders in Drosophila. Methods Mol Biol 2022; 2540:219-237. [PMID: 35980580 DOI: 10.1007/978-1-0716-2541-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The direct manipulation of proteins by nanobodies and other protein binders has become an additional and valuable approach to investigate development and homeostasis in Drosophila. In contrast to other techniques, that indirectly interfere with proteins via their nucleic acids (CRISPR, RNAi, etc.), protein binders permit direct and acute protein manipulation. Since the first use of a nanobody in Drosophila a decade ago, many different applications exploiting protein binders have been introduced. Most of these applications use nanobodies against GFP to regulate GFP fusion proteins. In order to exert specific protein manipulations, protein binders are linked to domains that confer them precise biochemical functions. Here, we reflect on the use of tools based on protein binders in Drosophila. We describe their key features and provide an overview of the available reagents. Finally, we briefly explore the future avenues that protein binders might open up and thus further contribute to better understand development and homeostasis of multicellular organisms.
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Affiliation(s)
| | - Milena Bauer
- Biozentrum der Universität Basel, Basel, Switzerland
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19
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Histone variant H2A.Z regulates zygotic genome activation. Nat Commun 2021; 12:7002. [PMID: 34853314 PMCID: PMC8636486 DOI: 10.1038/s41467-021-27125-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
During embryogenesis, the genome shifts from transcriptionally quiescent to extensively active in a process known as Zygotic Genome Activation (ZGA). In Drosophila, the pioneer factor Zelda is known to be essential for the progression of development; still, it regulates the activation of only a small subset of genes at ZGA. However, thousands of genes do not require Zelda, suggesting that other mechanisms exist. By conducting GRO-seq, HiC and ChIP-seq in Drosophila embryos, we demonstrate that up to 65% of zygotically activated genes are enriched for the histone variant H2A.Z. H2A.Z enrichment precedes ZGA and RNA Polymerase II loading onto chromatin. In vivo knockdown of maternally contributed Domino, a histone chaperone and ATPase, reduces H2A.Z deposition at transcription start sites, causes global downregulation of housekeeping genes at ZGA, and compromises the establishment of the 3D chromatin structure. We infer that H2A.Z is essential for the de novo establishment of transcriptional programs during ZGA via chromatin reorganization. During embryogenesis, the genome becomes transcriptionally active in a process known as zygotic genome activation (ZGA); how ZGA is initiated is still an open question. Here the authors show histone variant H2A.Z deposition precedes RNA polymerase II binding on chromatin, before ZGA. H2A.Z loss causes transcriptional downregulation of ZGA genes and leads to changes in the 3D genome organization.
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20
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Diaz-Cuadros M, Pourquié O, El-Sherif E. Patterning with clocks and genetic cascades: Segmentation and regionalization of vertebrate versus insect body plans. PLoS Genet 2021; 17:e1009812. [PMID: 34648490 PMCID: PMC8516289 DOI: 10.1371/journal.pgen.1009812] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Oscillatory and sequential processes have been implicated in the spatial patterning of many embryonic tissues. For example, molecular clocks delimit segmental boundaries in vertebrates and insects and mediate lateral root formation in plants, whereas sequential gene activities are involved in the specification of regional identities of insect neuroblasts, vertebrate neural tube, vertebrate limb, and insect and vertebrate body axes. These processes take place in various tissues and organisms, and, hence, raise the question of what common themes and strategies they share. In this article, we review 2 processes that rely on the spatial regulation of periodic and sequential gene activities: segmentation and regionalization of the anterior-posterior (AP) axis of animal body plans. We study these processes in species that belong to 2 different phyla: vertebrates and insects. By contrasting 2 different processes (segmentation and regionalization) in species that belong to 2 distantly related phyla (arthropods and vertebrates), we elucidate the deep logic of patterning by oscillatory and sequential gene activities. Furthermore, in some of these organisms (e.g., the fruit fly Drosophila), a mode of AP patterning has evolved that seems not to overtly rely on oscillations or sequential gene activities, providing an opportunity to study the evolution of pattern formation mechanisms.
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Affiliation(s)
- Margarete Diaz-Cuadros
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, United States of America
| | - Ezzat El-Sherif
- Division of Developmental Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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21
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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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22
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Asma H, Halfon MS. Annotating the Insect Regulatory Genome. INSECTS 2021; 12:591. [PMID: 34209769 PMCID: PMC8305585 DOI: 10.3390/insects12070591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022]
Abstract
An ever-growing number of insect genomes is being sequenced across the evolutionary spectrum. Comprehensive annotation of not only genes but also regulatory regions is critical for reaping the full benefits of this sequencing. Driven by developments in sequencing technologies and in both empirical and computational discovery strategies, the past few decades have witnessed dramatic progress in our ability to identify cis-regulatory modules (CRMs), sequences such as enhancers that play a major role in regulating transcription. Nevertheless, providing a timely and comprehensive regulatory annotation of newly sequenced insect genomes is an ongoing challenge. We review here the methods being used to identify CRMs in both model and non-model insect species, and focus on two tools that we have developed, REDfly and SCRMshaw. These resources can be paired together in a powerful combination to facilitate insect regulatory annotation over a broad range of species, with an accuracy equal to or better than that of other state-of-the-art methods.
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Affiliation(s)
- Hasiba Asma
- Program in Genetics, Genomics, and Bioinformatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA;
| | - Marc S. Halfon
- Program in Genetics, Genomics, and Bioinformatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA;
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- Department of Biomedical Informatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- Department of Biological Sciences, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- NY State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY 14203, USA
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23
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Abstract
Arthropod segmentation and vertebrate somitogenesis are leading fields in the experimental and theoretical interrogation of developmental patterning. However, despite the sophistication of current research, basic conceptual issues remain unresolved. These include: (i) the mechanistic origins of spatial organization within the segment addition zone (SAZ); (ii) the mechanistic origins of segment polarization; (iii) the mechanistic origins of axial variation; and (iv) the evolutionary origins of simultaneous patterning. Here, I explore these problems using coarse-grained models of cross-regulating dynamical processes. In the morphogenetic framework of a row of cells undergoing axial elongation, I simulate interactions between an 'oscillator', a 'switch' and up to three 'timers', successfully reproducing essential patterning behaviours of segmenting systems. By comparing the output of these largely cell-autonomous models to variants that incorporate positional information, I find that scaling relationships, wave patterns and patterning dynamics all depend on whether the SAZ is regulated by temporal or spatial information. I also identify three mechanisms for polarizing oscillator output, all of which functionally implicate the oscillator frequency profile. Finally, I demonstrate significant dynamical and regulatory continuity between sequential and simultaneous modes of segmentation. I discuss these results in the context of the experimental literature.
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Affiliation(s)
- Erik Clark
- Department of Systems Biology, Harvard Medical School, 210 Longwood Ave, Boston, MA 02115, USA
- Trinity College Cambridge, University of Cambridge, Trinity Street, Cambridge CB2 1TQ, UK
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24
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Larson ED, Marsh AJ, Harrison MM. Pioneering the developmental frontier. Mol Cell 2021; 81:1640-1650. [PMID: 33689750 PMCID: PMC8052302 DOI: 10.1016/j.molcel.2021.02.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/28/2021] [Accepted: 02/16/2021] [Indexed: 12/16/2022]
Abstract
Coordinated changes in gene expression allow a single fertilized oocyte to develop into a complex multi-cellular organism. These changes in expression are controlled by transcription factors that gain access to discrete cis-regulatory elements in the genome, allowing them to activate gene expression. Although nucleosomes present barriers to transcription factor occupancy, pioneer transcription factors have unique properties that allow them to bind DNA in the context of nucleosomes, define cis-regulatory elements, and facilitate the subsequent binding of additional factors that determine gene expression. In this capacity, pioneer factors act at the top of gene-regulatory networks to control developmental transitions. Developmental context also influences pioneer factor binding and activity. Here we discuss the interplay between pioneer factors and development, their role in driving developmental transitions, and the influence of the cellular environment on pioneer factor binding and activity.
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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
| | - Audrey J Marsh
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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25
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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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