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Zygotic Pioneer Factor Activity of Odd-Paired/Zic Is Necessary for Establishing 8 the Drosophila Segmentation Network 9 10 Isabella V

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Zygotic Pioneer Factor Activity of Odd-Paired/Zic Is Necessary for Establishing 8 the Drosophila Segmentation Network 9 10 Isabella V bioRxiv preprint doi: https://doi.org/10.1101/852707; this version posted November 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 2 3 4 5 6 7 Zygotic pioneer factor activity of Odd-paired/Zic is necessary for establishing 8 the Drosophila Segmentation Network 9 10 Isabella V. Soluri1, Lauren M. Zumerling1, Omar A. Payan Parra2,3, Eleanor G. Clark2, Shelby A. 11 Blythe1,4 12 1) Department of Molecular Biosciences, Northwestern University, Evanston, IL 13 2) Program in Interdisciplinary Biological Sciences, Northwestern University, Evanston, IL 14 3) Department of Neurobiology, Northwestern University, Evanston, IL 15 4) For correspondence: [email protected] 16 17 18 19 20 21 22 23 24 25 26 27 28 29 Running title: Patterning-dependent chromatin accessibility 30 bioRxiv preprint doi: https://doi.org/10.1101/852707; this version posted November 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 31 Abstract 32 Because regulatory networks of transcription factors drive embryonic patterning, it is possible that 33 chromatin accessibility states impact how networks interact with information encoded in DNA. To 34 determine the interplay between chromatin states and regulatory network function, we performed 35 ATAC seq on Drosophila embryos over the period spanning the establishment of the segmentation 36 network, from zygotic genome activation to gastrulation. Chromatin accessibility states are 37 dynamic over this period, and establishment of the segmentation network requires maturation of 38 the ground chromatin state. Elimination of all maternal patterning information allows 39 identification of patterning-dependent and -independent dynamic chromatin regions. A significant 40 proportion of patterning-dependent accessibility stems from pioneer activity of the pair-rule factor 41 Odd-paired (opa). While opa is necessary to drive late opening of segmentation network cis- 42 regulatory elements, competence for opa to pioneer is regulated over time. These results indicate 43 that dynamic systems for chromatin regulation directly impact the interpretation of embryonic 44 patterning information. 45 Introduction 46 Embryonic patterning systems direct a set of initially uncommitted pluripotent cells to 47 differentiate into a variety of cell types and complex tissues. Over developmental time spans, 48 regulatory networks of transcription factors drive the acquisition of unique cell fates by integrating 49 patterning information and determining the set of genes to be activated or repressed in response to 50 developmental cues [1]. The critical nodes of these regulatory networks are cis-regulatory modules 51 (CRMs) where transcription factors bind in order to enhance or silence target gene activity. 52 However, additional epigenetic determinants such as the organization of chromatin structure likely 53 influence how genomic information is accessed by regulatory networks. For instance, because 54 nucleosome positioning can hinder transcription factor-DNA interactions [2, 3] chromatin 55 effectively serves as a filter either to highlight or obscure regulatory information encoded in DNA. 56 But embryonic chromatin states themselves are dynamic [4-9]. The mechanisms that drive 57 developmental progression can also trigger remodeling of chromatin accessibility patterns on both 58 large and small scales, thereby changing over time what genetic information is available to gene 59 regulatory systems. While in many cases we have near comprehensive understanding of both the 60 genetic components of certain developmental networks and the critical CRMs whereby these 61 components interact, much less is known about how chromatin accessibility states constrain 62 network function and how mechanisms for controlling chromatin accessibility are systematically 63 woven into the developmental program. 64 In the case of Drosophila melanogaster, decades of investigation into the mechanisms of 65 development have exhaustively identified the critical patterning cues and transcription factors that Soluri et al.: Patterning-dependent chromatin accessibility 2 bioRxiv preprint doi: https://doi.org/10.1101/852707; this version posted November 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 66 drive early cell fate specification and differentiation of select developmental lineages. Patterning 67 is initiated by four distinct maternal pathways that alone are sufficient to initiate zygotic regulatory 68 networks that specify all of the primary cell identities that arise along the major embryonic axes 69 [10-17]. At the outset of patterning, nuclei have what can be considered a ‘ground state’ of 70 chromatin structure that contains the initial set of accessible CRMs and promoters that will define 71 the first regulatory network interactions [7]. The ground state effectively provides a baseline for 72 determining the influence of epigenetic mechanisms of gene regulation on developmental 73 processes. The early Drosophila embryo therefore provides an ideal starting point to observe both 74 how regulatory networks are constrained by chromatin states, and how these states evolve as a 75 function of progression through the developmental program. 76 Before embryos can respond zygotically to maternal patterning cues, they must first 77 undergo a series of 13 rapid, synchronous mitotic divisions that serve to amplify the single nucleus 78 formed after fertilization into a set of ~6000 largely uncommitted, pluripotent cells [18, 19]. These 79 mitotic divisions occur in a state of general transcriptional quiescence that effectively prevents 80 nuclei from responding prematurely to regulatory stimuli [20-23]. The shift from the initial 81 proliferative phase to later periods of differentiation comes at a major developmental milestone 82 termed the midblastula transition (MBT) during which the zygotic genome activates, and cells 83 become competent to respond to maternal patterning information [24]. A major component of 84 zygotic genome activation (ZGA) is the establishment of the chromatin ground state by a subset 85 of transcription factors known as pioneer factors that gain access to closed or nucleosome- 86 associated DNA and direct the establishment of short tracts of open and accessible chromatin [25- 87 31]. Because maternal pioneer factors such as Zelda are expressed uniformly in all cells [25], it is 88 inferred that the initial ground state is common to all cells of the embryo at ZGA. However, 89 maternal patterning systems can directly influence chromatin accessibility states at ZGA [32], and 90 because their activities are by definition spatially restricted, this gives rise to heterogeneous 91 embryonic chromatin states. Indeed, ATAC-seq measurements of chromatin accessibility in 92 subdivided post-ZGA embryos, sampled either as posterior and anterior halves [33], sorted cells 93 purified from restricted positions along the anterior-posterior (AP) axis [34], or as single cells [8] 94 identify spatial heterogeneities in accessibility patterns that begin to emerge shortly after embryos 95 undergo ZGA and initiate patterning. These observations raise the question of what mechanisms 96 drive the reshaping of the chromatin landscape following ZGA. Soluri et al.: Patterning-dependent chromatin accessibility 3 bioRxiv preprint doi: https://doi.org/10.1101/852707; this version posted November 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 97 In this study, we have investigated how chromatin accessibility states change following 98 ZGA and to what extent these changes are dependent on the mechanisms of embryonic patterning. 99 We find that the ZGA chromatin state must continue to evolve in order to support the establishment 100 of accessible CRMs within the regulatory network that confers embryonic segmental identities. 101 By measuring changes in chromatin accessibility over the one-hour period between ZGA and 102 gastrulation comparing wild-type and mutant embryos in which all graded maternal inputs to 103 patterning are either eliminated or flattened, we define sites that display dynamic regulation of 104 accessibility downstream of either localized pattern-dependent or global patterning-independent 105 cues. We find that although maternal patterning systems are limited in their ability to influence 106 directly chromatin accessibility states, distinct downstream components of zygotic gene regulatory 107 networks make major contributions to patterning-dependent alterations of the chromatin 108 accessibility landscape. We focus on the characterization of one such factor, Odd-paired (Opa), 109 which we demonstrate is both necessary and sufficient to pioneer open chromatin states for a set 110 of cis-regulatory elements critical for the function of the embryonic
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