Zygotic pioneer factor activity of Odd-paired/Zic is necessary for establishing theDrosophilaSegmentation Network

Abstract

31Because regulatory networks of transcription factors drive embryonic patterning, it is possible that 32 chromatin accessibility states impact how networks interact with information encoded in DNA. To 33 determine the interplay between chromatin states and regulatory network function, we performed 34 ATAC seq on Drosophila embryos over the period spanning the establishment of the segmentation 35 network, from zygotic genome activation to gastrulation. Chromatin accessibility states are 36 dynamic over this period, and establishment of the segmentation network requires maturation of 37 the ground chromatin state. Elimination of all maternal patterning information allows 38 identification of patterning-dependent and -independent dynamic chromatin regions. A significant 39proportion of patterning-dependent accessibility stems from pioneer activity of the pair-rule factor 40Odd-paired (opa). While opa is necessary to drive late opening of segmentation network cis-41 regulatory elements, competence for opa to pioneer is regulated over time. These results indicate 42 that dynamic systems for chromatin regulation directly impact the interpretation of embryonic 43 patterning information. 44In this study, we have investigated how chromatin accessibility states change following 97ZGA and to what extent these changes are dependent on the mechanisms of embryonic patterning. 98We find that the ZGA chromatin state must continue to evolve in order to support the establishment 99 of accessible CRMs within the regulatory network that confers embryonic segmental identities. 100By measuring changes in chromatin accessibility over the one-hour period between ZGA and 101 gastrulation comparing wild-type and mutant embryos in which all graded maternal inputs to 102 patterning are either eliminated or flattened, we define sites that display dynamic regulation of 103 accessibility downstream of either localized pattern-dependent or global patterning-independent 104 cues. We find that although maternal patterning systems are limited in their ability to influence 105 directly chromatin accessibility states, distinct downstream components of zygotic gene regulatory 106 networks make major contributions to patterning-dependent alterations of the chromatin 107 accessibility landscape. We focus on the characterization of one such factor, Odd-paired (Opa), 108 which we demonstrate is both necessary and sufficient to pioneer open chromatin states for a set 109 of cis-regulatory elements critical for the function of the embryonic segmentation network. These 110 results highlight that individual components of gene regulatory networks may operate not simply 111 to activate or repress target gene expression, but to dictate how and when network components 112 interact by controlling dynamic cis-regulatory element accessibility. 113 114 Results 115 The ZGA Chromatin State is Insufficient to Support Embryonic Segmentation 116To estimate the sufficiency of the ZGA chromatin state to support early embryonic 117 development, we scored all known enhancer...

Establishment of chromatin accessibility by the conserved transcription factor Grainy head is developmentally regulated

“…These results suggest that Forkhead-like, D, Grh, and other factors such as Dref and Odd-paired (Opa) may have active roles in facilitating chromatin accessibility at gastrulation. Indeed, an important role for Opa in shaping chromatin accessibility during gastrulation was recently demonstrated ( Koromila et al, 2019 preprint; Soluri et al, 2019 preprint). This contrasts with regions that lost accessibility.…”

“…D binds to core promoters and enhancers in the embryo and is required for proper gene expression of thousands of genes ( Aleksic et al, 2013 ). Indeed, recent evidence has shown that Opa is required for hundreds of regions of accessible chromatin in the gastrulating embryo, demonstrating that individual factors can drive chromatin accessibility at this stage of development ( Koromila et al, 2019 preprint; Soluri et al, 2019 preprint). Opa, Grh and D are all factors that are broadly expressed at the transition to gastrulation and are required for proper gene expression.…”

Nasoniasegmentation is regulated by an ancestral insect segmentation regulatory network also present in flies

“…D is required for normal expression of some pair rule genes in Drosophila and for spider segmentation, and the expression of D orthologues in the segment addition zone is conserved throughout panarthropoda (Nambu & Nambu, 1996; Russell et al, 1996; Ma et al, 1998; Clark & Peel, 2018; Janssen et al, 2018; Paese et al, 2018; Baudouin-Gonzalez et al, 2020). In Drosophila, opa is required for late network activation and genome-wide regulatory changes (Clark & Akam, 2016; Koromila et al, 2019; Soluri et al, 2019). In other insects, opa is expressed in a band at the end of the segment addition zone, where a putative late network would be active, though Oncopeltus lack this pattern, implying this timer gene role may not be conserved across all insects (Green & Akam, 2013; Xiang et al, 2017; Janssen et al, 2011; Auman & Chipman, 2018).…”

A Comprehensive Review of Various Therapeutic Strategies for the Management of Skin Cancer

“…60 One study found that CGIs primarily reside in the transcriptionally active regions and are unaffected by methylation through a variety of mechanisms like occupied TFs, RNA pol II, or H3K4me3, and nucleosome positioning is driven by DNMT blockage. 61 It becomes transcriptionally silenced if CGI becomes condensed in the promoter region. In contrast, via a sequence of enzymes, i.e., 10−11 translocases (TETs) known as TET1/2/3-governed-reactions, DNA that has been methylated can be changed back to its original cytosine base.…”