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Regulatory Functions and Chromatin Loading Dynamics of Linker Histone H1 During Endoreplication in Drosophila

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Regulatory Functions and Chromatin Loading Dynamics of Linker Histone H1 During Endoreplication in Drosophila Downloaded from genesdev.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Regulatory functions and chromatin loading dynamics of linker histone H1 during endoreplication in Drosophila Evgeniya N. Andreyeva,1,5 Travis J. Bernardo,2,5 Tatyana D. Kolesnikova,1,3,5 Xingwu Lu,2,4,5 Lyubov A. Yarinich,1,3 Boris A. Bartholdy,2 Xiaohan Guo,2 Olga V. Posukh,1 Sean Healton,2 Michael A. Willcockson,2 Alexey V. Pindyurin,1 Igor F. Zhimulev,1,3 Arthur I. Skoultchi,2 and Dmitry V. Fyodorov2 1Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation; 2Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; 3Novosibirsk State University, Novosibirsk 630090, Russian Federation Eukaryotic DNA replicates asynchronously, with discrete genomic loci replicating during different stages of S phase. Drosophila larval tissues undergo endoreplication without cell division, and the latest replicating regions occa- sionally fail to complete endoreplication, resulting in underreplicated domains of polytene chromosomes. Here we show that linker histone H1 is required for the underreplication (UR) phenomenon in Drosophila salivary glands. H1 directly interacts with the Suppressor of UR (SUUR) protein and is required for SUUR binding to chromatin in vivo. These observations implicate H1 as a critical factor in the formation of underreplicated regions and an upstream effector of SUUR. We also demonstrate that the localization of H1 in chromatin changes profoundly during the endocycle. At the onset of endocycle S (endo-S) phase, H1 is heavily and specifically loaded into late replicating genomic regions and is then redistributed during the course of endoreplication. Our data suggest that cell cycle- dependent chromosome occupancy of H1 is governed by several independent processes. In addition to the ubiquitous replication-related disassembly and reassembly of chromatin, H1 is deposited into chromatin through a novel pathway that is replication-independent, rapid, and locus-specific. This cell cycle-directed dynamic localization of H1 in chromatin may play an important role in the regulation of DNA replication timing. [Keywords: linker histone H1; suppressor of underreplication; polytene chromosomes; endoreplication; replication timing; intercalary heterochromatin] Supplemental material is available for this article. Received December 31, 2016; revised version accepted March 3, 2017. In eukaryotic organisms, DNA replication does not occur 2010; Duronio 2012; Farrell et al. 2012). Following em- synchronously throughout the genome but, rather, in dis- bryogenesis, asynchronous DNA replication continues crete domains at different stages of S phase (Nakamura in the imaginal tissues that will eventually form adult et al. 1986; Zink 2006). This asynchrony in replication structures as well as in the differentiated tissues compris- timing has been well documented in Drosophila. During ing the larval body. embryogenesis, the Drosophila genome initially repli- Drosophila is a powerful model to study asynchronous cates rapidly and synchronously. The cell cycle then replication timing owing to the polyploid nature of the lar- lengthens, and replication becomes asynchronous, result- val tissues. The cells of larval tissues undergo endoreplica- ing in segregation of early and late replicating regions. As tion, resulting in multiple copies of the genome present in in other eukaryotes, active euchromatin replicates in ear- each cell. The homologous regions of each chromosome ly S phase, whereas repetitive DNA and other sequences align and form giant polytene chromosomes that can be vi- assembled into condensed transcriptionally inert hetero- sualized by DNA staining to reveal characteristic patterns chromatin are copied later in S phase (Shermoen et al. of intensely stained bands and lightly stained interbands. For instance, salivarygland polytenechromosomes consist 4Present address: Department of Genetics and Genomic Sciences, Mount Sinai Medical Center, New York, NY 10029, USA. © 2017 Andreyeva et al. This article is distributed exclusively by Cold 5These authors contributed equally to this work. Spring Harbor Laboratory Press for the first six months after the full-issue Corresponding authors: [email protected], arthur. publication date (see http://genesdev.cshlp.org/site/misc/terms.xhtml). [email protected] After six months, it is available under a Creative Commons License (At- Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.295717. tribution-NonCommercial 4.0 International), as described at http:// 116. creativecommons.org/licenses/by-nc/4.0/. GENES & DEVELOPMENT 31:603–616 Published by Cold Spring Harbor Laboratory Press; ISSN 0890-9369/17; www.genesdev.org 603 Downloaded from genesdev.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Andreyeva et al. of >1000 genome copies per cell by the end of the third in- (van Steensel et al. 2010). H1 has also been implicated in star (Zhimulev et al. 2004; Edgar et al. 2014). During endor- suppression of replication initiation by several in vitro eplication, heterochromatic regions that replicate near and in vivo studies (Lu et al. 1998; Thiriet and Hayes the end of S phase fail to replicate fully, leading to underre- 2009; for review, see Flickinger 2015). Thus, similar to plicated loci that have a reduced ploidy compared with SUUR, H1 may negatively regulate DNA endoreplication. other regions of the polytene chromosomes. Underreplica- The localization of both SUUR and H1 to underreplicated tion (UR) of intercalary heterochromatin (IH) in the chro- chromatin suggests that they may work in concert to mosome arms produces physical constrictions or “weak maintain its underreplicated status in Drosophila larvae. points” with an increased incidence of chromosome The paradigmatic view of linker histone H1 as a global breaks, while UR of pericentric heterochromatin (PH) regulator of higher-order chromatin structure was derived yields condensed unstructured chromatin that coalesces principally from in vitro studies and the fact that, after core in a single chromocenter (Zhimulev et al. 2004). histones, H1 is the next most abundant chromatin protein. The mechanisms underlying late replication and UR are Earlier studies demonstrated that H1 condenses chroma- still not fully understood. However, the Suppressor of UR tin, protects the linker DNA, and regulates the spacing be- (SuUR) gene has been shown to be essential for the estab- tween nucleosome particles (Wolffe 1997; Woodcock et al. lishment of UR (Belyaeva et al. 1998). SuUR encodes a 2006). However, more recent work has shown that H1 also protein with no known mammalian homolog but moder- has locus-specific effects that are rendered through highly ate similarity in its N terminus to the ATPase domain of specific interactions between H1 and a variety of transcrip- the SNF2/SWI2 family (Makunin et al. 2002). Its mutation tional and epigenetic regulatory proteins. For example, by a 6-kb insertion in the last exon (SuURES) results in full Drosophila H1 has been shown to be critical for the struc- polytenization of IH. Cytological bands of normal ploidy tural integrity of PH (Lu et al. 2009) by directly interacting are formed instead of the “weak points,” and chromosome with and recruiting the histone methyltransferase (HMT) break frequency is reduced (Belyaeva et al. 1998; Belyakin Su(var)3-9, thereby promoting dimethylation of H3K9 at et al. 2005; Yarosh and Spradling 2014). Additionally, a PH and transposon repression (Lu et al. 2013). Likewise, portion of PH proximal to each of the chromosome arms mammalian H1b has been shown to interact with the mus- forms a structured banding pattern similar to normal pol- cle-specific transcription factor Msx1, leading to repres- ytenized chromatin (Belyaeva et al. 1998). SUUR protein sion of MyoD expression and inhibition of myogenesis exhibits a highly dynamic spatial and temporal distribu- (Lee et al. 2004). Several mammalian H1s were also shown tion pattern in polytene chromosomes. Whereas SUUR to interact directly with DNA methyltransferases associates with PH throughout the endocycle, it emerges DNMT1 and DNMT3b to promote DNA methylation at at IH only during the late endocycle S (endo-S) phase, the H19 and Meg3 (Gtl2) imprinting control regions when it colocalizes with the replication fork (Kolesnikova (Yang et al. 2013). Even though functional consequences et al. 2013). Several recent studies suggest that SUUR may have not yet been established, physical interactions be- promote the formation of UR by inhibiting replication tween linker histones and numerous other chromatin- fork progression. The occupancy of ORC2, a component bound proteins have been reported (for review, see McBry- of the origin recognition complex (ORC), is reduced at ant et al. 2010), suggesting that H1 may partner with a va- sites of UR in salivary glands. It is not increased at under- riety of additional factors to regulate a wide variety of replicated sites in SuURES mutants, indicating that en- transactions occurring within chromatin. hanced replication at these regions is not due to the In this study, we show that H1 is essential for the forma- increased appearance of initiation sites; rather, SuUR mu- tion of underreplicated domains in both IH and PH of lar- tation increases the rate of DNA replication (Belyaeva val polytene chromosomes. H1 and SUUR
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