The Curious Case of Bivalent Marks

The Curious Case of Bivalent Marks

Developmental Cell Previews The Curious Case of Bivalent Marks Hans-Martin Herz,1 Shima Nakanishi,1 and Ali Shilatifard1,* 1Stowers Institute for Med...

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Developmental Cell

Previews The Curious Case of Bivalent Marks Hans-Martin Herz,1 Shima Nakanishi,1 and Ali Shilatifard1,* 1Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA *Correspondence: [email protected] DOI 10.1016/j.devcel.2009.08.014

Bivalently marked chromatin, containing both histone H3 lysine 4 (H3K4) and H3K27 trimethylation, is a hallmark of developmentally regulated paused promoters in mammalian embryonic stem cells. In this issue of Developmental Cell, Akkers et al. report that Xenopus tropicalis embryos transition through early development without the requirement for bivalently marked promoters. DNA encodes basic genetic information that guides the development of living organisms. How this information is read in space and time depends mainly on the interaction of DNA with proteins called histones, which package DNA into nucleosomes. The N-terminal tails of histones protrude from the nucleosomes and are subject to various posttranslational modifications that affect the accessibility of DNA to factors involved in transcriptional regulation. One of these modifications, histone H3K4 trimethylation (H3K4me3), is implemented by the mammalian Set1/Trithorax-related, COMPASS-like complexes, and is associated with transcriptionally active genes (Shilatifard, 2006) (Figure 1A). On the other hand, histone H3K27me3, implemented by the Polycomb-group protein EZH2 within the Polycomb Repressive Complex 2 (PRC2), is found with repressed chromatin (Shilatifard, 2006) (Figure 1B). Interestingly, both modifications are found simultaneously on promoters in mouse and human embryonic stem (ES) cells (Bernstein et al., 2006; Mikkelsen et al., 2007; Pan et al., 2007; Zhao et al., 2007). The finding that active and repressive marks can coexist led to the ‘‘bivalent domain’’ model. In this model, the repressive H3K27me3 mark is considered dominant over the usually activating H3K4me3 mark, suggesting that bivalently marked genes are held in a repressed mode. Many of the repressed genes are pivotal for differentiation or are important developmental regulators. Their promoters are bound by RNA polymerase II (RNAPII) and are held in a poised state at very low levels of transcription. During differentiation, H3K4 methylation remains at these genes, while H3K27me3 disappears, thereby initiating

a transcriptional response. However, the molecular mechanism by which the bivalent domain causes RNAPII to pause, and how the combination of such marks holds RNAPII at the promoters of developmentally regulated genes, is not clear at this time. In this issue of Developmental Cell, Akkers et al. follow up on these questions and test the co-occupancy of H3K4me3 and H3K27me3 in Xenopus tropicalis during embryogenesis, finding that Xenopus does not follow the mammalian model (Akkers et al., 2009). Akkers et al. perform genome-wide Chromatin Immunoprecipitation followed by DNA sequencing (ChIP-seq) experiments for H3K4me3 and H3K27me3 histone marks combined with an RNA-sequencing approach in gastrula-stage embryos. Since to date almost all of the studies regarding bivalent domains have been performed in cell lines, this study is the first to address the issue of bivalency in vertebrate embryos. As in studies with ES cells, the authors find regions that are enriched only for H3K4me3 or H3K27me3, but also regions that are marked for both H3K4me3 and H3K27me3. The numbers of bivalent regions detected with this approach versus H3K4me3- and H3K27me3-only regions are similar to the ones reported previously for human ES cells. However, the majority of genes with both H3K4me3 and H3K27me3 marks are nonetheless expressed and show no signs of RNAPII pausing. It turns out that true ‘‘bivalency’’ does not exist in Xenopus embryos. Subsequent sequential ChIP experiments failed to detect nucleosomes simultaneously bearing both modifications. Instead, studies with dissected embryos showed that spatial control of gene expression underlies the finding that antibodies to either H3K4me3 or

H3K27me3 can immunoprecipitate some of the same genes: the combination of H3K4me3 and H3K27me3 has its origin in genes being transcribed in one part of the embryo, but being repressed in other parts. The study by Akkers et al. reveals that Xenopus diverges from the bivalency model in yet another way. In Xenopus, the H3K4me3 mark first appears after the midblastula transition, when zygotic transcription starts. H3K27me3 is undetectable until even later in midgastrulastage embryos. It is not clear whether H3K4me3 and H3K27me3 are completely absent before the midblastula transition in Xenopus or whether initial H3K4me3 and H3K27me3 marks are erased before the midblastula transition. Either way, the lack of bivalent marks right before the onset of zygotic transcription in Xenopus embryos does not fit the paradigm for the transition of promoters from bivalency to either H3K4me3/active or H3K27me3/ repressed upon differentiation. Rather, Xenopus embryos appear to start from a blank slate or use other mechanisms to poise genes for later developmental decisions. The Akkers et al. study suggests that bivalent marks, as described for mammalian ES cells, do not exist in Xenopus (Figure 1D). Rather, the Xenopus pattern resembles that found during Drosophila embryogenesis, wherein H3K4 methylation first emerges around the onset of zygotic transcription (Rudolph et al., 2007; Schaner et al., 2003). Furthermore, genome-wide ChIP-on-chip studies in Drosophila embryos only found a minor overlap between H3K4me3- and H3K27me3-enriched regions (Schuettengruber et al., 2009), suggesting that bivalency may not exist in Drosophila embryos. The nature of the H3K4 and

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Figure 1. Transcriptional Regulation and Chromatin Modifications (A) RNA polymerase II and its basal transcription machinery initiate transcription. The macromolecular complex COMPASS, containing the Set1 and/or MLL1–4 proteins, marks active chromatin by trimethylation on lysine 4 of histone H3 (K4me3) (green spheres). (B) Transcriptionally repressed regions of chromatin are marked by trimethylation on lysine 27 of histone H3 (K27me3) (red spheres through PRC2), which can recruit the PRC1 complex, resulting in repression. (C) In mammalian ES cells, developmentally regulated genes are marked by histone H3 trimethylation on both H3K4 and H3K27, a state known as bivalent. (D) In this issue of Developmental Cell, Akkers et al. demonstrate that Xenopus tropicalis transitions through early development without the requirement for bivalently marked promoters.

H3K27 methylation overlap in Drosophila has not yet been determined and may reflect a mixed population of cells within the embryo as was found for Xenopus embryos. In light of these observations, how essential are bivalent domains for developmental processes, given that Xenopus embryos apparently undergo differentiation without bivalently marked genes? Is there some aspect of mammalian development that requires this additional level of regulation? There is no doubt, based on published studies, that promoter bivalency exists in mammalian ES cells and to a certain extent even in differentiated cells (Bernstein et al., 2006; Pan et al., 2007; Roh et al., 2006). However, it is curious that eukaryotes such as Drosophila and

Xenopus, whose Trithorax and Polycomb machineries are similar to those of mammals, can transition through early development without bivalently marked promoters. At present, it is not clear whether the bivalent mark observed in mammalian ES cells is required for the proper expression of genes during differentiation, or whether it reflects a nonfunctional, mixed state of modifications in cells that have not yet committed to a particular developmental fate. Bivalency might therefore indicate a special ‘‘transition state’’ between inactive and active on developmentally regulated genes. Without a doubt, future experiments in various model organisms at different developmental stages are required

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to paint a clearer picture of the occurrence or absence of bivalent marks. Ultimately, if bivalency is a hallmark of undifferentiated mammalian cells, questions regarding its coexistence on the same histone tail or nucleosome, its molecular role in the regulation of paused RNAPII, and its release from promoter proximal pausing sites need to be addressed in order to solidify a regulatory role for bivalent domains in development.

REFERENCES Akkers, R.C., van Heeringen, S.J., Jacobi, U.G., Janssen-Megens, E.M., Franc¸oijs, K.J., Stunnenberg, H.G., and Veenstra, G.J.C. (2009). Dev. Cell 17, this issue, 425–434.

Developmental Cell

Previews Bernstein, B.E., Mikkelsen, T.S., Xie, X., Kamal, M., Huebert, D.J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006). Cell 125, 315–326. Mikkelsen, T.S., Ku, M., Jaffe, D.B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.K., Koche, R.P., et al. (2007). Nature 448, 553–560. Pan, G., Tian, S., Nie, J., Yang, C., Ruotti, V., Wei, H., Jonsdottir, G.A., Stewart, R., and Thomson, J.A. (2007). Cell Stem Cell 1, 299–312.

Roh, T.Y., Cuddapah, S., Cui, K., and Zhao, K. (2006). Proc. Natl. Acad. Sci. USA 103, 15782– 15787. Rudolph, T., Yonezawa, M., Lein, S., Heidrich, K., Kubicek, S., Schafer, C., Phalke, S., Walther, M., Schmidt, A., Jenuwein, T., et al. (2007). Mol. Cell 26, 103–115. Schaner, C.E., Deshpande, G., Schedl, P.D., and Kelly, W.G. (2003). Dev. Cell 5, 747–757.

Schuettengruber, B., Ganapathi, M., Leblanc, B., Portoso, M., Jaschek, R., Tolhuis, B., van Lohuizen, M., Tanay, A., and Cavalli, G. (2009). PLoS Biol. 7, e13. Shilatifard, A. (2006). Annu. Rev. Biochem. 75, 243–269. Zhao, X.D., Han, X., Chew, J.L., Liu, J., Chiu, K.P., Choo, A., Orlov, Y.L., Sung, W.K., Shahab, A., Kuznetsov, V.A., et al. (2007). Cell Stem Cell 1, 286–298.

Shugoshin and PP2A: Collaborating to Keep Chromosomes Connected Anna V. Kateneva1 and Jonathan M.G. Higgins1,* 1Division of Rheumatology, Immunology and Allergy, Brigham & Women’s Hospital, Harvard Medical School, Smith Building Room 538A, 1 Jimmy Fund Way, Boston, MA 02115, USA *Correspondence: [email protected] DOI 10.1016/j.devcel.2009.08.016

Timely release of sister chromatid cohesion is essential for accurate chromosome segregation during cell division. Shugoshin forms a complex with the phosphatase PP2A that has been proposed to dephosphorylate cohesin proteins to prevent premature loss of centromeric cohesion. A recent study in Molecular Cell by Xu et al. presents the structure of Shugoshin bound to PP2A and provides evidence that this interaction is required for cohesion protection. To ensure accurate segregation during mitosis, sister chromatids remain associated following replication, separating only once all chromosomes are biorientated on the spindle (Figure 1A). The association of sister chromatids in mitosis depends on cohesin complexes (Figure 1C; Peters et al., 2008). Meiosis is more complex: segregation of homologous chromosomes in the first division is followed by segregation of sister chromatids in the second division (Figure 1B). The cohesin complex again plays a crucial role, although meiotic cells employ additional meiosis-specific cohesin subunits (Figure 1D; Brar and Amon, 2008; Clarke and Orr-Weaver, 2006). In both mitosis and meiosis the protease Separase cleaves a cohesin subunit—Scc1 in mitosis or Rec8 in meiosis—to release cohesin from chromosomes, but the spindle assembly checkpoint (SAC) keeps Separase activity in check until all chromosomes are properly oriented on the spindle (Brar and Amon, 2008; Peters et al., 2008). In

meiosis (Figure 1B), cohesion is removed from chromosome arms during meiosis I to allow homolog segregation but is protected at centromeres to maintain sister chromatid association needed for meiosis II. In vertebrate mitosis (Figure 1A), the bulk of cohesin on chromosome arms is removed during prophase in a cleavageindependent manner, while a small population at centromeres is shielded from this ‘‘prophase pathway’’ and provides cohesion until the metaphase-anaphase transition (Peters et al., 2008). Experiments in various model organisms have shown that Shugoshin (Sgo) family proteins protect centromere cohesion in meiosis and mitosis and also play a role in chromosome biorientation and the SAC. Sgo1 copurifies with the protein phosphatase PP2A, specifically with PP2A-AB0 C (Kitajima et al., 2006; Riedel et al., 2006; Tang et al., 2006). This discovery was intriguing because cohesin phosphorylation, perhaps by Polo kinases, regulates cohesion release in both meiosis and mitosis (Figures 1C

and 1D). Sgo1 is required for PP2A localization to centromeres during meiosis, where PP2A might maintain Rec8 in a dephosphorylated state and thereby prevent sister separation. A similar model has been proposed for protection of centromeric cohesion from the prophase pathway, though PP2A centromere localization does not require Sgo1 in vertebrate mitosis (Kitajima et al., 2006; Riedel et al., 2006; Tang et al., 2006). The exact roles of Sgo therefore remain unclear. In a recent Molecular Cell paper, Xu, Nasymth, and coworkers test the relationship between PP2A and Sgo proteins (Xu et al., 2009). First, they demonstrate that there is a direct interaction between human Sgo1 and PP2A-AB0 C. They narrow down the interacting segment of Sgo1 to a conserved N-terminal region (Sgo1cc) that also dimerizes Sgo1. A crystal structure revealed that Sgo1cc forms parallel coiled-coil dimers that are sandwiched between two PP2A-AB0 C holoenzymes. Based on solution studies, however, the authors conclude that an

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