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Short Communication Mysterious Role of H3k56ac in Embryonic Stem Cells

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Short Communication Mysterious Role of H3k56ac in Embryonic Stem Cells Short Communication Mysterious Role of H3K56ac in Embryonic Stem Cells (H3K56ac / p300/CBP / pluripotency / chromatin) S. STEJSKAL, L. TESAŘOVá, I. KOUTNá Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic Abstract. Posttranslational modifications of histones consequence of increased conformation entropy in α-N belong to epigenetic mechanisms that regulate gene helix (Xu et al., 2005). The nucleosome remodelling ac- expression by chromatin structure changes. General- tivity is first modestly in hands (SWI/SNF or RSC) and ly, histone acetylation reduces its positive charge and then even dramatically enhanced (INO80) after recruit- consequently weakens the stability of the nucleo- ment of chromatin remodellers on the chromatin com- some. Acetylation of lysine 56 on histone H3 is impli- posed of H3K56ac nucleosomes (Neumann et al., 2009; cated in the processes associated with loosened chro- Watanabe et al., 2013). Artificially prepared chromatin matin structure. H3K56ac is a mark for histones containing H3K56ac histones showed no evidence of with high nucleosome turnover in the nuclear pro- affecting the nucleosome stability. On the contrary, cesses such as gene transcription, DNA replication H3K56ac noticeably increased nucleosome breathing, and reparation in yeasts. During evolution, the main the state of nucleosome with partially unwrapping DNA H3K56ac regulatory pathway was lost and the level (Neumann et al., 2009). H3K56ac incorporated into nu- of H3K56ac remained very low in mammalian cells. cleosomes facilitates partial DNA unwrapping from the Moreover, the function of this modification still re- histone octamer and uncovers DNA regulatory binding mains unclear. In this minireview, we summarize the sites for other proteins (Neumann et al., 2009). In con- recent knowledge of the ambiguous role of H3K56ac clusion, H3K56ac relaxes chromatin fibres not by af- in mammalian embryonic stem cells. fecting the nucleosome stability, as is the case of acety- lation on N-tail lysines, but mostly by changing the Introduction chromatin dynamics. Unlike N-end lysines, lysine 56 is positioned at the H3K56ac regulation in mammalian cells amino-terminal α-N helix in the globular, central part of histone H3. This area is in contact with a place where H3K56ac is a common and relatively well-described DNA enters and exits the nucleosome (Hyland et al., histone modification in yeasts. Histones with such a 2005; Ozdemir et al., 2005). Acetylation of histones in modification are mainly a mark of newly synthesized the lateral surface of nucleosomes can directly influence nucleosomes (Hyland et al., 2005; Masumoto et al., histone-DNA interactions and weaken the nucleosome 2005; Han et al., 2007a; Li et al., 2008). H3K56ac is stability even in the absence of potential binding pro- involved in nuclear processes that need to rebuild im- teins (Fenley et al., 2010; Tropberger and Schneider, paired nucleosomes during DNA replication and repara- 2013). The lysine residue stabilizes the helical structure tion, or replenish histones behind processing RNA poly- of α-N helix by its positive charge. After histone acety- merases (Recht et al., 2006; Han et al., 2007b; Tsubota lation, DNA is more accessible for specific proteins as a et al., 2007; Wurtele et al., 2012). H3K56ac also serves as a marker, favouring sister chromatid recombination before other DNA reparation mechanisms when ena- Received June 27, 2014. Accepted July 27, 2014. bling recognition of newly synthetized chromatid by This study was generously supported by the Ministry of Educa- DNA repairing complexes (Muñoz-Galván et al., 2013). tion, Youth and Sports of the Czech Republic grants CZ.1.07/ Moreover, the modification is also important for pro- 2.3.00/30.0030 and the Grant Agency CZE grant 302/12/G157. tecting DNA against small insertions/deletions or hy- Corresponding author: Stanislav Stejskal, Centre for Biomedical peramplification of ribosomal RNA (Ide et al., 2013; Image Analysis, Faculty of Informatics, Masaryk University, Bo- Ka dyrova et al., 2013). Participation in many different tanická 68a, 602 00 Brno, Czech Republic. Phone: (+420) 549 nuclear processes points to the importance of H3K56ac 483 976; fax: (+420) 549 498 360; email: [email protected] in the yeasts. Abbreviations: ESCs – embryonic stem cells, H3K56ac – histone In Saccharomyces cerevisiae, the transfer of the H3 lysine 56 acetylation, HATs – histone acetyltransferases, acetyl group to H3K56 is catalysed by HAT Rtt109 in HDACs – histone deacetyltransferases, TSS – transcription start complex with the H3-H4 dimer (Fillingham et al., 2008; site. Kolonko et al., 2010). Because of the lack of Rtt109 ho- Folia Biologica (Praha) 60 (Suppl 1), 71-75 (2014) 72 S. Stejskal et al. Vol. 60 mology protein and the modification rarity, first re- mammalian and yeasts cells. ASF1 is necessary for searchers had not predicted the presence of H3K56ac in H3K56ac interaction with p300/CBP. ASF1 probably mammalian cells (Xu et al., 2005; Bazan, 2008; Drogaris directs H3 histone into the HAT domain of the enzyme et al., 2012). (Das et al., 2014). ASF1A enhances the level of H3K56ac In the mammalian system (Fig.1A), three HATs were in a dose-dependent manner not only for free histones, identified as enzymes responsible for transfer of the but also for chromatin-bound histones (Groth et al., acetyl group to H3K56ac: p300, CBP and Gcn5. HATs 2007). Another chaperone, CAF1, is responsible for cor- from the p300-CBP co-activator family contain motifs rect incorporation of H3K56ac histones into the newly that are structurally close to Rtt109 (Das et al., 2009). folded nucleosome (Das et al., 2009). CAF-1 also com- Both p300 and CBP can transfer the acetyl group to ly- municates with the replication complex through the sine residues on H3 and H4, even on H3K56 (Das et al., p150 subdomain and PCNA protein (Shibahara and 2009; Vempati et al., 2010; Henry et al., 2013; Li et al., Stillman, 1999). However, there is no clear evidence 2014). Through acetylation, p300/CBP orchestrates tis- that CAF-1 is involved in the incorporation of H3K56ac sue- or signal-dependent gene expression and conse- into chromatin during S phase like in the yeasts. quently regulates different cellular processes such as K56 deacetylation in mammalian cells is catalysed by proliferation, differentiation, pluripotency or apoptosis many different HDACs: HDAC1, HDAC2, and mem- (Das et al., 2009; Zhong and Jin, 2009; Goodman and bers of the sirtuin family: SIRT1, SIRT2, SIRT3, and Smolik, 2000; He et al., 2011; Xu et al., 2011). p300/ SIRT6 (Das et al., 2009; Michishita et al., 2009; Yang et CBP also promotes acetylation of K56 on free histones. al., 2009; Miller et al., 2010; Vempati et al., 2010). Similarly to p300, the CBP bromodomain interacts with H3 and catalyses the acetyl group transfer to K56 only if H3K56ac and pluripotency the CBP protein is auto-acetylated (Filippakopoulos et al., 2012; Das et al., 2014). Gcn5 is a member of several The chromatin of pluripotent embryonic stem cells co-activator complexes implicated in transcription regu- (ESCs) has an in vivo potential to activate the develop- lation and acetylation of H3K56 (Brownell et al., 1996; ment of all cell lineages. In contrast to differentiated Kuo et al., 1996; Kong et al., 2011). As a part of SAGA cells, the ESC chromatin is homogenous, highly dynam- and ATAC complexes, Gcn5 is involved in H3K56 ace- ic and structurally distinct (Meshorer and Misteli, 2006; ty lation in mammalian cells (Fillingham et al., 2008; Efroni et al., 2008). Nucleosomes contain a larger Tjeertes et al., 2009; Jin et al., 2011). amount of acetylated H3 and interact loosely with het- Two mammalian sequence homologous proteins, erochromatic binding proteins, such as HP1 or histone ASF1A and ASF1B, are responsible for incorporation of H1 (Meshorer et al., 2006; Bártová et al., 2008; Krejcí et H3K56ac into the nucleosome (Yuan et al., 2009). ASF1 al., 2009; Bhattacharya et al., 2009). Generally, ESCs is a modulator of K56 acetylation specificity in both contain the largest proportion of transcriptionally active DNA with little restriction for chromatin integration a b proteins (Meshorer and Misteli, 2006; Gaspar-Maia et al., 2011). Even in ESCs, the level of H3K56ac remains very low. What is the role of K56ac during the cell pluripo- tency regulation? Studies of human ESCs confirm an important role for H3K56ac in transcription induction of the most active genes regulated by SOX2, OCT4 and less by NANOG (Xie et al., 2009; Tan et al., 2013). Almost 79 % of highly active genes regulated by at least one of SOX2, NANOG or OCT4 contain nucleosomes with K56ac at promoter sites. Surprisingly, modifica- tions were also created in co-localization with inactive Fig. 1. Possible p300-dependent regulation of H3K56ac in gene promoters, but mostly on promoters with bound mammalian cells poised RNA polymerase II. Poised RNA polymerase II A) The complex composed of acetylated p300, ASF1 and is poised on transcription start sites (TSS) of the genes histone octamer catalyses the transfer of an acetyl group that are important for the fast entry to differentiation. (red dot) to H3K56. Together with another chaperone and During differentiation, H3K56ac marks relocate from CAF1, the H3K56ac is incorporated into a new nucleo- pluripotency-related gene promoters to promoters of some. The p300 activity, as well as that of H3K56ac, is tissue-specific developmental genes (Xie et al., 2009). regulated by HDACs (for example SIRT1). B) H3K56ac in Moreover, H3K56ac together with H3K18ac and the regulation of poised RNA polymerase II. The first nu- H4K20me1 overlap with replication origins in ESCs, cleosome downstream to TSS is targeted by p300. H3 is but not in differentiated cells (Li et al., 2014). K56ac- then acetylated on K56 and the modification promotes in- modified H3 histones also probably promote interaction teraction with chromatin remodelling complexes followed of Oct4 with destabilized nucleosomes. Oct4 strongly by nucleosome decomposition.
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