ABSTRACT
In eukaryotic cell nuclei, DNA is wrapped around a histone octamer, consisting of two copies each of the core histones (H2A, H2B, H3, and H4), to form a single nucleosome, which is the fundamental unit of chromatin (Luger et al. 1997). Posttranslational modifications of these core histones play an important role in genome function, including the regulation of gene expression, DNA damage recovery, and accurate chromosome segregation (Figure 12.1) (Bhaumik et al. 2007; Bannister and Kouzarides 2011; Greer and Shi 2012). In particular, acetylation and methylation on specific lysine residues are important for epigenetic gene regulation. Although only a single acetyl group is added on the primary amine on lysine residues, methylation can occur at three different levels: monomethylation (me1), dimethylation (me2), and trimethylation (me3). These modifications are added and removed by modification and demodification
12.1 Introduction 317 12.2 FRET-Based Enzymatic Activity Sensors 321 12.3 Sensors for Endogenous Histone Modifications 323
12.3.1 Fab-Based Live Endogenous Modification Labeling 323 12.3.2 Histone Modification Dynamics as Revealed by FabLEM 325 12.3.3 Modification-Specific Intracellular Antibodies as In Vivo
Sensors 326 12.4 Perspectives 328 Acknowledgments 329 References 329
enzymes, respectively. For example, an acetyl group is added by histone acetyltransferase (HAT) and removed by histone deacetylase (HDAC) (Shahbazian and Grunstein 2007). Similarly, the methylation status is controlled by lysine (K) methyltransferase (KMT) and demethylase (KDM) (Dillon et al. 2005; Greer and Shi 2012). With the regulation of these enzymes, histone modifications change locally and globally during the cell cycle, development and differentiation, and in response to external stimuli. Some acetylations and phosphorylations turn over rapidly (Waterborg 2002; Clayton et al. 2006; Zheng et al. 2013), possibly playing a role in balancing transcription kinetics and signaling pathways. In contrast, some methylations are more stably maintained (Zee et al. 2010; Xu et al. 2012) and can be inheritable epigenetic markers, because core histones, particularly H3 and H4, bind stably with DNA over cell generations (Kimura and Cook 2001).
