1.3.1 Epigenetics and chromatin plasticity
Now diving to an even deeper and more basic level under learning and memory, right to the eukaryotic cell nuclei, scientists have been trying to explain plasticities happening in the brain on an epigenetic level.
The notion “epigenetics” was first proposed by C. H. Waddington in 1942 to describe that the genes might interact with each other and with their environment to produce a phenotype (Waddington, 1953).
A gene is a locus or region of DNA and the molecular unit of heredity (Alberts, Johnson, Lewis, Raff, Roberts, & Walter, 2002). Genes are compactly stored on chromosomes (the condensed form) or chromatins (the unraveled form) (Figure 1.14).
The more condensed form of chromatin is called heterochromatin, and the genes located in heterochromatic region usually are less active or not active, while euchromatin is dispersed and loose, making the genes located at euchromatic regions relatively active (Grewal & Moazed, 2003).
Approximately 146 base pair (bp) of DNA strand is wrapped around a histone octamer core protein, forming a structure called nucleosome. The "linker DNA"
between two nucleosomes can be up to 80 bp long. The histone octamer consists of 4 types of histones: H2A, H2B, H3, and H4, with two copies of each (Luger, Mader, Richmond, Sargent, & Richmond, 1997). The histone proteins are overall positively charged, making them attracted to negatively charged DNAs. Importantly, each histone protein has an N-terminal tail sticking out, which is subject to many forms of modifications, such as acetylation, methylation, phosphorylation, ubiquitylation and ADP-ribosylation (Strahl & Allis, 2000; Vaquero, Loyola, & Reinberg, 2003).
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Figure 1.14. Schematic representation of chromosome, chromatin, nucleosome, and histone octamers.
A. Illustration showing how DNA is packaged into a chromosome. DNA wraps around the histone cores to form nucleosomes. These units then condense into a chromatin fiber, which condenses further to form a chromosome. Image copyright: Genome Research Ltd. B. Nucleosome as a “beads-on-a-string” structure. The nucleosome core is comprised of a histone octamer with histone 2A, 2B, 3 and 4, two copies each. The DNA double helix strand is wrapped around (~1.7 times) the histone octamer. Image copyright: Pearson Education Inc.
These post-translational modifications on histone tails actively regulate the interaction between DNA and histones. If the positive charge is reduced by the modification, the attractive force between histone and DNA decreases, thus making DNA more accessible for translational machinery; conversely, when the positive charge is increased, DNAs are less likely to be translated.
1.3.2 Histone Methylation as a transcription regulator
Unlike histone acetylation, which almost always facilitates local gene expression, histone methylation can either promotes or represses gene expression, depending on which residue is modified (Justin, De Marco, Aasland, & Gamblin, 2010; Scharf &
Imhof, 2011; Shi & Whetstine, 2007; Shilatifard, 2008). It occurs on lysine (K) or arginine (R) residues of histone tails, and it can happen more than once on the same
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residue, resulting in monomethylation, dimethylation or trimethylation (Mosammaparast & Shi, 2010; Santos-Rosa et al., 2002; Schneider et al., 2005). A summary of known histone methylation types is listed in Table 1.3 (Di Lorenzo &
Bedford, 2011).
Table 1.3 Histone tail methylations.
Histone Modification Role Reference
H3 H3K4me2 Permissive euchromatin (Santos-Rosa et al., 2002)
H3K4me3 Transcriptional elongation; active
H3R17me Transcriptional activation (Bauer, Daujat, Nielsen, Nightingale, & Kouzarides, 2002; Chen et al., 1999) H3K27me3 Transcriptional silencing; X-inactivation;
bivalent genes/gene poising
(K. Zhang et al., 2002)
H3K36me3 Transcriptional elongation (K. Zhang et al., 2002) H4 H4R3me Transcriptional activation (Wang et al., 2001)
H4K20me Transcriptional silencing (Nishioka et al., 2002)
H4K20me3 Heterochromatin (Schotta et al., 2004)
H3K4 is the one of the most extensively targeted positions among all possible histone methylation sites (Vallianatos & Iwase, 2015), and is always facilitating translation. With the advances of technological nowadays, especially chromatin immunoprecipitation (ChIP) together with quantification of associated DNA by next-generation sequencing (ChIP-seq), it has been shown that H3K4 methylation has wide-ranging roles on a genome-wide scale, and is closely related to transcriptional regulation and epigenetic tagging of promoter and enhancer sequences in both neurodevelopment and neuropsychiatric diseases (Barski et al., 2007).
ChIP-seq studies have shown that the distribution of the trimethylated form of histone 3 (H3K4me3) in the human brain shows approximately 30 000 sharp “peaks”
genome-wide (Cheung et al., 2010; Shulha, Crisci, et al., 2012). These “peaks” (1–2 kb in length) can differ among different cell types, and are mostly located around transcription start sites (TSSs) of proximal gene promoters and other regulatory
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sequences (e.g. CpG islands) (Barrera et al., 2008; Guenther, Levine, Boyer, Jaenisch,
& Young, 2007). In contrast, the di- and mono-methylated forms of histone 3 (H3K4me2 and H3K4me1) are organized as much broader peaks and appear in a much larger proportion of open chromatin, including promoters and enhancers (Barski et al., 2007; Maston, Landt, Snyder, & Green, 2012).
1.3.3 H3K4me3 in learning and memory
As is mentioned in the last chapter, H3K4me3 markers appear in promoter areas across the genome in a more concentrated and cell-type specific manner compared to H3K4me1 and H3K4me2 (Guenther et al., 2007), and is thought to be an important additional layer of transcriptional regulation (Shilatifard, 2008, 2012).
One study showed that H3K4me3 level is upregulated in hippocampus 1 h following contextual fear conditioning and returned to baseline levels at 24 h (Gupta et al., 2010). In a more recent study, people have found that retrieval of a recent contextual fear conditioned memory increased global levels H3K4me3 in hippocampal CA1 area, and in vivo knockdown of the H3K4me3 methyltransferase Mll1 in CA1 impaired fear memory (Webb et al., 2017). Another report stated that baseline resting levels of H3K4me3 were altered in the aged rat hippocampus as compared to young adults, and object learning can increase hippocampal H3K4me3 levels in young adult rats but not aged ones with memory deficits, which can be rescued by increasing H3K4me3 levels in aged rats with a histone demethylase inhibitor treatment (Morse, Butler, Davis, Soller,
& Lubin, 2015). In line with these results, increased levels of H3K4me3 were found in the hippocampus of mice with enhanced hippocampal-dependent learning and memory (offspring of high licking/grooming mothers), and this results in higher expression of mGluR1 in hippocampus together with increased mGluR1-induced LTD and paired-pulse depression (PPD) (Bagot et al., 2012)
Moreover, altered levels of H3K4me3 were also found in a few mouse models with intellectual disabilities. For example, a ketogenic diet modulated H3K4me3 levels in the granule cell layer, rescuing both the neurogenesis defect and hippocampal memory abnormalities in a mouse model of Kabuki syndrome (Benjamin et al., 2017).
Disruption of KDM5C in mice, which predominantly represses genes with high levels of H3K4me3 at the promoters, recapitulates adaptive and cognitive abnormalities seen in human patients with X-linked intellectual disability (XLID) (Iwase et al., 2016).
Interestingly, abnormal levels of H3K4me3 were also observed in brains of
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patients with other neuropsychiatric disorders, such as Huntington disease (Vashishtha et al., 2013), autism (Shulha, Cheung, et al., 2012), schizophrenia (Kano et al., 2013), and addiction to cocaine or alcohol (Zhou, Yuan, Mash, & Goldman, 2011).
Collectively, these findings suggest that the levels of H3K4me3, especially in the hippocampus, are actively regulated and closely correlated with learning and memory functions.