What is a chemical modification of a nucleosome that could impact gene expression?

Histone Modification

Histones are highly basic proteins that function to compress DNA within the nucleus to form chromatin, which provides a platform for regulating gene transcription. Therefore histone modification, which can occur as a consequence of DNA methylation (see earlier) or independent of DNA methylation, provides mechanisms for epigenetic tagging of the genome and gene transcription.162,163 The interaction between histone and DNA is mediated by the amino-terminal (N-terminal) tail of histone proteins, which serve as a platform for “histone code,” a specific pattern of posttranslational modification of histone octamer in chromatin. A number of posttranslational modification sites are present within the N-terminal tails of histone proteins.

Posttranslational modification of histone tails occurs by means of acetylation, methylation, ubiquitylation, and phosphorylation. Acetylation of histone tails correlates with transcriptional activity in many genes.Acetylation of lysine residues is catalyzed by histone acetyl-transferases, resulting in neutralization of their positive charge, which transfer an acetyl group from acetyl-coenzyme A to the ε-NH+ group of a lysine residue within a histone. Histone acetylation is a reversible processes that is catalyzed by histone deacetylases. Histone deacetylation is associated with repression of gene expression.Histone methylation also occurs on the ε-NH+ group of a lysine residue and is mediated by histone methyltransferases. However, methylation of lys residues preserves their positive charge.Ubiquitylation of histones, similar to other proteins, occurs through the attachment of ubiquitin (a 76-amino-acid protein) to the ε-NH+ group of a lysine residue; most histones are monoubiquitylated.Phosphorylation of histones H1 and H3 was discovered in the context of chromosome condensation during meiosis. Phosphorylation of Ser10 on H3 is mediated by ribosomal protein S6kinase 2, which is downstream of extracellular signal–regulated kinase, and phosphorylation of Ser28 on H3 is mediated by aurora kinases.

3.3.2 Histone Modifications and Nuclear Organization

The first evidence that histone modifications may affect three-dimensional (3D) chromatin organization was obtained a long time ago when it was shown that chromatin formed dense compact fibers, and that histone acetylation led to the formation of a decompacted beads-on-a-string structure.98 Later it was shown that other histone modifications could also affect the macrostructure of chromatin. For example, an increase in H3K9 acetylation and H3K4 dimethylation leads to chromatin decondensation and the formation of chromatin loops, which separate out actively transcribed genes from more compact chromosome regions in the HOX cluster of human ESCs.99 Inhibition of HDACs with trichostatin A was shown to result in a large-scale movement of centromeric and pericentromeric chromatin to the nuclear periphery.100

The development of techniques based on chromosome conformation capture (3C), and related methods (4C, 5C, and Hi-C),101 extended the possibility of studying the genome 3D architecture and allowed the question of how histone modifications affect chromatin organization to be addressed with high resolution. Genome-wide Hi-C mapping at a megabase scale revealed that inter- and intrachromosomal interactions are represented by two compartments, A and B. The A compartments contain highly expressed genes, harbor active chromatin marks such as H3K36me3, H3K79me2, H3K27ac, and H3K4me1, and are depleted in the nuclear lamina and in nucleolus-associated domains (NADs). B subcompartments correlate positively with H3K27me3 and negatively with H3K36me3, some include more than 60% of pericentromeric heterochromatin and are enriched at the nuclear lamina and/or NADs.102, 103

Compartments are organized into a set of self-interacting domains called Topologically Associating Domains (TADs) with a size from one to several thousand kb.104 The presence of TADs or similar 3D domains has been documented in most species from bacteria and yeast to mammals and plants.105 These domains are characterized by high internal interactions and are separated from each other by regions called boundary elements.106 Deletion of a TAD boundary reconfigures the topology of chromatin loops between the distal enhancer and target promoters and could alter gene expression patterns.107, 108 Different experimental data revealed that the epigenomic composition of TADs is rather uniform in either active or inactive epigenetic marks.103 In both mammals and Drosophila, inactive TADs correspond to regions of strong attachment to the nuclear lamina thus forming Lamina-associated domains (LADs). High-resolution genome-wide mapping showed that nearly 40% of the human genome consisted of LADs. LADs are enriched in heterochromatin marks (H3K9me2/3 and H3K27me3) and are highly compacted. The borders of LADs are defined by binding sites of the insulator protein CTCF, or by CpG islands, suggesting possible mechanisms of LAD confinement. During differentiation, LADs containing genes to be activated shift from the periphery to the center of the nucleus.

Active TADs include many transcriptionally active genes and their regulatory elements. They correlate with open chromatin marks, such as acetylated histones, and contain typical histone marks for enhancers, promoters and active genes.109 Active TADs are characterized by lower frequencies of lamina association.106, 110 A correlation between TAD partitioning and active/inactive genomic regions suggests that gene-rich regions with histone modifications for active chromatin are less capable of forming compact structures. As mentioned above, histone acetylation decreases the histone charge and prevents internucleosome interaction.111 On the other hand, a nucleosome with histone modifications for inactive chromatin may form higher order folds due to interactions between the positively charged N-terminal tail of histones and a negatively charged patch on the surface of adjacent nucleosomes.112

The mechanisms responsible for defining TAD boundaries and establishing TADs are still unclear. TAD boundaries in human and mouse genomes contain sites for different chromatin-binding proteins (e.g., CTCF or cohesin) and are enriched in tRNA genes, SINE retrotransposons, housekeeping genes and active histone marks H3K4me1 and H3K36me3106, suggesting that both CTCF binding and a high level of transcription activity may contribute to TAD formation. Indeed, histone marks (e.g., H3K4me1) and CTCF were shown to be highly effective in predicting chromatin interaction hubs (compartments) and TAD boundaries.113

Based on the findings that architectural proteins, such as cohesion and CTCF, are enriched in TAD boundaries, it was proposed that they play a key role in defining TADs114. 3D folding of the genome may be based on loop extrusion where chromatin fiber looping is driven by certain cis-acting loop-extruding factors, likely cohesins.115 These factors bind to chromatin and extrude DNA loops until unbinding or pausing at a CTCF-occupied boundary.

Other mechanisms could also participate in the partitioning and formation of TADs. Indeed, it was shown that depletion of various insulator proteins had no effect on the partitioning of the chromosome into TADs, but rather decreased intra-TAD interactions.116 Studies in different Drosophila cell lines did not demonstrate an appreciable enrichment of binding sites for dCTCF and Su(Hw) in TAD boundaries.117

The role of methyltransferases was recently shown in the regulation of 3D genome organization. Specifically, SETDB1 is required for shielding the genome from excess CTCF binding and thus contributes to the structural maintenance of particular large-scale chromatin domains.118 A role for the PRMT1-mediated arginine methylation in the regulation of dynamic chromatin structures was demonstrated on the chicken β-globin locus.113

Further epigenetic and 3D chromatin organization studies, as well as development of models describing epigenomic-driven interactions, will allow us to gain insight into the principles of genome folding and its roles in pathophysiology.

Chromatin and Histone Modifications Regulate Inflammatory Gene Expression

In order to package DNA within the nucleus, 146 bp are wrapped around a histone octamer (two each of histones 2A, 2B, 3, and 4) to produce nucleosomes.83,84 The tails of these histones protrude beyond the ring of DNA and are susceptible to posttranslational modifications that are associated with gene expression. The most studied of these modifications are histone acetylation and methylation, which are deposited by specific enzymes.83,84 Binding of NF-κB to specific DNA sites results in the recruitment of transcriptional coactivators such as CBP, which possess intrinsic histone acetyltransferase (HAT) activity. This results in a localized acetylation of specific histone lysine residues, which acts as a tag that can be read by bromodomain-containing proteins (Brds). Bromodomain-containing proteins, such as Brd4, form a link between histone acetylation and the recruitment of basal transcription factors and the initiation of gene transcription.83,84 In general, histone acetylation is linked with enhanced gene expression. Histone acetylation is reversed by the actions of histone deacetylases (HDACs), which remove this activation tag and attenuate gene expression.85 The development of bromodomain mimics that prevent Brd4 interaction with acetylated lysines suppress inflammation in primary human cells and in animal models of asthma and COPD.86,87

Enhanced histone acetylation is linked to changes in chromatin structure. This may result from altered electrostatic attraction between histones and DNA or from active ATP-dependent processes that move nucleosomes. This movement is driven by chromatin remodeling engines such as SWI/SNF (SWItch/Sucrose NonFermentable)88 and enable the large RNA polymerase 2 complex to move along DNA-transcribing mRNA.

Histone methylation, although again involving proteins that write (histone methyltransferases, HMTs), read (chromodomain-containing proteins), and erase (histone demethylases, HDM) methyl tags at specific lysing and arginine residues, is more complex. The functional outcome is dependent upon the target amino acid with histone H3 lysine 4 tri-methylation (H3K4me3) being associated with gene activation, whereas H3K9 and H3K27 methylation tags generally are markers of gene repression.83,84

Histone Modification

Histone modification includes acetylation, methylation, phosphorylation, ubiquitination, and sumoylation.132,142 Histone acetylation, addition of acetyl groups to lysine residue at the histone tail, is important for histones packaging of DNA into nucleosomes, the basic unit of chromatin (seeFig. 73.5). Histones physically regulate transcription by either facilitating or restricting access of transcription factors to DNA promoter regions.143 Histone acetyltransferases (HATs) are a group of enzymes responsible for both histone and non-histone acetylation. HAT activity can relax chromatin structure and regulate transcriptional activity by acetylation of lysine 56 (K56) of histone 3 (H3).144 On the other hand, acetylation of lysine (K16) on histone 4 (H4) regulates chromatin compaction and folding.145 HDACs are enzymes that remove acetylated lysine on histone tails.146 Histone deacetylation condenses the chromatin structure and prevents the accessibility of transcription factors.147,148

In HNSCCs, changes in the expression level of HDACs can increase tumor growth and aggressiveness.85 Loss of histone H3K9ac was associated with elevated NFkB signaling, leading to cisplatin resistance.149 Other modifications such as histone methylation in lysine, arginine, and histidine moieties result in activation or repression of gene expression.

Other Diseases

Histone modifications are more difficult to detect in a locus-specific manner in the absence of fresh/frozen samples, making the biomarker utility of this class lag behind DNA methylation and miRNAs. However, histone modification changes are beginning to be associated with the diagnosis of neurological diseases including schizophrenia and AD and for the prognosis of several cancer types [78–80]. We expect that the next decade will yield an exciting number of advances in technology and decoding of histone complexity that will result in a more robust panel of histone modification biomarkers across human disease.

Table 22.2. Epigenetic Biomarkers of Human Disease

4.3.1 Histone modifications

Histone modifications are strongly implicated in playing an important role in epigenetic regulation. There are several types of histone modifications, including histone acetylation, methylation, ubiquitination, and phosphorylation, with acetylation and methylation being the two most well studied and the ones we will discuss here. Histone modifications are catalyzed by enzymes that act primarily on the N-terminal tail, most frequently on lysine and arginine, serine, threonine, and tyrosine residues (Alaskhar Alhamwe et al., 2018). Histone acetylation is typically associated with higher levels of gene expression and histone methylation with either increased or repressed levels of gene expression.

Crosstalk of Histone Modification and DNA Methylation

Histone modification and DNA methylation link together to regulate epigenetic control of gene expression in eukaryotes. Histone modification and DNA methylation in plants associate together in a codependent feed forward loop, with both mechanisms enhancing RNA-directed DNA methylation [30]. During salinity stress in soybean, transcription factors including AP2/EREB, bZIP, NAC, and MYB were activated with a reduction in DNA methylation and at the same time increase of histone modification marks H3K4me3 and H3K9ac. In addition, there are reports on the inclusion of HDA6 as an important component in gene silencing, involved with RNA-directed DNA methylation (RdDM) and in the maintenance of transposable elements and ribosomal RNA silencing [63].

Abstract

Histone modifications provide an important layer of regulation for chromatin functions and are critical for processes ranging from DNA replication to transcription, from cell-cycle regulation to differentiation, and from tissue specification during development to numerous diseases. Various histone modifications are also linked to DNA methylation and cell identity determination; hence they are now considered epigenetic markings. Distinct epigenetic changes, including changes in certain histone modifications, have been observed in various aged cells and tissues. However, are these changes simply marks of the consequences of aging, or are these changes a cause of aging? In this review, we summarize recent findings regarding epigenetic changes during aging and highlight evidence that suggest some of these changes are causal for aging and age-related diseases.

Dynamics of histone modification in the female germ line

Histone modifications including histone acetylation, histone methylation, and histone phosphorylation also undergo a dynamic change in mammalian oocyte growth and maturation [33,34]. For example, deacetylases (HDACs) remove most of the acetylation from histone, such as acetylation at histone 4 lysine 12 (H4K12ac), which is involved in the formation and location of heterochromatin structure in murine oocytes [35,36]. Another important removal of histone modification is histone methylation in oocytes, such as the arginine methylation at histone 3 and 4 (H3/4) [37,38].