Encyclopedia of Cancer, 2015
Chromatin modification; Nucleosome remodeling
Chromatin remodeling is regulated by reorganization of nucleosome position by ATP-dependent nucleosome remodeling factors (ADNR) and covalent modifications of histone proteins. Because chromatin structure affects the binding of proteins including transcription factors to DNA, it is involved in many essential cellular processes.
Nucleosome (nucleosomes) consists of 147 bp DNA wrapped around the histone octamer comprising histone proteins, H2A, H2B, H3, and H4. Since the position of nucleosomes on DNA and the chromatin structure can affect the binding of proteins to DNA, chromatin remodeling is required for all the key processes such as gene expression (epigenetic gene silencing), DNA replication, repair, chromosomal recombination, and mitosis. ADNR factors, SWI-/SNF-type factors, which are the part of multiprotein complexes, shuffle the nucleosomes and change chromatin structure and organization (nucleosome mobility), leading to either activation or repression of gene expression.
The N-terminal domains of all core histones are subjected to chemical modifications, such as acetylation, methylation, and phosphorylation at certain residues (Fig. 1). Histone-modifying enzymes (histone deacetylases; HDACs) bring complexity of posttranslational modifications that can either activate or repress transcription, depending on the type of chemical modification and its location in the histone protein. The modification pattern of histone has been functionally linked to transcription and acts as a “histone code,” which alters the structure of higher-order chromatin and helps recruit effector molecules. Various observations have suggested a connection between nucleosome remodeling and covalent histone modifications.
Recent study suggested that histones at transcriptionally active loci can be selectively replaced in a manner that is independent of DNA replication, that is, replacement of canonical histone H3 with variant histone H3.3, which is a highly conserved histone variant. Mutation or dysfunction of these “epigenetic mechanisms” has been implicated in human cancers (epigenetics).
Mechanisms and clinical aspects
In order to obtain the access of proteins to the DNA inside nucleosomes, chromatin-remodeling ATPases are required to unwrap the nucleosomal DNA or to slide the nucleosome along the DNA to expose the buried sequences (Fig. 2). SWI-/ SNF-type chromatin-remodeling factors have been shown to be required to this process. These factors are multiprotein complexes containing a central nucleic acid substrate stimulated ATPase belonging to the SWI2/SNF2 family. SWI2/ SNF2 family is thought to be involved in gene expression, although their regulation and functions are not fully understood. The mammalian homologues, Brahma gene (BRM) and Brahma-related gene 1 (BRG1), are major components with ATPase enzymatic activities in the nucleosome remodeling SWI/SNF complex. BRM and BRG1 have a high degree of homology and either one of them might be contained in each SWI/SNF complex. Mutations or lack of expression of BRG1 has been identified in pancreatic, breast, lung, and prostate cancer cell lines. Germline and somatic mutations in SNF5 (also called INI1), which is another mammalian SWI/SNF complex component but itself does not possess a chromatin-remodeling function, cause malignant rhabdoid tumor. Although BRM and BRG1 make a chromatin-remodeling complex with SNF5, mutation in SNF5 resulted in more sever phenotype than the tumor harboring either BRM or BRG1 mutations. There could be a degree of functional redundancy between BRM and BRG1, though the functions of SWI/SNF complexes containing BRG1 or BRM might not be interchangeable in some cases. BRG1 is involved in preventing cell cycle progression through its interaction with RB that has been shown to function as a brake on the cell cycle at least in part by establishing stable epigenetic silencing of the target genes. The SWI2/ SNF2 family also contains generally one or more domains in addition to helicase-like and ATPase domains. A number of these domains have been shown to interact with surfaces on the nucleosome, which are often the targets of posttranslational modifications (see below). For example, bromodomain and chromodomain could bind acetylated lysine and methylated lysine, respectively.
Histone modifications are important in transcriptional regulation and are stably maintained during cell division. The less structured N-terminal domains of all core histones protrude from the nucleosomes and are subjected to chemical modifications, such as acetylation, methylation, and phosphorylation at certain residues. The modification patterns of histone have been functionally linked to transcription and act as a “histone code,” which implies that transcription states can be predicted simply by deciphering this code. Generally, acetylation of lysine (K) residues on histone H3 and H4 leads to the formation of an open chromatin structure, with transcription factors accessible to promoters. Phosphorylation on serine 10 and acetylation on K14 on histone H3 work antagonistically to K9 methylation on H3 leading to the gene activation. Methylation at lysine is considered as a stable modification. There are the extra complications that histone lysine methylation can be either activating (e.g., H3K4 and H3K36) or repressing (e.g., H3K9, H3K27, and H4K20), and the respective enzymes vary in their potential to induce mono-, di-, or trimethylation. Trimethylation at K9 on histone H3 or K20 on histone H4 has been shown to be a marker of heterochromatin from yeast to human. Dimethylation at K9 is associated with inactivation of gene expression. Trimethylation at histone H3K27 is a distinct histone modification involved in the regulation of homeotic (Hox) genes (homeobox genes and cancer) expression and in early steps of X-chromosome inactivation in women. Di- or trimethylation on K4 on histone H3 localizes to sites of active transcription and this modification may be stimulatory for transcription. These different combinations of histone tail modifications influence transcription by affecting chromatin structure. Modifications on the lateral surface of core histone could also affect the histone–DNA interactions as well. Control of nucleosome mobility could be regulated by the valance of modifications of acetylation, methylation, and phosphorylation on the lateral surface amino acid residues.
DNA methylation is a crucial epigenetic mechanism for silencing tumor suppressor genes in human cancers, which also affect the chromatin structures. The link between DNA methylation and the histone modifications is mediated by a group of proteins with methyl–DNA binding activity, including MeCP2, MBD1, and Kaizo; these proteins localize to DNA-methylated promoters and recruit a protein complex that contains HDACs and histone methyltransferases. The DNA methyltransferases may also play a role in direct repression of transcription through cooperation with HDACs in late S-phase. While evidences for interactions between the DNA methylation and histone modifications are accumulating, the critical initiating events in silencing remain to be defined. In fungi, mutations of a histone H3K9 methyltransferase reduced DNA methylation indicate a simple linear model in which H3K9 methylation acts as an upstream epigenetic mark which signals to DNA methylation. However, in mammalian cells, DNA methylation inhibition could also rapidly changes histone methylation, and in plants histone and DNA methylation play distinct roles depending on the locus studied. The interactions between DNA methylation and histone H3K9 methylation currently best fit a model whereby these two changes form a reinforcing silencing loop, and this may explain why silencing is less stable in organisms that lack DNA methylation.
At transcriptionally active loci, histone H3.3 variant substitutes for the canonical H3 histones. This replacement is independent of DNA replication. Histone modifications that may change histone–DNA or histone–histone contacts also affect catalyzing histone variant exchange. This replacement process is also catalyzed by ATP-dependent nucleosome-remodeling complexes. Histone replacement, which presumably is associated with activating transcription factors on the promoter region, offers an explanation for gene reactivation that were previously silenced via histone methylation. Whether histone replacement might be perturbed in cancer cells remains an open question.
The most promising aspect of this field is the restoring gene function silenced by epigenetic changes including chromatin remodeling in cancer. “Epigenetic therapy” has the potential of “normalizing” cancer cells, which may lead to differentiation, senescence, or apoptosis. This could have a novel impact on the prevention and treatment of human cancers. HDAC inhibitors (valproic acid) lead to the accumulation of acetylation in histones resulted in changes of chromatin status and of transcriptional activity to a normal state. P21 is a good example that is induced by HDAC inhibitors. However, exact mechanism through which the HDAC inhibitors mediate antitumor activity remains to be unclear, although these agents have been known to induce apoptosis and to inhibit angiogenesis and metastasis.
In a mouse model of colonic tumorigenesis, reducing DNA methylation genetically and/or pharmacologically has been shown to have tumor-preventive effects, a finding which was recently confirmed. The cytosine analogues, 5- azacytidine, and 5-aza-20-deoxycytidine are powerful inhibitors of DNA methylation, which are incorporated into DNA during cell division and trap DNA methyltransferases and lead to cell differentiation and growth repression. Indeed these demethylating agents have been widely studied in hematological diseases and received FDA approval for the treatment of myelodysplastic syndrome. Further, the synergistic effects between DNA-demethylating agent and HDAC inhibitors suggest clinical trials of this approach to restore gene function silenced by aberrant chromatin changes in cancers.
Fig. 1. (a) DNA is compacted in the nucleus through a hierarchy of histone-dependent interactions. The fundamental repeating unit of chromatin is the nucleosome, which consists of 147 bp of DNA wrapped around an octamer of core histone proteins, H2A, H2B, H3, and H4. (b) Core histone proteins consist of less structured amino–terminal tails (histone tail domain) protruding from the nucleosome and globular carboxy-terminal domains making up the nucleosome scaffold (histone fold domain). Histone tail domain could be a target of a variety of posttranslational modifications, including acetylation (Ac), methylation (Me) and ubiquitination of lysine (K) residues, phosphorylation (P) of serine (S) and threonine (T) residues, and methylation of arginine (R) residues
Fig. 2. (a) The nucleosome is a substrate of ATP-dependent nucleosome remodeling factor (ADNR). Nucleosome mobility is regulated by ADNR. (b) The SWI2/SNF2 family of ATP-dependent nucleosome remodeling proteins in mammals is classified into different subfamilies. SWI2/SNF2 family contains one or more domains in addition to helicase-like and ATPase domains. SANT (SWI3, ADA2, N-CoR, TFIIIB), DBINO (DNA-binding domain of INO80), Bromo (bromodomain), and Chromo (chromodomain) might interact with surfaces on the nucleosomes
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