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A comprehensive view of the epigenetic landscape. Part II: Histone post-translational modification, nucleosome level, and chromatin regulation by ncRNAs.

Sadakierska-Chudy A, Filip M - Neurotox Res (2014)

Bottom Line: Epigenetic machinery is involved in various biological processes, including embryonic development, cell differentiation, neurogenesis, and adult cell renewal.In the last few years, it has become clear that the number of players identified in the regulation of chromatin structure and function is still increasing.The present paper provides the current state of knowledge about the role of 16 different histone post-translational modifications, nucleosome positioning, and histone tail clipping in the structure and function of chromatin.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Drug Addiction Pharmacology, Institute of Pharmacology Polish Academy of Sciences, Smetna 12, 31-343, Kraków, Poland, annasc@if-pan.krakow.pl.

ABSTRACT
The complexity of the genome is regulated by epigenetic mechanisms, which act on the level of DNA, histones, and nucleosomes. Epigenetic machinery is involved in various biological processes, including embryonic development, cell differentiation, neurogenesis, and adult cell renewal. In the last few years, it has become clear that the number of players identified in the regulation of chromatin structure and function is still increasing. In addition to well-known phenomena, including DNA methylation and histone modification, new, important elements, including nucleosome mobility, histone tail clipping, and regulatory ncRNA molecules, are being discovered. The present paper provides the current state of knowledge about the role of 16 different histone post-translational modifications, nucleosome positioning, and histone tail clipping in the structure and function of chromatin. We also emphasize the significance of cross-talk among chromatin marks and ncRNAs in epigenetic control.

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Cross-talk between chromatin marks. Intranucleosomal interaction: cis configuration—interaction between the modifications at the same histone tail (a) and trans configuration—interaction between the modification of the different histone tails (b). Intranucleosomal interaction between DNA methylation and histone modification (c)
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Fig1: Cross-talk between chromatin marks. Intranucleosomal interaction: cis configuration—interaction between the modifications at the same histone tail (a) and trans configuration—interaction between the modification of the different histone tails (b). Intranucleosomal interaction between DNA methylation and histone modification (c)

Mentions: Many studies have shown that the histone post-translational modifications can be influenced by neighboring PTMs and work in a coordinated manner. In 2000, Strahl and Allis proposed the histone code hypothesis, which states that “multiple histone modifications, acting in a combinatorial or sequential fashion on one or multiple histone tails, specify unique downstream function” (Strahl and Allis 2000). However, the relationships between chromatin marks, including DNA methylation and histone modifications, seem to be much more complex because these processes could mutually influence each other (Zhang and Reinberg 2001; Fischle et al. 2003). It has been proposed to define them as an”epigenetic code” that shapes the structure of chromatin and thus affects transcriptional activity. The cross-talk between different modifications can occur via diverse mechanisms. First, communication at the level of a single histone tail (the cis effect), for example, methylation on H3K9, can inhibit acetylation of the H3 tail and methylation of H3K4 (Fig. 1a) (Wang et al. 2001; Fischle et al. 2003). In addition, the identification of specific lysine residues as acceptor sites for several different modifications (e.g., acetylation, methylation, ADP-ribosylation, propionylation, and butyrylation) indicates direct competition for the same amino acid residues. Second, interactions at the level of nucleosomes mean that the modifications on different histones can affect each other (the trans effect). For example, trimethylation on H3K9 is required for the induction of H4K20 trimethylation (Fig. 1b) (An 2007). Third, DNA methylation and histone modification pathways can influence each other and establish the epigenetic landscape important for development, somatic cell reprogramming, and tumorigenesis. Relationships between DNA methylation and histone H3 methylation, particularly H3K4, H3K9, and H3K27, have been observed (Fig. 1c). There is also a strong anti-correlation between different DNA methylations; for example, the presence of the H3K4me mark prevents de novo methylation of CpG islands in the embryo (Cedar and Bergman 2009). The cross-talk between DNA methylation and histone modification most likely is mediated by SET domain HMTs and DNMTs (Cedar and Bergman 2009).Fig. 1


A comprehensive view of the epigenetic landscape. Part II: Histone post-translational modification, nucleosome level, and chromatin regulation by ncRNAs.

Sadakierska-Chudy A, Filip M - Neurotox Res (2014)

Cross-talk between chromatin marks. Intranucleosomal interaction: cis configuration—interaction between the modifications at the same histone tail (a) and trans configuration—interaction between the modification of the different histone tails (b). Intranucleosomal interaction between DNA methylation and histone modification (c)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4300421&req=5

Fig1: Cross-talk between chromatin marks. Intranucleosomal interaction: cis configuration—interaction between the modifications at the same histone tail (a) and trans configuration—interaction between the modification of the different histone tails (b). Intranucleosomal interaction between DNA methylation and histone modification (c)
Mentions: Many studies have shown that the histone post-translational modifications can be influenced by neighboring PTMs and work in a coordinated manner. In 2000, Strahl and Allis proposed the histone code hypothesis, which states that “multiple histone modifications, acting in a combinatorial or sequential fashion on one or multiple histone tails, specify unique downstream function” (Strahl and Allis 2000). However, the relationships between chromatin marks, including DNA methylation and histone modifications, seem to be much more complex because these processes could mutually influence each other (Zhang and Reinberg 2001; Fischle et al. 2003). It has been proposed to define them as an”epigenetic code” that shapes the structure of chromatin and thus affects transcriptional activity. The cross-talk between different modifications can occur via diverse mechanisms. First, communication at the level of a single histone tail (the cis effect), for example, methylation on H3K9, can inhibit acetylation of the H3 tail and methylation of H3K4 (Fig. 1a) (Wang et al. 2001; Fischle et al. 2003). In addition, the identification of specific lysine residues as acceptor sites for several different modifications (e.g., acetylation, methylation, ADP-ribosylation, propionylation, and butyrylation) indicates direct competition for the same amino acid residues. Second, interactions at the level of nucleosomes mean that the modifications on different histones can affect each other (the trans effect). For example, trimethylation on H3K9 is required for the induction of H4K20 trimethylation (Fig. 1b) (An 2007). Third, DNA methylation and histone modification pathways can influence each other and establish the epigenetic landscape important for development, somatic cell reprogramming, and tumorigenesis. Relationships between DNA methylation and histone H3 methylation, particularly H3K4, H3K9, and H3K27, have been observed (Fig. 1c). There is also a strong anti-correlation between different DNA methylations; for example, the presence of the H3K4me mark prevents de novo methylation of CpG islands in the embryo (Cedar and Bergman 2009). The cross-talk between DNA methylation and histone modification most likely is mediated by SET domain HMTs and DNMTs (Cedar and Bergman 2009).Fig. 1

Bottom Line: Epigenetic machinery is involved in various biological processes, including embryonic development, cell differentiation, neurogenesis, and adult cell renewal.In the last few years, it has become clear that the number of players identified in the regulation of chromatin structure and function is still increasing.The present paper provides the current state of knowledge about the role of 16 different histone post-translational modifications, nucleosome positioning, and histone tail clipping in the structure and function of chromatin.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Drug Addiction Pharmacology, Institute of Pharmacology Polish Academy of Sciences, Smetna 12, 31-343, Kraków, Poland, annasc@if-pan.krakow.pl.

ABSTRACT
The complexity of the genome is regulated by epigenetic mechanisms, which act on the level of DNA, histones, and nucleosomes. Epigenetic machinery is involved in various biological processes, including embryonic development, cell differentiation, neurogenesis, and adult cell renewal. In the last few years, it has become clear that the number of players identified in the regulation of chromatin structure and function is still increasing. In addition to well-known phenomena, including DNA methylation and histone modification, new, important elements, including nucleosome mobility, histone tail clipping, and regulatory ncRNA molecules, are being discovered. The present paper provides the current state of knowledge about the role of 16 different histone post-translational modifications, nucleosome positioning, and histone tail clipping in the structure and function of chromatin. We also emphasize the significance of cross-talk among chromatin marks and ncRNAs in epigenetic control.

Show MeSH
Related in: MedlinePlus