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Review
. 2015 Feb;27(2):172-97.
doi: 10.1007/s12640-014-9508-6. Epub 2014 Dec 17.

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

Anna Sadakierska-Chudy  1 , Małgorzata Filip
Affiliations
Review

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

Anna Sadakierska-Chudy et al. Neurotox Res. 2015 Feb.

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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Figures

Fig. 1
Fig. 1
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)
Fig. 2
Fig. 2
Protein domains capable of recognizing specific histone modifications. Kac acetylated lysine, Kme methylated lysine, Tph phospotylated threonine, Sph phosphorylated serine, Kprop propionylated lysine, Kbuty butyrylated lysine. For more abbreviations see Table 4
Fig. 3
Fig. 3
Schematic ncRNAs and chromatin regulatory network. ncRNAs influence different epigenetic events. Regulation involving miRNAs is the best known, particularly interesting is their participation in epigenetic heredity. miRNA-mediated inheritance is provided by the paramutation. Paramutation is an allelic interaction, one allele (called paramutagenic) causes heritable epigenetic changes in the second allele (called paramutable) of the same gene mediated by miRNA or siRNA. lncRNAs are also involved in epigenetic network, one of the first identified was Xist, the master regulator of X chromosome inactivation. Air, Kenq1ot1, Xist—the name of RNA genes
Fig. 4
Fig. 4
Effects exerted by ncRNA on the epigenetic regulations. Mature miRNAs after the incorporation into RISC complex bind to the complementary sequence in the 3′-UTR region of target transcript. miRNAs negatively regulate their targets by one of the four ways: (1) mRNA cleavage, (2) translation repression, (3) mRNA deadenylation, and (4) mRNA P-body localization. piRNA associated with PIWI proteins mediated in histone modifications and de novo DNA methylation. lncRNAs guide chromatin-remodeling complexes to specific site and also serve as scaffolds for modifying complexes
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