Linking the epigenetic 'language' of covalent histone modifications to cancer

Abstract

Covalent modifications of histones, such as acetylation, methylation, and phosphorylation, and other epigenetic modulations of the chromatin, such as methylation of DNA and ATP-dependent chromatin reorganisation, can play a major part in the multistep process of carcinogenesis, with far-reaching implications for human biology and human health. This review focuses on how aberrant covalent histone modifications may contribute to the development of a variety of human cancers, and discusses the recent findings with regard to potential therapies.

Figure 1

‘Writing’ and ‘reading’ of certain covalent marks in human histone H3 and H3.3 variant. (A) Dominant methyl marks are found on lysines 4, 9, and 27 in histone H3, all adjacent to threonine or serine, potential phosphomark carriers (Fischle et al, 2003a). Methylation of lysine 4 is generated by the SET domain of MLL, and is connected to gene activation of ceratin target genes (green=‘ON’ mark) (Milne et al, 2002). Protein(s) that ‘read’ this mark are not yet identified. Marks that correlate with gene silencing are methylation of lysines 9 and 27, generated by the HMTs SUV39H1 and EZH2, respectively (red=‘OFF’ marks). ‘Readers’ of these repressive marks are HP1 for lysine 9 methylation and Pc for lysine 27 methylation (Fischle et al, 2003c). Serines, adjacent to lysines 9 and 27, are shown to be phosphorylated by Aurora B kinase (orange), and might play a role in preventing ‘readers’ from recognising methyl marks. It is not yet known if threonine 3 is also a phospho mark (orange circle). Sequence alignment of the N-termini of H3 with H3.3 variant shows an almost identical sequence, except that alanine 31 in H3 is replaced by serine in H3.3, another potential phospho mark. (B) Lower eukaryotes maintain an epigenetic active or permissive state, whereas higher eukaryotes show an epigenetic repressive phenotype. Histone H3 from yeast and Tetrahymena are strongly methylated at lysine 4 (‘ON’ mark), but not at lysine 9 (‘OFF’ mark). The opposite was observed for H3 in chicken and humans, where lysine 9 was strongly methylated, but not lysine 4 in H3 (Briggs et al, 2001).

Figure 2

Epigenetic modifications leading to gene silencing. (A) Gene repression through histone methylation. Histone deacetylase deacetylates lysine 9 in H3, which can then be methylated by HMTs. Methylated lysine 9 in H3 is recognised by HP1, resulting in maintenance of gene silencing. (B) Gene repression involving DNA methylation. DNA methyltransferases methylate DNA by converting SAM to SAH, a mechanism that can be inhibited by DNMT inhibitors (DNMTi). MBPs recognise methylated DNA and recruit HDACs, which deacetylate lysines in the histone tails, leading to a repressive state. (C) Interplay between DNMTs and HMTs results in methylation of DNA and lysine 9 in H3, and consequent local heterochromatin formation. The exact mechanism of this cooperation is still poorly understood. (D) Specific gene repression by small RNAs (sRNAs). Transcription of repetitive DNA sequences lead to double-strand RNA (dsRNA) generation by still poorly understood mechanisms, and dsRNA is later processed to sRNAs. sRNAs associate with and recruit HMTs to the complementary DNA sequence, where HMTs locally methylate lysine 9 in H3. Methylated lysine 9 is recognised by ‘HP1’ that forms a complex with HMTs to spread the repressive mark to other histones, until reaching a boundary. ‘Writers’ and ‘readers’ of DNA epigenetic marks are shown in blue, and proteins involved with repressive histone marks are depicted in red. Tail length has been exaggerated for clarity.

Figure 3

Epigenetic modifications leading to gene activation. (A) Setting ‘ON’ marks in histone H3 to activate gene transcription. Lysine 4 in H3 is methylated by HMT (for example MLL) and lysine 9 is acetylated by HAT, allowing genes to be transcribed. It is not known, if HMTs and HATs have a direct connection to each other. (B) In the postulated ‘switch’ hypothesis (Fischle et al, 2003a), phosphorylation of serines or threonines adjacent to lysines displaces histone methyl-binding proteins, accomplishing a binding platform for other proteins with different enzymatic activities. For example, phosphorylation of serine 10 in H3 may prevent HP1 from binding to the methyl mark on lysine 9. Other lysines in H3 may be acetylated by HATs, therefore overwriting the repressive lysine 9 methyl mark and allowing activation. (C) Although there is no HDM identified to date, one can speculate that, if this enzyme exists, serine 10 phosphorylation in H3, for example, by Aurora kinases, can lead to recruitment of HDMs that in turn demethylate lysine 9 in H3. Histone acetyltransferases might then acetylate lysine 9 and HMTs methylate lysine 4, resulting in the loosening of the chromatin structure and allowing gene transcription. (D) Repressive-marked histones are exchanged with unmodified (or active) counter parts (dark circles) that are then acetylated at lysine 9 by HATs and methylated at lysine 4 in H3 by HMTs, for example, MLL, leading to gene activation. Proteins involved with repressive histone marks are depicted in red, ‘writers’ and ‘readers’ of histone activation marks are shown in green, kinases are orange and phospho marks are depicted as orange circles.

Figure 4

Histone variants and their importance in diverse biological pathways. (A) Histone variants, such as H3.3, shown in Figure 1A, are integrated into nucleosomes by a yet not understood mechanism. New data suggest that an ATP-dependent chromatin remodelling complex related to SWI/SNF is involved in the replacement of histones with their variant counterparts (shown here is the exchange of H2A with the variant H2A.X (depicted in blue)). (B) Importance of the histone variant H2A.X (depicted in blue) in DNA damage repair. Upon DSB, serine 139 in H2A.X is phosphorylated by phosphatidylinositol 3-kinase, a mark that is recognised by a complex of DNA repair proteins (DRP) that restore the structure of the DNA. After successful DSB repair, serine 139 is dephosphorylated by a yet unknown phosphatase. (C) Deficiency of histone variant H2A.X (blue circle) has critical implications for genomic stability. As shown in Figure 4B, H2A.X is important in DNA damage repair and needs p53 to arrest the cell to allow DSB repair. Alternatively, if the DNA damage is severe, p53 activates the apoptosis pathway, preventing thereby mutations and/or chromosome translocations (left site). Loss of both H2A.X and p53 can lead to chromosomal rearrangements after DSB and result in cancer (right site).