# Molecular and Hormonal Mechanisms Regulating Fleshy Fruit Ripening
## 4 Accessibility of Genes for Transcription during Fruit Development and Ripening
### Histone Marks  
Histone post-translational modifications (PTMs) are also involved in regulating the accessibility of genes for expression. PTMs include phosphorylation, methylation, acetylation or ubiquitination, and depend on a wide range of enzymes that determine their distribution and abundance [206]. Several different histone marks have been identified in plants by chromatin immunoprecipitation combined with microarray analysis (ChIP-chip) or deep sequencing (ChIP-seq), and histone modification, as recently reported [207]. Functional histone marks include H3K9 ac (histone H3 lysine 9 acetylation), H3K4 me3/2/1 (histone3 lysine K4 trimethylation/demethylation/monomethylation) and H3K27 me3 (histone lysine 27 trimethylation). The removal or addition of these marks is associated with gene activation or repression and is, to some extent, conserved in animals and plants [204; 208; 209; 210; 211; 212; 213; 214]. In rice, condensed heterochromatin, which often contains inactive genes, has less H3K4 me2 and H3K4 me3 and more methylated DNA than the less compact euchromatin [215], and genes with predominantly H3K4 me3 are actively transcribed, whereas genes with predominantly H3K4 me2 are transcribed at lower levels. H3K9 ac and H3K4 me3 have been correlated with gene activation during different developmental processes in plants [216; 217; 218; 219; 220; 221; 222]. [PERSON] et al. [223] showed that three types of H3K4 methylations were present in Arabidopsis (H3K4 me1, H3K4 me2 and H3K4 me3), and H3K4 me-containing genes were highly expressed, although only H3K4 me3 was thought to be directly related to transcriptional activation. Tomato proteins HP1 and HP2, involved in fruit carotenoids metabolism, which are affected in the tomato mutations _hp1_ and _hp2_, are capable of forming a complex with CULLIN 4 (CUL4), a ubiquitin E3 ligase component that participates in chromatin remodelling [224]. Two tomato polycomb repressive complex 2 (PRC2) constituents, the ENHANCER OF ZESTE homologs SIEZ1 and SIEZ2, encoding putative histonelysine-\(N\)-methyltransferaseases, are involved in fruit morphology [225; 226]. [PERSON] et al. [132] showed that a ripening-related polycomb-group protein encoded by a _MULTICOPY SUPPRESSOR OF IRAI_ (_MSII_) gene, _SIMSII_, inhibits ripening, possibly through repression of _MADS-RIN_ expression. In contrast to histone marks associated with gene activation, the trimethylation of lysine 27 at histone H3 (HK27 me3) by polycomb complexes is a conserved gene silencing mechanism [227]. Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) are involved in histone modifications that cause the epigenetic repression of animal and plant genes [228]. PRC1 is required for proper H3K27 me3 deposition to specific targets [229], but the animal and plant versions have diverged [230]. Recently, [PERSON] et al. [231] showed that in tomato, one component of PCR1 (Like Heterochromatin Protein 1 (LHP1)) has two variants, SILHP1a and SILHP1b. _SLHP1b_ is expressed during ripening and co-localizes with H3K27 me3 marks in chromatin from tomato fruit. Inhibiting _SLHP1b_ by RNAi in tomato fruits upregulated genes for ethylene synthesis (_ACS2_, _ACS4_, _ACOI_) carotenoid production (_PSY1_) and cell wall modification (_PL_), and the regulator genes _MADS-RIN_ and _NACNOR_ were also upregulated, whereas overexpressing _SILHP1b_ in fruits downregulated these genes [231]. [PERSON] et al. [232] identified SJJMJ6 as a H3K27 me3 demethylase that specifically demethylates H3K27 me3, thereby activating the expression of ripening-related genes, and showed that overexpression of tomato _SJJMJ6_ accelerated tomato fruit ripening. RNA-seq and chromatin immunoprecipitation identified 32 genes directly targeted by SJJMJ6, including ripening-related genes such as _MADS-RIN_, _ACS4_, _ACO1_, _PL_, _TBG4_ and _DML2_. [PERSON] et al.