Partitioning of the Maize Epigenome by the Number of Methyl Groups on Histone H3 Lysines 9 and 27

Abstract

We report a detailed analysis of maize chromosome structure with respect to seven histone H3 methylation states (dimethylation at lysine 4 and mono-, di-, and trimethylation at lysines 9 and 27). Threedimensional light microscopy and the fine cytological resolution of maize pachytene chromosomes made it possible to compare the distribution of individual histone methylation events to each other and to DNA staining intensity. Major conclusions are that (1) H3K27me2 marks classical heterochromatin; (2) H3K4me2 is limited to areas between and around H3K27me2-marked chromomeres, clearly demarcating the euchromatic gene space; (3) H3K9me2 is restricted to the euchromatic gene space; (4) H3K27me3 occurs in a few (roughly seven) focused euchromatic domains; (5) centromeres and CENP-C are closely associated with H3K9me2 and H3K9me3; and (6) histone H4K20 di-and trimethylation are nearly or completely absent in maize. Each methylation state identifies different regions of the epigenome. We discuss the evolutionary lability of histone methylation profiles and draw a distinction between H3K9me2-mediated gene silencing and heterochromatin formation.

Plasticity in the Meiotic Epigenetic Landscape of Sex Chromosomes inCaenorhabditisSpecies

“…In mammals and maize, H3K9me2 has been shown to be associated with facultative heterochromatin, while H3K9me3 has been shown to be associated with constitutive heterochromatin (Peters et al 2003;Rice et al 2003;Shi and Dawe 2006). Our analyses of germ-line chromatin marks in Caenorhabditis species indicate that either H3K9me2 or H3K9me3 can be enriched on sex chromosomes and mediate transcriptional silencing, suggesting that these chromatin marks are interchangeable in this context.…”

DNA methylation and histone modification in onion chromosomes

“…We were not able to detect specific accumulation of methylated cytosines on the terminal heterochromatin regions in this microscopy analysis. Further Chromosomal distribution of histone methylation We used 4 representative antibodies against histone methylation (H3K4me2, H3K9me2, H3K27me1, and H3K27me3) to detect chromosomal distribution of the histone codes, because these antibodies are highly reliable, and commonly used in the immunohistochemical staining of plant chromosomes (Fuchs et al, 2006(Fuchs et al, , 2008Shi and Dawe, 2006;Carchilan et al, 2007;Marschner et al, 2007). In angiosperms, euchromatin is marked by H3K4me2, while heterochromatin is marked by H3K9me2 and H3K27me1.…”

A super-resolution map of the vertebrate kinetochore

“…H3K4me2 and lower levels of H3K9me3 were readily detected within the kinetochore of a human artificial chromosome by ChIP (38). In contrast, levels of H3K4me2 were much lower in one human neocentromere (39) and in maize centromeres (11,12). Clearly, more work is required to understand the role of particular histone modifications in kinetochore chromatin structure and function.…”

“…A similar pattern is also found in neocentromeres, rare chromosomal aberrations in which functional kinetochores assemble on unique sequence noncentromeric DNA (9). This pattern of H3 modifications is not universal, however, and a different pattern is observed at maize and rice centromeres (10)(11)(12).…”