Histone Code and Higher-Order Chromatin Folding: A Hypothesis

Abstract

Histone modifications alone or in combination are thought to modulate chromatin structure and function; a concept termed histone code. By combining evidence from several studies, we investigated if the histone code can play a role in higher-order folding of chromatin. Firstly using genomic data, we analyzed associations between histone modifications at the nucleosome level. We could dissect the composition of individual nucleosomes into five predicted clusters of histone modifications. Secondly, by assembling the raw reads of histone modifications at various length scales, we noticed that the histone mark relationships that exist at nucleosome level tend to be maintained at the higher orders of chromatin folding. Recently, a high-resolution imaging study showed that histone marks belonging to three of the five predicted clusters show structurally distinct and anti-correlated chromatin domains at the level of chromosomes. This made us think that the histone code can have a significant impact in the overall compaction of DNA: at the level of nucleosomes, at the level of genes, and finally at the level of chromosomes. As a result, in this article, we put forward a theory where the histone code drives not only the functionality but also the higher-order folding and compaction of chromatin.

Keywords: chromatin folding; chromatin organization; epigenetic regulation; histone code; histone modification; meiosis; nucleosome; super-resolution microscopy.

Figure 1:. Histone modification associations at the nucleosome level.

Five clusters of histone modifications were identified based on 186,492 predicted nucleosome positions using hierarchical clustering. Coefficient of correlation of histone marks at the nucleosome level are presented by a coloring scheme from red (negative correlation) to blue (positive correlation) while white represents an absence of correlation. Black boxes highlight the identified clusters.

Figure 2:. Histone code at lower order tends to be maintained at higher orders.

From top to bottom, browser tracks of the different histone modifications shown in the same order as they appear in figure 1, with clusters displayed on the left (I, II, III, IV and V corresponding to the clusters of figure 1 in order that appeared top to bottom). Density of reads is represented by a gray scale, with darker regions depicting higher densities. From left to right, three different levels of zoom show the distribution of marks around the locus of gene BCOR. The left panel is the highest magnification at 200 kb, while the right panel is the lowest magnification with a range of 5kb. Genomic positions on X chromosome are indicated on the top of the different graphs for reference.Boxes and arrows in green and orange show the relationship between the three levels of zoom. The reference human genome used is hg18.

Figure 3:. Histone code at the level of chromosomes.

Chromatin during pachytene stage of meiosis prophase one is shown to be constrained by anti-correlating distinct clusters of histone modifications (in pink) along the synaptonemal complex (SC) (in green). Active chromatin (H3K4me3) emanates radially in loop-like structures (top right) while repressive chromatin (H3K27me3) is confined to axial regions (bottom) of the SC. Finally, centromeric chromatin (H3K9me3) is found at one end of the SC (top left) [18].

Figure 4:. A model for the histone code and its consequences for chromatin structure and function.

We propose that the same kind of information (for instance an active mark of chromatin) is clustering at all levels of chromatin folding, in a hierarchical fashion. From left to right, functionally different histone modifications separate in distinct chromatin domains at the chromosome level (left panel, the mouse pachytene chromosomes as a platform to test this hypothesis); separation holds true at the level of genomic regions (middle panel, for instance, an active mark tends to come in arrays/domains); finally information at nucleosome level: histone modifications combinatorially combine to define status of a gene and the future condensation states of chromatin (the so-called histone code, right panel).