Scheme of chromodomain protein structure and expression

The chromosomes of the fission yeast, Schizosaccharomyces pombe , contain a number of heterochromatic regions, including centromeres, telomeres and the mating-type region. The configuration and function of chromatin in these domains is studied as a model of how chromatin organization achieves its repressive effects in other species, including our own. Generally, the formation of higher-order chromatin structure can be divided, at least, into two processes; the establishment and maintenance. Researchers at the RIKEN Center for Developmental Biology (CDB; Kobe, Japan) Laboratory for Chromatin Dynamics (Jun-ichi Nakayama, Team Leader) now report the identification of a role for the protein, Chp1, in the establishment of heterochromatin. This protein had previously been implicated as important to chromatin organization by studies that showed that yeast lacking the chp1 gene suffered defects in chromosome segregation and centromeric transcriptional silencing, and that the Chp1 localizes to centromeric heterochromatic regions. It is also related to other known chromatin assembly molecules by virtue of its possession of a conserved motif, known as the chromodomain, shared by many of the protein players involved in epigenetic control of gene expression. Different chromodomain-containing proteins have been thought to play discrete roles in the chromosome's various heterochromatic regions.

Nakayama and colleagues started to analyze the localization of three chromodomain proteins, Chp1, Chp2, and Swi6. Swi6 is a homolog of heterochromatin protein 1 (HP1) in mammals, and has been shown to play a crucial role in the formation of heterochromatin. The researchers found that Chp1 does indeed associate with all three heterochromatic regions in S. pombe , the first demonstration of its presence outside of the centromere . A detailed analysis of the differences in the localization patterns of Swi6 and Chp2 in mutant strains of fission yeast lacking Chp1 suggested that this protein plays a vital role in the localization of Swi6 and Chp2 specifically to the centromeric heterochromatin.

This sparked the team's interest in whether its function might be linked to RNA interference (RNAi), a nearly universal process responsible for post-transcriptional gene silencing and known to be linked to both the establishment of heterochromatin and to centromere-specific gene silencing activity in fission yeast. Their further experiments showed that loss of chp1 function had similar effects on the accumulation of RNA transcripts to that of the loss of RNAi machinery components, indicating a role in either the production or processing of centromeric RNA, either of which might involve heterochromatin establishment. These similarities suggest that RNAi machinery and Chp1 work together; however, it remained unclear why mutations in chp1 or RNAi cause centromere-specific defects. Given Chp1's universal association at centromeres, telomeres and the mating-type region, they reasoned that the protein must have common function in all heterochromatic domains.

Histone proteins in chromatin, heterochromatin in particular, are subject to a form of epigenetic modification called methylation, which affects the expression of genes within the methylated region, generally by inactivating them. The introduction of methyl modification on histones is thought to be an initial and critical step in the establishment of heterochromatin. Nakayama and colleagues designed experiments to analyze the establishment steps using the histone methyltransferase, Clr4. When the function of the gene, clr4 , is disturbed, methylation is drastically reduced; reintroduction of clr4 restores this defect. However, in a chp1 mutant, the restoration of clr4 failed to re-establish methylation not only at centromeres, but also at the mating-type region and telomeres. These experiments elegantly demonstrated the common function of Chp1 in the establishment of all heterochromatic domains. Interestingly, tests of the chromodomain proteins Swi6 and Chp2 revealed that both were essential, possibly overlapping, factors in the maintenance of H3-K9 methylation. They concluded that these three chromodomain proteins play distinct and cooperative roles in the establishment and maintenance of heterochromatin structure.