High-affinity binding of Chp1 protein is key, according to paper in Molecular Cell.

The assembly of heterochromatin in the nucleus depends on the strength with which a protein called Chp1 binds to a specific target site on a histone that has attached to the double helix, according to researchers. The team from Cold Spring Harbor Laboratory (CSHL) and St. Jude Children’s Research Hospital believe that Chp1’s strength is at least as important as the availability of siRNAs in the process.

Since this study, published online April 9 in Molecular Cell, was done in yeast, the scientists point out that it is still unclear whether this mechanism of heterochromatin assembly occurs in mammalian cells; a mammalian equivalent to Chp1 has not been found.

In a typical chromosome, heterochromatin is concentrated at and supports the structure of the centromere. Heterochromatin depends on the density of methyl groups called H3K9me, which are added to the tail of histone H3 at a specific spot. The precise pattern of methylation depends on RNAi, which involves: the enzyme that copies DNA into RNA, which is diced into siRNAs; a part of the RNAi machinery known as the RITS complex; and various enzymes that are able to alter the configuration of chromatin.

“In trying to understand the interplay between each of these components,” explains Leemor Joshua-Tor, Ph.D., of CSHL, “there has been a longstanding debate over how the RITS complex initially gets recruited to the regions at the centromere that are destined to become heterochromatin.”

At first, scientists thought that the siRNA molecules acted as guides to recruit RITS. After latching on to the chromatin, RITS was in turn thought to recruit the other components: the enzyme that adds the methyl marks; and the protein Chp1, which keeps the RITS complex firmly attached to the methyl-decorated chromatin.

In the current study, the investigators found that siRNAs cannot do the job of heterochromatin assembly by themselves. Rather, the siRNA-guided interaction relies on the strength with which the Chp1 binds to methylated chromatin.

“We found that a part of Chp1 known as the chromodomain binds with high affinity to methylated chromatin,” explains Thomas Schalch, Ph.D., a postdoctoral researcher in the Joshua-Tor lab who led the current study. By teasing apart the origin of this unique affinity, the CSHL team stumbled across Chp1 mutants that would produce siRNAs but could not assemble heterochromatin.

The team then went on to look for the exact points of contact between Chp1 and its target and how these interactions contributed to the strength of binding. Disrupting each point of interaction between Chp1 and its target by engineering various mutations into the Chp1 protein decreased the strength of binding to different levels. Even a fivefold decrease in binding strength prevented the mutation-bearing cells from assembling new heterochromatin even though some of the mutants were able to generate siRNAs.

This paper titled “High-affinity binding of Chp1 chromodomain to K9 methylated histone H3 is required to establish centromeric heterochromatin” reveals that siRNAs cannot by themselves establish heterochromatin when Chp1’s binding to H3K9me the methylated chromatin is impaired.

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