Cross-talking epigenetic marks in yeast
Diaries, journals, knotted belts and blogs…we turn to these memory aids because keeping written records of our pasts help us to plan for the future. We acknowledge the fallibility of our own memories: “I wrote it down in my diary so I wouldn’t have to remember!” retorts Henry Jones Snr to his son Indiana Jones in the film The Last Crusade.
Cells too contain a record of their past adventures, recorded in epigenetic marks – reversible modifications made to DNA and to histone proteins that DNA wraps around inside the nucleus. These marks change how the DNA is packaged, making genes more or less exposed to the transcriptional machinery that makes proteins, ultimately defining cellular type. The sum total of each cell’s developmental story makes up the organism’s epigenome – each individual nuanced story contributing to a grand, heritable history for the organism.
Just as a diary or journal has particular places on the page for each day’s entry, there are particular places on the epigenome that are written to more than others. Of the histone proteins that are epigenetically modified, histone H3 has five such distinct places – lysine amino acids groups that dangle from the histone protein – that can be ‘written to’ by adding one, two or three methyl (–CH3) chemical groups, a job carried out by an enzyme called methyltransferase. Methylation of lysine 4 of histone H3 (‘H3K4’) is a mark associated with gene promotion – a cellular ‘to do’ mark that increases the priority of that gene in the cell’s workload. It is one of the most studied epigenetic modifications. In contrast, H3K4 acetylation (H3K4ac) – where an acetyl (–COCH3) is added – has not received as much attention, primarily because of the difficulties in distinguishing its function from H3K4me.
Di- and trimethylation of H3K4 has been linked to acetylation on the same histone, however, by inviting in acetyltransferase. “These results suggest that there is a highly dynamic and coordinated interplay between histone H3K4 methylation and the enzymes that control H3 acetylation during transcription,” says Professor Richard Festenstein of the CSC Gene Control Mechanisms and Disease group, who in collaboration with universities in Europe, Canada and Japan have investigated the prevalence and function of H3K4ac in yeast.
In order to separate H3K4ac from H3K4me function, the team developed a new antibody that can accurately distinguish between the two marks, binding to H3K4ac but not H3K4me and then allowing the acetylated histone to be separated. They then used mass spectrometry to measure the masses of tell-tale fragments of the protein that indicate acetylation. By the using the complementary technique of chromatin immunoprecipitation (‘ChIP’), the team was able to probe the function of acetylation in the H3 histone. And using yeast in this study was key: it allowed the team to turn particular genes involved in acetylation on or off to probe the function of these marks.
Yeast is an extremely important model organism – about half of all yeast genes have a counterpart in humans. Crucially, genetic mutations that remove the ability of the cell to make specific epigenetic marks, including methylation or acetylation of histones, can be readily introduced. In higher organisms such mutations would be fatal.
The researchers found that acetylation was more prevalent at the promoters of active genes, indicating a role in transcription, the process of turning DNA instructions into the proteins that do the work of the cell. They found 37 genes that require acetylation to function. However, in comparison to the ‘writing regions’ that exist on histones other than H3, usually either exclusively methylated or acetylated, H3 features both marks overlapping. One suggestion for both marks occurring together is that they are in direct competition for H3K4, but an alternative hypothesis proposes that methylation finetunes the level of acetylation. “This may contribute to prevent spurious transcriptional initiation events,” says Richard Festenstein.
“The potential to restrict the spreading of histone H3K4ac suggests a novel function for H3K4 methylation and reveals a previously unrecognised layer of chromatin regulation linked to the regulation of transcription in vivo.”
This work appears in PloS Genetics
Guillemette, B., Drogaris, P., Lin, H.-H. S., Armstrong, H., Hiragami-Hamada, K., Imhof, A., Bonneil, Ã., Thibault, P., Verreault, A., Festenstein, R. J., Mar. 2011. H3 lysine 4 is acetylated at active gene promoters and is regulated by h3 lysine 4 methylation. PLoS Genet 7 (3), e1001354+.