Lysine Crotonylation and the Histone Code

A recent study has identified 67 new histone modifications, bringing the current total of known histone marks to 163. Two new classes of modification were discovered: lysine crotonylation and tyrosine hydroxylation. Tan et al go on to show that crotonylated lysine marks active promoters and potentially plays an important role in male germ cell differentiation.

Eukaryotic chromosomal DNA is condensed by being wound around octamers of histone proteins to form nucleosomes. Post-translational modifications (PTMs) of histones can modulate chromatin structure, altering its biological activity (for example it’s transcription status). Different combinations of histone proteins and their PTMs are found through the genome and between different cell types. Deciphering this ‘histone code’ is crucial to our understanding of cellular regulation and differentiation, and is therefore the focus of huge amounts of current biological research.

Prior to this new paper at least twelve different types of histone PTM, at over sixty different amino acid residues had been reported. These include the most commonly discussed such as methylation and acetylation, as well as esoterica like citrullination. By performing a highly comprehensive survey of histone PTMs based on mass spectrometry, Tan et al have identified two new types of modification and 67 new histone marks.

The structure of the nucleosome. The four core histones are in different colours. Their N terminal tails are protruding from the nucleosome.

Nucleosomal cores consist of histone octamers containing two molecules each of histones H2A, H2B, H3, and H4. Interactions between histone proteins and between histones and DNA are generally mediated within the globular core domains of the histone proteins, whilst their N-terminal tails protrude from the nucleosome and have been considered the primary sites for post-translational modifications. However, this new study identified many histone PTMs within the globular cores, suggesting that previous methods of PTM identification have been biased against their discovery.

Tan et al also report further characterisation of one of the new types of histone PTM: lysine crotonylation (KCr). Crotonylation was found at 28 different lysine residues from all four core histones and the linker histone H1. KCr was detected in histones isolated from yeast, nematodes and fruit flies, as well as mice and humans.

Using an antibody that recognised all lysine crotonylation, chromatin immunoprecipitation followed by sequencing (ChIP-seq) showed that histone KCr was associated with active chromatin and was particularly enriched at promoter and enhancer regions.

Tan et al went on to find that during mouse spermatogenesis histone KCr is highly enriched in post-meiotic spermatids, coinciding with a general transcriptional shutdown. By using ChIP-seq in combination with transcriptomic data, they showed that KCr was marking a group of genes on the sex chromosomes that are transcriptionally active, whilst the rest of the sex chromosome is inactivated.

Lysine crotonylation appears to be an important new PTM adding even more complexity to an already complex field of study. The comprehensiveness of the technique employed for PTM identification used in this study, however, suggests that there may not be too many more histone marks to add to the list. The next questions to ask will be whether crotonylation of different lysine residues correlates with different biological events? What enzymes are responsible for the addition and removal of crotonyl modification? And what effects does the disruption of their activity have? What proteins interact with KCr? As can be ascertained from this taster, deciphering the histone code is going to keep a lot of people busy for a long time.

Tan, M., Luo, H., Lee, S., Jin, F., Yang, J., Montellier, E., Buchou, T., Cheng, Z., Rousseaux, S., Rajagopal, N., Lu, Z., Ye, Z., Zhu, Q., Wysocka, J., Ye, Y., Khochbin, S., Ren, B., & Zhao, Y. (2011). Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification Cell, 146 (6), 1016-1028 DOI: 10.1016/j.cell.2011.08.008

2 responses to “Lysine Crotonylation and the Histone Code

  1. Nice summary. I would think the donor would be crotonyl-CoA. There are not a huge number of possible candidates for adding this PTM given that the vast majority of yeast proteins with good homologs in human are wholly inappropriate (already assigned). Removal might be harder to get at if it is just hydrolysis though conceivably it might be a back reaction of the same enzyme.

    • Hi, thanks for the comment. One of the things I didn’t mention from Tan et al was details about biosynthesis of Kcr. To investigate whether Kcr was the result of additional reactions to acetylated lysine, they analysed Kcr after overexpression of histone acetyltransferases, or lysine deacetylases, and found no significant effects. They also state that different lysine residues are targets for the 2 marks, and different genetic loci have different Kac and Kcr profiles. Therefore, they consider the two marks biosynthesis to be unrelated. The authors assume that crotonyl-CoA will be the donor, and give the impression that a whole new set of biosynthetic enzymes will be regulating addition and removal of Crotonyl groups. It’s an important point that you make with regard to there not being many unassigned yeast candidate proteins. All the best to whomever is working this out.

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