There is nothing permanent except change. -Heraclitus
There is perhaps no more fundamental property of life than change, both in personal experience and, as the basis of evolution, in the nature of biology itself. same. The constant genetic permutations that fuel the evolutionary process have given rise to an incredible complexity and diversity of life, but even in the face of this unstoppable force, some aspects of life are so fundamental that they remain essentially unchangeable. The inevitability of death. The fact of reproduction. The chemical nature of the genetic code. Not surprisingly, some of the genes associated with these phenomena are themselves quite resistant to evolutionary change. Take, for example, histones. The oldest of these proteins, which form the scaffolding around which our DNA wraps, appeared billions of years ago and have changed little since. But some histone genes, in an apparent reversal of this trend, have evolved much more recently and in some cases are still evolving rapidly. In a new article from Molecular biology and evolutionDr. Pravrutha Raman, postdoctoral fellow, and Dr. Harmit Malik, a professor in Fred Hutch’s Basic Sciences Division and connoisseur of genes that evolve faster than they seem to, in collaboration with Dr. Toshi Tsukiyama and the Dr. Antoine Molaro of the Institute of Genetics, Reproduction and Development has identified several new and rapidly evolving histone genes in mammals.
Histone genes can be broadly categorized into main and variant genes. Ancient and extremely conserved base histones (H2A, H2B, H3, and H4) “package genomes after DNA replication,” the authors write. “In contrast, histone variants promote specialized chromatin functions, including DNA repair, genome stability, and epigenetic inheritance.” While a number of variant histone proteins have already been identified, the group noted that very few variants of the H2B protein have been identified in animals. This suggests that our understanding of the histone repertoire in animals may be incomplete. They closely examined 18 mammalian genomes to identify regions showing homology with known histone variants. “We were able to obtain an almost complete list of all variant H2B open reading frames,” they explained, which contained considerable diversity in sequence and length. By performing phylogenetic analysis to understand the evolutionary relationships between these sequences, they found seven distinct classes of H2B variants (Figure 1), five of which are widely present in mammals.
The authors then compared the H2B variants to the H2B core protein to understand what sets these proteins apart. They found a range of differences among proteins that could affect histone function, including those with potential impacts on DNA binding or packaging, post-translational modifications of proteins, protein-protein interactions , or even those that might promote function outside the nucleus. Thus, it seems that each variant has developed a distinct function in the body.
Next, the group examined the evolutionary dynamics of each variant to determine the extent to which they diversified or remained stable during evolution. They observed high rates of purifying selection in all genes, suggesting that they likely have important biological roles and are therefore somewhat limited in the sequence changes that can be tolerated by the animal, but they also found evidence evolutionary change. All variants of H2B, for example, seemed to evolve faster than the core H2B protein, some of them much faster. Likewise, they observed that many variants had been lost or duplicated in particular animal lines. “Overall, our strong purifying selection results suggest that H2B variants perform vital functions leading to their overall retention, while our positive selection results suggest that they have been the subject of recurrent genetic innovation,” summed up the authors.
Finally, as a step towards understanding the function of these variants, the authors examined tissue-specific RNA sequencing data to determine when and where they are expressed in the body. They found that most of the variants are expressed in the testis, which is known to be a common site for the expression of histone variants. However, two of the variants were primarily expressed in the ovaries and early embryos, an “unusual site of expression for histone variants”, according to Dr Raman, suggesting the tantalizing likelihood that they evolved new functions in line with their new patterns of expression.
Dr Raman, reflecting on the importance of this work, says: “Although histones are generally highly conserved and slowly evolving, we are finding mammalian H2B variants that have highly divergent sequences and display high evolutionary turnover with gains and species-to-species losses…our work reveals that even fundamental protein repertoires like histones can be continually modified by biological forces in the germline.Looking forward, she notes that the main missing piece is an understanding of what these histone variants do.” Most mammalian H2B variants, and in particular our newly discovered H2B variants, have not been functionally characterized. We plan to use human cells to decipher the molecular properties of these histones. Additionally, germline histone variants, including some H2B variants, can be aberrantly expressed in cancer cells. We are interested in the causes and consequences of this aberrant expression on human cancers. Dr. Raman was also keen to point out that two other members of the Malik Lab, undergraduate student Callie Rominger and staff scientist Dr. Janet Young, have made significant contributions to this work.