A focus on histone modifications in development and disease

The DNA of eukaryotes is not naked; instead, it is packed in a membrane-bound nucleus as a nucleoprotein complex called chromatin. This complex consists of proteins and nucleic acids in about a 50/50 mix. 

Histone proteins are a key component of chromatin. These small proteins help compact the DNA and carry several dynamic posttranslational modifications associated with local activity. These include acetylation, methylation and many others that directly or indirectly prepare the region of the genome for cellular functions including DNA replication, DNA damage response and gene transcription. 

Numerous studies highlight the significance of histone mutations in developmental disorders and cancers, shedding light on the intricate interplay between chromatin structure and cellular function. 

Modifications of histone proteins and DNA in chromatin are often interconnected. A well-studied example of such cross-regulation is histone H3 methylations at lysines 27 and 36 and DNA methylation. So-called methylation writer enzymes are said to read each other’s marks and deposit their own modifications accordingly. Mutations in these histone and DNA methylation enzymes cause a class of developmental disorders that present with abnormal childhood growth, intellectual disability and sometimes components of autism spectrum disorder. 

Courtesy of Alexey Soshnev

Four histone types, top, together with associated DNA, make up the nucleosome core particle, the basic subunit of chromatin. The fifth type, linker histone H1, bottom, dynamically associates with the nucleosomes and facilitates chromatin condensation.

Alexey Soshnev and his team at the University of Texas at San Antonio study the role of linker histone H1 in gene expression and chromatin structure. “Linker histone H1 serves as the ultimate compaction machine of the chromatin,” Soshnev said.

They and collaborators previously found that H1 stimulates the function of the H3 lysine 27-specific methyltransferase Polycomb Repressive Complex 2, or PRC2, and negatively regulates H3 lysine 36-specific methyltransferases. 

While studying how individual mutations in H1 genes contribute to progression of blood cancer lymphoma, graduate student Dustin Fetch and undergraduate assistant Amina Jumamyradova in Soshnev’s lab focused on an unusual mutation cluster. Unlike the missense mutations, where DNA change alters a single amino acid, these mutations cause a shift of the reading frame during mRNA translation, meaning that a section of the protein is replaced by an entirely different sequence of amino acids. 

Although these frameshift mutations never happen in lymphoma, they were reported in over 100 unrelated patients diagnosed with a developmental disorder that had clinical features of abnormal childhood growth and intellectual disability – similar to the syndromes caused by mutations in DNA- and histone H3-methyltransferase genes, and suggesting that a common pathway is disrupted. 

However, this specific mutation does not appear to affect the activity of any of the other chromatin factors, indicating that all four may converge on a common target downstream that in turn contributes to the development of these disorders. 

The team is now focused on identifying this common target and validating its role in cell culture and animal models. By unraveling the molecular mechanisms underlying these mutations, they hope to gain insights into the causes of developmental disorders and potentially identify new therapeutic targets. 

Research assistant Cameron Chapa and a team in Soshnev’s lab have studied the gain and loss of histone H3 lysine 27 methylation in embryonic stem cells and pluripotency. Typically, this methylation is associated with gene repression and chromatin compaction, which plays a crucial role in regulating pluripotency and differentiation. 

This team found that the level of H3 lysine 27 methylation correlates with the expression of stemness markers, indicating a positive relationship the researchers did not expect. To understand the mechanism, researchers manipulated polycomb components and found that both loss and gain of lysine 27 methylation induce pluripotency phenotypes. The researchers hypothesized that so-called reader proteins interpret H3 lysine 27 methylation to drive chromatin compaction, and two opposite mechanisms — erasing the mark or filling in gaps — may lead to a similar final outcome. The team’s study suggests a complex interplay between histone modifications and chromatin structure. 

Courtesy of Alexey Soshnev

Left to right, Dustin Fetch, Cameron Chapa and Amina Jumamyradova will present research from Alexey Soshnev’s lab at Discover BMB in San Antonio.

Further research is needed to validate these findings and determine their biological significance, especially regarding the role of histone H3 lysine 27 methylation in early stem cell development. Recent work by Leonid Mirny proposes that the quantity of a writer is crucial for maintaining chromatin modification memory during cell divisions, so the team now wants to explore how lysine 27 methylation expansion might influence epigenetic memory in stem cells.

Studies of histone modifications and mutations present their own challenges. The intricate web of interactions among chromatin-modifying enzymes, histone variants and DNA-binding proteins challenges researchers who attempt to unravel the complexities of epigenetic regulation. For example, labs rely on antibodies for many chromatin assays, introducing potential biases and limitations, underscoring the need for rigorous experimental validation and cross-validation. 

The research can lead to unexpected discoveries. For example, over a decade ago Aaron Goldberg and Laura Banaszynski — then in the Allis lab at Rockefeller  — found out that histone variant H3.3 has a dual role in chromatin, contributing to both active and repressive genomic regions. Such findings highlight the complexity of histone research and suggest that other histones and modifications may have undiscovered functions.

 “This came as a huge surprise but opened up a whole new field of study,” Soshnev said. “I have a feeling that other histones and histone modifications, which we label as singularly ‘active’ and ‘repressive,’ behave the same way, and have a shadow life elsewhere in the genome. 

“It is an exciting field, and a great time to be doing science.”