08 January, 2025
As an epigeneticist, my knowledge of histones largely centres around what they do in the confined space of the nucleus, and how these bead-like proteins, particularly their ‘tails’ are modified to regulate the access of cellular machinery to DNA, which allows for gene expression to be switched on or off. However, it is becoming increasingly clear that histones have functional roles outside of the genomic architecture, and as more is revealed about the function of histones outside of the nucleus and the cell, we are left asking more questions.
Histones as storage molecules
There is estimated to be approximately two metres of DNA in a human cell, so how is this all packaged into the nucleus of the cell on a microscopic scale? The answer lies in histones. Histones help wind up DNA so that it fits into the nucleus. About 147 base pairs of DNA wraps around a histone, then eight histone proteins cluster together to form what is known as a nucleosome and together these chains of nucleosomes form chromatin, which makes up chromosomes (Figure 1a).
But if all the DNA is wrapped up and condensed, how do cells access the DNA in order to express genes and make proteins, or change which parts of the genome can be used in response to environmental cues? This is what some research groups within the Epigenetics programme at the Babraham Institute are interested in, and it is something that I am investigating during my PhD.
A central mechanism regulating chromatin structure is through histone post translational modifications (PTMs). At a basic level, histones can be modified by enzymes which add or remove chemical marks (PTMs) to the histones. These modifications either directly or indirectly control the structure of chromatin, by closing or silencing regions of chromatin (heterochromatin), or opening the chromatin (euchromatin) and allowing for gene expression (Figure 1b). This process is dynamic and allows for tightly regulated gene expression. However, it is now clear that histone functionality is not confined to the storage and regulation of genetic material.
Histones as antimicrobials
As far back as the 1940s, histones were known to have antimicrobial properties, however a tangible link to this property was not made until 2004 when Brinkmann and their team showed that a type of immune cell, called neutrophils, can release histones and DNA into the space between cells by a process called NETosis.
In response to pathogens, the neutrophils undergo a controlled cell death, where their cellular contents are expelled into the extracellular space (Figure 2). Histones are a major component of neutrophil extracellular traps (NETs) and kill microbes that become trapped in the web-like DNA. Specifically, the DNA serves as a net to trap and localise the microbes, and ensures a high concentration of antimicrobial agents (histones and other granular proteins) to kill the microbes.
Chromatin expulsion is not a process confined to immune cells, it has been shown that when cancer cells undergo apoptosis, they can expel their chromatin into the extracellular space, this has been termed nuclear expulsion, and has been shown to promote metastasis.
Histones as danger signals
Normally, when cells reach the end of their lifespan they receive signals which trigger a type of controlled cell death called apoptosis, resulting in the release of cell fragments, which can contain histones. In addition to this, in response to damage or extreme stress, cells can also undergo a type of uncontrolled cell death, known as necrosis where the cell membrane ruptures and the cellular contents spill out. Both types of cell death can result in the release of histones and DNA into the extracellular space.
In this circumstance, the histones act as warning signals to alert other cells close by that there is cellular damage. Specifically, the histones bind to and interact with toll-like receptors (TLRs) on cells which promotes inflammation.
For this reason, abnormal levels of histones in circulation are drivers of inflammation in the presence of pathogens, but also in the absence of pathogens (sterile inflammation). This means they have been linked to lots of health issues such as sepsis, rheumatoid arthritis, and cancer progression. In fact, the increased awareness of histones as drivers of certain diseases has resulted in development of histone neutralising polyanions, which have proven successful in alleviating mice models of sepsis.
Histones as enzymes
It has been suggested that originally, histones were thought to protect the genome from damage that may have resulted from the extreme environments that certain organisms such as archaea were found in, as opposed to facilitating genetic regulation. To this end, Kurdistani and colleagues discovered that histone H3 and H4 can bind to copper ions and enzymatically reduce them. It is thought, in an evolutionary context, this function helped organisms such as archaea protect themselves from otherwise damaging increases in atmospheric oxygen concentrations.
Emerging role of histones in cell signalling
Aside from histones now well-established roles in the innate immune response, inflammatory disease, and cancer, there is emerging evidence which indicates that extracellular histones may have more widespread roles in cell signalling. For example, it has been shown that histones from NETs can bind to toll-like receptor 2 on naïve T-cells- a type of stem cell- which promotes their differentiation into T-helper 17 cells.
In addition, researchers have shown that when extracellular histone concentrations remain low, they promote a type of cell recycling required for normal cell function (autophagy). However, when histone concentrations are high and exceed a threshold, they promote apoptosis. These findings suggest there is a fine line between histone levels that can orchestrate a tuned signalling response and those that are cytotoxic and detrimental to the cell.
What might we find next?
There is still a lot we do not know, indeed our work in the Christophorou lab aims to uncover more insights into the extracellular functions of histones, we believe we are only just scratching the surface of what these proteins may be doing. If you are interested in reading more about unconventional functions of histones, please see our recently published review: ‘Fantastic proteins and where to find them- histones, in the nucleus and beyond’. It is a really exciting field of research; watch this space!
Read the Christophorou lab review in the Journal of Cell Science: Fantastic proteins and where to find them – histones, in the nucleus and beyond
Further reading
Attar, N., Campos, O. A., Vogelauer, M., Cheng, C., Xue, Y., Schmollinger, S., Salwinski, L., Mallipeddi, N. V., Boone, B. A., Yen, L., et al. (2020). The histone H3-H4 tetramer is a copper reductase enzyme. Science 369, 59–64.
Brinkmann, V., Reichard, U., Goosmann, C., Fauler, B., Uhlemann, Y., Weiss, D.S., Weinrauch, Y. and Zychlinsky, A., 2004. Neutrophil extracellular traps kill bacteria. Science (New York, N.Y.) [Online], 303(5663), pp.1532–1535. Available from: https://doi.org/10.1126/science.1092385.
Ibañez-Cabellos, J.S., Aguado, C., Pérez-Cremades, D., García-Giménez, J.L., Bueno-Betí, C., García-López, E.M., Romá-Mateo, C., Novella, S., Hermenegildo, C. and Pallardó, F.V., 2018. Extracellular histones activate autophagy and apoptosis via mTOR signaling in human endothelial cells. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease [Online], 1864(10), pp.3234–3246. Available from: https://doi.org/10.1016/j.bbadis.2018.07.010.
Park, W.-Y., Gray, J.M., Holewinski, R.J., Andresson, T., So, J.Y., Carmona-Rivera, C., Hollander, M.C., Yang, H.H., Lee, M., Kaplan, M.J., Cappell, S.D. and Yang, L., 2023. Apoptosis-induced nuclear expulsion in tumor cells drives S100a4-mediated metastatic outgrowth through the RAGE pathway. Nature Cancer [Online], 4(3), pp.419–435. Available from: https://doi.org/10.1038/s43018-023-00524-z.
Wilson, A.S., Randall, K.L., Pettitt, J.A., Ellyard, J.I., Blumenthal, A., Enders, A., Quah, B.J., Bopp, T., Parish, C.R. and Brüstle, A., 2022. Neutrophil extracellular traps and their histones promote Th17 cell differentiation directly via TLR2. Nature Communications [Online], 13(1), p.528. Available from: https://doi.org/10.1038/s41467-022-28172-4.
Xu, J., Zhang, X., Monestier, M., Esmon, N.L. and Esmon, C.T., 2011. Extracellular Histones Are Mediators of Death through TLR2 and TLR4 in Mouse Fatal Liver Injury. The Journal of Immunology [Online], 187(5), pp.2626–2631. Available from: https://doi.org/10.4049/jimmunol.1003930.
Image description: Extracellular histones marked by citrullination (red). DNA in blue. Credit: Johanna Grinat
08 January 2025
By Noah Shriever