Enzymatic cleavage of histone H3: a new consideration when measuring histone modifications in human samples
Clinical Epigenetics volume 7, Article number: 7 (2015)
Histone modifications are increasingly being used as biomarkers of cancer prognosis and survival. However, we identified a cleavage product of histone H3 in human peripheral blood mononuclear cells, which interferes with measures of certain H3 modifications. Therefore, the potential for enzymatic cleavage of histones should be considered when measuring histone modifications in human samples. Furthermore, the enzymatic cleavage of human H3 is itself a fascinating area of research and two important questions remain to be answered: 1) Does cleavage of human H3 occur in vivo, as it does in other organisms? and 2) Does it serve a biologically important function?
Enzymatic cleavage of histones
Histone modifications are increasingly being used as biomarkers of cancer prognosis . However, histones are very sensitive to enzymatic degradation by proteases , and there is evidence from many organisms that histones are enzymatically cleaved in vivo; this topic is receiving increasing attention and has been reviewed recently by several groups [3-5]. Enzymatic cleavage of H3 has been observed in tetrahymena , yeast [7,8], chicken , quail , and mouse [11,12]. Furthermore, certain viruses can cleave host cell H3 [13,14], and antimicrobial peptides derived from the N-terminal region of various histones (e.g., H2A, H2B, H1) have been identified in several organisms, including fish [15-20], molluscs [21,22], frogs , and even from the gastrointestinal tract  and wound fluids  of humans.
Until recently, there were few reports of histone cleavage in human cells. However, last year, Vossaert et al. reported histone H3 clipping in human embryonic stem cell (ESC) lines , and our group recently identified a cleavage product of H3 in human peripheral blood mononuclear cells (PBMCs) (Figure 1). We observe this H3 cleavage product in spite of the use of protease inhibitors during histone isolation, including a protease inhibitor cocktail (Roche), which inhibits enzymatic cleavage of H3 in human ESCs , and E-64, which inhibits cathepsins, including Cathepsin L, which cleaves H3 in mouse ESCs . The H3 cleavage product that we observe in human PBMCs is similar in size to the H3 cleavage product observed in mouse ESCs . Extensive cleavage of H3 is observed in approximately one-third of these PBMC histone samples (Figure 2).
Based on Western blot, we have determined that H3 cleavage interferes with the measurement of certain histone modifications. Figure 1A illustrates the known enzymatic cleavage sites in H3 for mouse ESCs . In Figure 1B, Western blots illustrate total H3 (top panel) with varying degrees of histone cleavage for 11 representative PBMC histone samples that were collected from participants enrolled in the Folic Acid and Creatine Trial (FACT), a randomized controlled trial of folic acid and creatine supplementation in Bangladeshi adults . Figure 1B also shows, for the same 11 PBMC samples, three histone modifications that vary in relation to their location on histone H3 (i.e., upstream or downstream of the cleavage sites shown in Figure 1A). For example, Figure 1B illustrates H3K9me2 (second panel), a modification located downstream of known H3 cleavage sites. Samples without large amounts of H3 cleavage (Lanes 1, 3–5, 8, 10, 11) have detectable H3K9me2. In contrast, samples with extensive cleavage of H3 (Lanes 2, 6, 7, 9) have no detectable H3K9me2. Figure 1B also illustrates H3K36me2 (third panel) and H3K79me2 (fourth panel), which are histone modifications located upstream of H3 enzymatic cleavage sites; H3K36me2 is located in the tail region of H3, and H3K79me2 is located in the core domain of H3 (Figure 1A). H3K36me2 and H3K79me2 can be detected both in the 17-kDa band of H3 that has not been cleaved and in the <17-kDa bands of H3 that have been cleaved (Figures 1B and 2). H3 cleavage is also detectable in histones from calf thymus (Figure 2). This has been described previously by several groups [3,29]. Similarly, cleavage of calf thymus H3 does not interfere with upstream histone modifications, such as H3K79me2 (Figure 2). Collectively, these data suggest that H3 cleavage only influences the ability to detect histone modifications that are situated downstream of histone cleavage sites.
Implications for molecular epidemiology studies
Since it is unclear when enzymatic cleavage of H3 occurs in human PBMC samples, it is difficult to know if it is of biological or methodological interest. Regardless, enzymatic cleavage of H3 has important implications for measuring global histone modifications in human samples. Currently, the most commonly studied histone modifications include methylation and acetylation marks on H3K4, H3K9, and H3K27, which all fall within the N-terminal tail region of H3. However, the portion of H3 that is clipped off in mouse and human cells includes these residues. Thus, measures of marks on H3K4, H3K9, and H3K27 may be underestimated if samples have experienced enzymatic cleavage of H3; this is particularly true for antibody-based methods, such as ELISA and immunohistochemistry methods, which cannot take into account H3 cleavage. Modifications that lie on amino acid residues upstream of H3 enzymatic cleavage sites, such as H3K36 and H3K79, do not appear to be affected by the enzymatic cleavage of H3 and therefore can be measured accurately, regardless of cleavage.
A better understanding of when and why enzymatic cleavage of H3 occurs is essential. If enzymatic cleavage of human H3 occurs in vivo, this may be an important biological phenomenon. Alternatively, if enzymatic cleavage occurs as a result of sample collection and processing, preventive measures must be developed such that all global histone modifications on H3, including modifications on H3K4, H3K9, and H3K27, can be accurately measured. In the meantime, for banked samples previously collected for the measurement of global histone marks, Western blot can be used to check samples for enzymatic cleavage of histones. If histone cleavage products are observed in samples, it may not be appropriate to measure certain histone marks based on their location.
Embryonic stem cells
Peripheral blood mononuclear cells
Chervona Y, Costa M. Histone modifications and cancer: biomarkers of prognosis? Am J Cancer Res. 2012;2(5):589–97.
Suganuma T, Workman JL. Crosstalk among histone modifications. Cell. 2008;135(4):604–7.
Dhaenens M, Glibert P, Meert P, Vossaert L, Deforce D. Histone proteolysis: a proposal for categorization into ‘clipping’ and ‘degradation’. Bioessays. 2014;37(1):70–9.
Azad G, Tomar RS. Proteolytic clipping of histone tails: the emerging role of histone proteases in regulation of various biological processes. Mol Biol Rep. 2014;41(5):2717–30.
Zhou P, Wu E, Alam HB, Li Y. Histone cleavage as a mechanism for epigenetic regulation: current insights and perspectives. Curr Mol Med. 2014;14(9):1164–72.
David A, Bowen C, Abraham JK, Glover GN, Claiborne VC, Gorovsky MA. Proteolytic processing of histone H3 in chromatin: a physiologically regulated event in Tetrahymena micronuclei. Cell. 1980;20(1):55–64.
Santos-Rosa H, Kirmizis A, Nelson C, Bartke T, Saksouk N, Cote J, et al. Histone H3 tail clipping regulates gene expression. Nat Struct Mol Biol. 2009;16(1):17–22.
Xue Y, Vashisht AA, Tan Y, Su T, Wohlschlegel JA. PRB1 is required for clipping of the histone H3 N terminal tail in Saccharomyces cerevisiae. PLoS One. 2014;9(2):e90496.
Mandal P, Azad GK, Tomar RS. Identification of a novel histone H3 specific protease activity in nuclei of chicken liver. Biochem Biophys Res Commun. 2012;421(2):261–7.
Mahendra G, Kanungo MS. Age-related and steroid induced changes in the histones of the quail liver. Arch Gerontol Geriatr. 2000;30(2):109–14.
Duncan E, Muratore-Schroeder TL, Cook RG, Garcia BA, Shabanowitz J, Hunt DF, et al. Cathepsin L proteolytically processes histone H3 during mouse embryonic stem cell differentiation. Cell. 2008;135(2):284–94.
Khalkhali-Ellis Z, Goossens W, Margaryan NV, Hendrix MJ. Cleavage of histone 3 by Cathepsin D in the involuting mammary gland. PLoS One. 2014;9(7):e103230.
Falk M, Grigera PR, Bergmann IE, Zibert A, Multhaup G, Beck E. Foot-and-mouth disease virus protease 3C induces specific proteolytic cleavage of host cell histone H3. J Virol. 1990;64(2):748–56.
Tesar M, Marquardt O. Foot-and-mouth disease virus protease 3C inhibits cellular transcription and mediates cleavage of histone H3. Virology. 1990;174(2):364–74.
Cho J, Park IY, Kim HS, Lee WT, Kim MS, Kim SC. Cathepsin D produces antimicrobial peptide parasin I from histone H2A in the skin mucosa of fish. FASEB J. 2002;16(3):429–31.
Birkemo G, Lüders T, Andersen Ø, Nes IF, Nissen-Meyer J. Hipposin, a histone-derived antimicrobial peptide in Atlantic halibut (Hippoglossus hippoglossus L.). Biochim Biophys Acta. 2003;1646(1):207–15.
Lüders T, Birkemo GA, Nissen-Meyer J, Andersen Ø, Nes IF. Proline conformation-dependent antimicrobial activity of a proline-rich histone H1 N-terminal peptide fragment isolated from the skin mucus of Atlantic salmon. Antimicrob Agents Chemother. 2005;49(6):2399–406.
Sathyan N, Philip R, Chaithanya ER, Anil Kumar PR, Sanjeevan VN, Singh IS. Characterization of Histone H2A derived antimicrobial peptides, Harriottins, from Sicklefin Chimaera Neoharriotta pinnata (Schnakenbeck, 1931) and its evolutionary divergence with respect to CO1 and Histone H2A. ISRN Mol Biol. 2013;2013:1–10.
Anil Kumar P. Molecular characterization and phylogenetic analysis of a histone-derived antimicrobial peptide teleostin from the marine teleost fishes, Tachysurus jella and Cynoglossus semifasciatus. ISRN Mol Biol. 2013;2013:1–7.
Park I, Park CB, Kim MS, Kim SC. Parasin I, an antimicrobial peptide derived from histone H2A in the catfish, Parasilurus asotus. FEBS Lett. 1998;437(3):258–62.
Sathyan N, Philip R, Chaithanya ER, Anil Kumar PR. Identification and molecular characterization of molluskin, a histone-H2A-derived antimicrobial peptide from molluscs. ISRN Mol Biol. 2012;2012:1–6.
De Zoysa M, Nikapitiya C, Whang I, Lee J-S, Lee J. Abhisin: a potential antimicrobial peptide derived from histone H2A of disk abalone (haliotis discus discus). Fish Shellfish Immunol. 2009;27(5):639–46.
Kawasaki H, Isaacson T, Iwamuro S, Conlon JM. A protein with antimicrobial activity in the skin of Schlegel’s green tree frog Rhacophorus schlegelii (Rhacophoridae) identified as histone H2B. Biochem Biophys Res Commun. 2003;312(4):1082–6.
Rose F, Bailey K, Keyte JW, Chan WC, Greenwood D, Mahida YR. Potential role of epithelial cell-derived histone H1 proteins in innate antimicrobial defense in the human gastrointestinal tract. Infect Immun. 1998;66(7):3255–63.
Frohm M, Gunne H, Bergman AC, Agerberth B, Bergman T, Boman A, et al. Biochemical and antibacterial analysis of human wound and blister fluid. Eur J Biochem. 1996;237(1):86–92.
Vossaert L, Meert P, Scheerlinck E, Glibert P, Van Roy N, Heindryckx B, et al. Identification of histone H3 clipping activity in human embryonic stem cells. Stem Cell Res. 2014;13(1):123–34.
Arita A, Niu J, Qu Q, Zhao N, Ruan Y, Nadas A, et al. Global levels of histone modifications in peripheral blood mononuclear cells of subjects with exposure to nickel. Environ Health Perspect. 2012;120(2):198.
Harper K, Peters BA, Gamble MV. Batch effects and pathway analysis: two potential perils in cancer studies involving DNA methylation array analysis. Cancer Epidemiol Biomarkers Prev. 2013;22(6):1052–60.
Huyen Y, Zgheib O, DiTullio Jr RA, Gorgoulis VG, Zacharatos P, Petty TJ, et al. Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks. Nature. 2004;432(7015):406–11.
This work was supported by funding from NIH grants P42 ES10349 and RO1 CA133595.
The authors declare that they have no competing interests.
CGH completed the laboratory analyses and wrote the letter with feedback from MVG. The samples described in this letter were collected for a study designed by MVG. Both authors read and approved the final manuscript.
About this article
Cite this article
Howe, C.G., Gamble, M.V. Enzymatic cleavage of histone H3: a new consideration when measuring histone modifications in human samples. Clin Epigenet 7, 7 (2015). https://doi.org/10.1186/s13148-014-0041-5