The Sperm Epigenome: 4D structure


Since the inception of my laboratory, we have focused our efforts on understanding the fundamentals of how two meters of DNA are packaged into the sperm nucleus to achieve a structure that is 13-times more compact than its oocyte complement. We developed the first humanized mouse model that faithfully recapitulates the expression of the entire suite of genes contained within the domain (1,2,3). This model system presented a pathway toward epigenetic analysis from a structural perspective. Our early clinical and mechanistic analyses showed that deletion of nuclear matrix attachment sites inhibited the expression of the protamine locus. In humans, this hampered histone replacement (4). Functional rescue of the human protamine locus was achieved with the insertion of nuclear matrix attachment sites in our humanized mouse model (5).

In sperm, these sites, and those surrounding promoters, remain histone bound even in this protamine compacted crystal-like structure. This observation led to the question: is this an exception to a rule or a fundamental property of the protamine packaged sperm nuclear genome? Resolution came with publishing the first genome-wide positioning of histones retained in both mouse and human sperm (6,7). This work revealed an additional layer of well-positioned nucleosomal bound CTCF sites segmenting the genome. Their frequency and distribution bore a marked resemblance to Topological Associated Domains observed in somatic cells (8), suggesting a preserved fundamental structure in the male somatic and gamete nucleus. This, along with our early clinical and structural studies (9), highlighted the significance of 4D structure (10) in the formation of healthy sperm.


  1. Choudhary, S. K, Wykes, S.M., Kramer, J.A., Mohamed, A.N., Koppitch, F., Nelson, J.E. and Krawetz, S.A. (1995) A Haploid expressed gene cluster exists as a single chromatin domain in human sperm. (pdf) (pdf) The Journal of Biological Chemistry 270:8755-8762.  PMID: 7721781
  2. Kramer, J.A., McCarrey, J. R., Djakiew, D. and Krawetz, S.A. (1998) Differentiation: the selective potentiation of chromatin domains.  (pdf) Development 125:4749-4755.  PMID: 9806923
  3. Kramer, J.A., McCarrey, J.R., Djakiew, D. and Krawetz, S.A. (2000) Human spermatogenesis as a model to examine gene potentiation. Molecular Reproduction and Development 56:254-258.  PMID: 10824979
  4. Kramer, J.A., Zhang, S., Yaron, Y., Zhao, Y. and Krawetz, S.A. (1997) Genetic testing for male infertility: a postulated role for mutations in sperm nuclear matrix attachment regions.  Genetic Testing 1:125-129.  PMID: 10464636
  5. Martins, R. P. and Krawetz, S.A. (2007) Decondensing the protamine domain for transcription.  (pdf) Proceedings of the National Academy of Sciences (U.S.A.) 104:8340-8345.  PMID: 17483471
  6. Wykes, S.M. and Krawetz, S.A. (2003) The Structural Organization of Sperm Chromatin, Journal of Biological Chemistry (pdf)278:29471-29477.  PMID: 12775710
  7. Arpanahi, A., Brinkworth, M., Iles, D., Krawetz, S.A., Paradowska, A., Platts, A.E., Saida, M., Steger, K., Tedder, P. and Miller, D. (2009) Endonuclease-sensitive regions of human spermatozoal chromatin are highly enriched in promoter and CTCF binding sequences. (pdf) Genome Research. 19:1338-1349.  PMID: 19584098
  8. Johnson, G.D., Jodar, M., Pique-Regi, R., Krawetz, S.A., (2016) Nuclease Footprints in Sperm Project Past and Future Chromatin Regulatory Events, Scientific Reports. (pdf)  6:25864 PMID: 27184706
  9. Martins, R.P., Ostermeier, G.C. and Krawetz, S.A. (2004) Nuclear matrix interactions at the human protamine domain: a working model of potentiation. (pdf)  Journal of Biological Chemistry 279:51862-51868.  PMID: 15452126
  10. Kocer, A., Henry-Berger, J., Noblanc, A., Champroux, A., Pogorelcnik, R., Guiton, R., Janny, L., Pons Rejraji, H., Saez, F., Johnson, G.D., Krawetz, S.A., Alvarez, J.G., Aitken, R.J., and Drevet, J.R. (2015) Oxidative DNA damage in mouse sperm chromosomes: Size matters. Free Radic Biol Med. 89:993-1002. PMID: 26510519