Kadauke, S. & Blobel, G. A. Chromatin loops in gene regulation. Biochim. Biophys. Acta 1789, 17–25 (2009).

Article  CAS  PubMed  Google Scholar 

Holwerda, S. & de Laat, W. Chromatin loops, gene positioning, and gene expression. Front. Genet. 3, 217 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zheng, H. & Xie, W. The role of 3D genome organization in development and cell differentiation. Nat. Rev. Mol. Cell Biol. 20, 535–550 (2019).

Article  CAS  PubMed  Google Scholar 

Misteli, T. The self-organizing genome: principles of genome architecture and function. Cell 183, 28–45 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stadhouders, R., Filion, G. J. & Graf, T. Transcription factors and 3D genome conformation in cell-fate decisions. Nature 569, 345–354 (2019).

Article  CAS  PubMed  Google Scholar 

Kubo, N. et al. Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. Nat. Struct. Mol. Biol. 28, 152–161 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Olbrich, T. et al. CTCF is a barrier for 2C-like reprogramming. Nat. Commun. 12, 4856 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Griswold, M. D. Spermatogenesis: the commitment to meiosis. Physiol. Rev. 96, 1–17 (2016).

Article  CAS  PubMed  Google Scholar 

Song, H. W. & Wilkinson, M. F. Transcriptional control of spermatogonial maintenance and differentiation. Semin. Cell Dev. Biol. 30, 14–26 (2014).

Article  PubMed  Google Scholar 

Alavattam, K. G., Maezawa, S., Andreassen, P. R. & Namekawa, S. H. Meiotic sex chromosome inactivation and the XY body: a phase separation hypothesis. Cell. Mol. Life Sci. 79, 18 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Sasaki, K. & Sangrithi, M. Developmental origins of mammalian spermatogonial stem cells: new perspectives on epigenetic regulation and sex chromosome function. Mol. Cell. Endocrinol. 573, 111949 (2023).

Article  CAS  PubMed  Google Scholar 

Kitamura, Y. & Namekawa, S. H. Epigenetic priming in the male germline. Curr. Opin. Genet. Dev. 86, 102190 (2024).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lesch, B. J., Dokshin, G. A., Young, R. A., McCarrey, J. R. & Page, D. C. A set of genes critical to development is epigenetically poised in mouse germ cells from fetal stages through completion of meiosis. Proc. Natl Acad. Sci. USA 110, 16061–16066 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hasegawa, K. et al. SCML2 establishes the male germline epigenome through regulation of histone H2A ubiquitination. Dev. Cell 32, 574–588 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sin, H. S., Kartashov, A. V., Hasegawa, K., Barski, A. & Namekawa, S. H. Poised chromatin and bivalent domains facilitate the mitosis-to-meiosis transition in the male germline. BMC Biol. 13, 53 (2015).

Article  PubMed  PubMed Central  Google Scholar 

Tomizawa, S. I. et al. Kmt2b conveys monovalent and bivalent H3K4me3 in mouse spermatogonial stem cells at germline and embryonic promoters. Development 145, dev169102 (2018).

Article  PubMed  Google Scholar 

Maezawa, S. et al. Super-enhancer switching drives a burst in gene expression at the mitosis-to-meiosis transition. Nat. Struct. Mol. Biol. 27, 978–988 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Turner, J. M. Meiotic silencing in mammals. Annu. Rev. Genet 49, 395–412 (2015).

Article  CAS  PubMed  Google Scholar 

Abe, H. et al. The initiation of meiotic sex chromosome inactivation sequesters DNA damage signaling from autosomes in mouse spermatogenesis. Curr. Biol. 30, 408–420 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alavattam, K. G. et al. Attenuated chromatin compartmentalization in meiosis and its maturation in sperm development. Nat. Struct. Mol. Biol. 26, 175–184 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Vara, C. et al. Three-dimensional genomic structure and cohesin occupancy correlate with transcriptional activity during spermatogenesis. Cell Rep. 28, 352–367 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Luo, Z. et al. Reorganized 3D genome structures support transcriptional regulation in mouse spermatogenesis. iScience 23, 101034 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang, Y. et al. Reprogramming of meiotic chromatin architecture during spermatogenesis. Mol. Cell 73, 547–561.e6 (2019).

Article  CAS  PubMed  Google Scholar 

Zuo, W. et al. Stage-resolved Hi-C analyses reveal meiotic chromosome organizational features influencing homolog alignment. Nat. Commun. 12, 5827 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Patel, L. et al. Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase. Nat. Struct. Mol. Biol. 26, 164–174 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bolcun-Filas, E. et al. A-MYB (MYBL1) transcription factor is a master regulator of male meiosis. Development 138, 3319–3330 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Maezawa, S., Yukawa, M., Alavattam, K. G., Barski, A. & Namekawa, S. H. Dynamic reorganization of open chromatin underlies diverse transcriptomes during spermatogenesis. Nucleic Acids Res. 46, 593–608 (2018).

Article  CAS  PubMed  Google Scholar 

Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bonev, B. et al. Multiscale 3D genome rewiring during mouse neural development. Cell 171, 557–572 (2017).

Article  CAS  PubMed