[ad_1]

  • Greenberg, M. V. C. & Bourc’his, D. The diverse roles of DNA methylation in mammalian development and disease. Nat. Rev. Mol. Cell Biol. 20, 590–607 (2019).

    CAS 
    PubMed 

    Google Scholar
     

  • Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 39, 457–466 (2007).

    CAS 
    PubMed 

    Google Scholar
     

  • Stadler, M. B. et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480, 490–495 (2011).

    CAS 
    PubMed 

    Google Scholar
     

  • Xie, W. et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153, 1134–1148 (2013).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gifford, C. A. et al. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell 153, 1149–1163 (2013).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yin, Y. et al. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science 356, eaaj2239 (2017).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Luo, C., Hajkova, P. & Ecker, J. R. Dynamic DNA methylation: In the right place at the right time. Science 361, 1336–1340 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lord, T. & Oatley, J. M. Regulation of spermatogonial stem cell maintenance and self-renewal. In The Biology of Mammalian Spermatogonia 91–129 (Springer, 2017).

  • Kubo, N. et al. DNA methylation and gene expression dynamics during spermatogonial stem cell differentiation in the early postnatal mouse testis. BMC Genomics 16, 624 (2015).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bourc’his, D., Xu, G.-L., Lin, C.-S., Bollman, B. & Bestor, T. H. Dnmt3L and the establishment of maternal genomic imprints. Science 294, 2536–2539 (2001).

    PubMed 

    Google Scholar
     

  • Kaneda, M. et al. Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting. Nature 429, 900–903 (2004).

    CAS 
    PubMed 

    Google Scholar
     

  • Barau, J. et al. The DNA methyltransferase DNMT3C protects male germ cells from transposon activity. Science 354, 909–912 (2016).

    CAS 
    PubMed 

    Google Scholar
     

  • Bourc’his, D. & Bestor, T. H. Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431, 96–99 (2004).

    PubMed 

    Google Scholar
     

  • Zamudio, N. et al. DNA methylation restrains transposons from adopting a chromatin signature permissive for meiotic recombination. Genes Dev. 29, 1256–1270 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yaman, R. & Grandjean, V. Timing of entry of meiosis depends on a mark generated by DNA methyltransferase 3a in testis. Mol. Reprod. Dev. 73, 390–397 (2006).

    CAS 
    PubMed 

    Google Scholar
     

  • Kato, Y. et al. Role of the Dnmt3 family in de novo methylation of imprinted and repetitive sequences during male germ cell development in the mouse. Hum. Mol. Genet. 16, 2272–2280 (2007).

    CAS 
    PubMed 

    Google Scholar
     

  • Lengner, C. J. et al. Oct4 expression is not required for mouse somatic stem cell self-renewal. Cell Stem Cell 1, 403–415 (2007).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shovlin, T. C. et al. Sex-specific promoters regulate Dnmt3L expression in mouse germ cells. Hum. Reprod. 22, 457–467 (2007).

    CAS 
    PubMed 

    Google Scholar
     

  • Shirane, K., Miura, F., Ito, T. & Lorincz, M. C. NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing. Nat. Genet. 52, 1088–1098 (2020).

    PubMed 

    Google Scholar
     

  • Okano, M., Bell, D. W., Haber, D. A. & Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247–257 (1999).

    CAS 
    PubMed 

    Google Scholar
     

  • Ohinata, Y. et al. Blimp1 is a critical determinant of the germ cell lineage in mice. Nature 436, 207–213 (2005).

    CAS 
    PubMed 

    Google Scholar
     

  • Yoshida, S. et al. The first round of mouse spermatogenesis is a distinctive program that lacks the self-renewing spermatogonia stage. Development 133, 1495–1505 (2006).

    CAS 
    PubMed 

    Google Scholar
     

  • Law, N. C., Oatley, M. J. & Oatley, J. M. Developmental kinetics and transcriptome dynamics of stem cell specification in the spermatogenic lineage. Nat. Commun. 10, 2787 (2019).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chan, F. et al. Functional and molecular features of the Id4+ germline stem cell population in mouse testes. Genes Dev. 28, 1351–1362 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Helsel, A. R. et al. ID4 levels dictate the stem cell state in mouse spermatogonia. Development 144, 624–634 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lord, T. & Oatley, J. M. A revised Asingle model to explain stem cell dynamics in the mouse male germline. Reproduction 154, R55–R64 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hermann, B. P. et al. The mammalian spermatogenesis single-cell transcriptome, from spermatogonial stem cells to spermatids. Cell Rep. 25, 1650–1667.e8 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Green, C. D. et al. A comprehensive roadmap of murine spermatogenesis defined by single-cell RNA-seq. Dev. Cell 46, 651–667.e10 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vasiliauskaitė, L. et al. Defective germline reprogramming rewires the spermatogonial transcriptome. Nat. Struct. Mol. Biol. 25, 394–404 (2018).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Roy Choudhury, D. et al. Microarray-based analysis of cell-cycle gene expression during spermatogenesis in the mouse. Biol. Reprod. 83, 663–675 (2010).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Suzuki, S., McCarrey, J. R. & Hermann, B. P. An mTORC1-dependent switch orchestrates the transition between mouse spermatogonial stem cells and clones of progenitor spermatogonia. Cell Rep. 34, 108752 (2021).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • La Manno, G. et al. RNA velocity of single cells. Nature 560, 494–498 (2018).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • King, A. D. et al. Reversible regulation of promoter and enhancer histone landscape by DNA methylation in mouse embryonic stem cells. Cell Rep. 17, 289–302 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jermann, P., Hoerner, L., Burger, L. & Schubeler, D. Short sequences can efficiently recruit histone H3 lysine 27 trimethylation in the absence of enhancer activity and DNA methylation. Proc. Natl Acad. Sci. U S A 111, E3415–E3421 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Brinkman, A. B. et al. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res. 22, 1128–1138 (2012).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cheng, K. et al. Unique epigenetic programming distinguishes regenerative spermatogonial stem cells in the developing mouse testis. iScience 23, 101596 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yamanaka, S. et al. Broad heterochromatic domains open in gonocyte development prior to de novo DNA methylation.Dev. Cell 51, 21–34.e5 (2019).

    CAS 
    PubMed 

    Google Scholar
     

  • Kawabata, Y. et al. Sex-specific histone modifications in mouse fetal and neonatal germ cells. Epigenomics 11, 543–561 (2019).

    CAS 
    PubMed 

    Google Scholar
     

  • Smith, A. M. et al. A novel mode of enhancer evolution: the Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity. Genome Res. 18, 1422–1432 (2008).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Domcke, S. et al. Competition between DNA methylation and transcription factors determines binding of NRF1. Nature 528, 575–579 (2015).

    CAS 
    PubMed 

    Google Scholar
     

  • Lea, A. J. et al. Genome-wide quantification of the effects of DNA methylation on human gene regulation. Elife 7, 1–27 (2018).


    Google Scholar
     

  • Stephens, D. C. & Poon, G. M. K. Differential sensitivity to methylated DNA by ETS-family transcription factors is intrinsically encoded in their DNA-binding domains. Nucleic Acids Res. 44, 8671–8681 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

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

    PubMed 

    Google Scholar
     

  • Zhang, T., Oatley, J., Bardwell, V. J. & Zarkower, D. DMRT1 is required for mouse spermatogonial stem cell maintenance and replenishment. PLoS Genet. 12, e1006293 (2016).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wu, H. et al. Dnmt3a-dependent nonpromoter DNA methylation facilitates transcription of neurogenic genes. Sci. (80-.). 329, 444–448 (2010).

    CAS 

    Google Scholar
     

  • Izzo, F. et al. DNA methylation disruption reshapes the hematopoietic differentiation landscape. Nat. Genet. 52, 378–387 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ketkar, S. et al. Remethylation of Dnmt3a−/− hematopoietic cells is associated with partial correction of gene dysregulation and reduced myeloid skewing. Proc. Natl Acad. Sci. U S A 117, 3123–3134 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Challen, G. A. et al. Dnmt3a is essential for hematopoietic stem cell differentiation. Nat. Genet. 44, 23–31 (2012).

    CAS 

    Google Scholar
     

  • Jeong, M. et al. Loss of Dnmt3a immortalizes hematopoietic stem cells in vivo. Cell Rep. 23, 1–10 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lewandoski, M., Wassarman, K. M. & Martin, G. R. Zp3–cre, a transgenic mouse line for the activation or inactivation of loxP-flanked target genes specifically in the female germ line. Curr. Biol. 7, 148–151 (1997).

    CAS 
    PubMed 

    Google Scholar
     

  • Miura, F. et al. Highly efficient single-stranded DNA ligation technique improves low-input whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. Nucleic Acids Res. 47, e85–e85 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Skene, P. J. & Henikoff, S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. Elife 6, 1–35 (2017).


    Google Scholar
     

  • Didion, J. P., Martin, M. & Collins, F. S. Atropos: specific, sensitive, and speedy trimming of sequencing reads. PeerJ 5, e3720 (2017).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Illingworth, R. S. et al. Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet. 6, e1001134 (2010).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Feng, H., Conneely, K. N. & Wu, H. A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data. Nucleic Acids Res. 42, e69–e69 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).

    CAS 

    Google Scholar
     

  • Velte, E. K. et al. Differential RA responsiveness directs formation of functionally distinct spermatogonial populations at the initiation of spermatogenesis in the mouse. Development 146, dev173088 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Qiu, X. et al. Reversed graph embedding resolves complex single-cell trajectories. Nat. Methods 14, 979–982 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lane, N. et al. Resistance of IAPs to methylation reprogramming may provide a mechanism for epigenetic inheritance in the mouse. Genesis 35, 88–93 (2003).

    CAS 
    PubMed 

    Google Scholar
     

  • Zhou, Y. et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun. 10, 1523 (2019).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • [ad_2]

    Source link