Abstract
Centromeres are defined epigenetically by the histone H3 variant CENP-A. The propagation cycle by which pre-existing CENP-A nucleosomes serve as templates for nascent assembly predicts the epigenetic memory of weakened centromeres. Using a mouse model with reduced levels of CENP-A nucleosomes, we find that an embryonic plastic phase precedes epigenetic memory through development. During this phase, nascent CENP-A nucleosome assembly depends on the maternal Cenpa genotype rather than the pre-existing template. Weakened centromeres are thus limited to a single generation, and parental epigenetic differences are eliminated by equal assembly on maternal and paternal centromeres. These differences persist, however, when the underlying DNA of parental centromeres differs in repeat abundance, as assembly during the plastic phase also depends on sufficient repetitive centromere DNA. With contributions of centromere DNA and the Cenpa maternal effect, we propose that centromere inheritance naturally minimizes fitness costs associated with weakened centromeres or epigenetic differences between parents.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
Data availability
Previously published microarray data for long poly-(A) tailed Cenpa mRNA in pre-implantation development is available freely on the NCBI Gene Expression Omnibus (GEO) database (accession no. GDS813 from reference series GSE1749). The 12 mouse genomes used for Cenpa 3′ UTR analysis are available from the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject) under accession no. PRJNA669840. Data supporting the findings of this study are available from the corresponding author on reasonable request. Source data are provided with this paper.
Code availability
All codes used for statistical and distribution analysis are freely available as part of the R package ‘multimode’, described in ref. 58.
References
Kixmoeller, K., Allu, P. K. & Black, B. E. The centromere comes into focus: from CENP-A nucleosomes to kinetochore connections with the spindle. Open Biol. 10, 200051 (2020).
Dumont, M. & Fachinetti, D. DNA sequences in centromere formation and function. Prog. Mol. Subcell. Biol. 56, 305–336 (2017).
Chmátal, L., Schultz, R. M., Black, B. E. & Lampson, M. A. Cell biology of cheating-transmission of centromeres and other selfish elements through asymmetric meiosis. Prog. Mol. Subcell. Biol. 56, 377–396 (2017).
Iwata-Otsubo, A. et al. Expanded satellite repeats amplify a discrete CENP-A nucleosome assembly site on chromosomes that drive in female meiosis. Curr. Biol. 27, 2365–2373.e8 (2017).
Akera, T., Trimm, E. & Lampson, M. A. Molecular strategies of meiotic cheating by selfish centromeres. Cell 178, 1132–1144 (2019).
Fishman, L. & Saunders, A. Centromere-associated female meiotic drive entails male fitness costs in monkeyflowers. Science 322, 1559–1562 (2008).
Voullaire, L. E., Slater, H. R., Petrovic, V. & Choo, K. H. A. A functional marker centromere with no detectable α-satellite, satellite III or CENP-B protein: activation of a latent centromere? Am. J. Hum. Genet. 52, 1153–1163 (1993).
Logsdon, G. A. et al. Human artificial chromosomes that bypass centromeric DNA. Cell 178, 624–639 (2019).
Depinet, T. W. et al. Characterization of neo-centromeres in marker chromosomes lacking detectable α-satellite DNA. Hum. Mol. Genet. 6, 1195–2204 (1997).
Du Sart, D. et al. A functional neo-centromere formed through activation of a latent human centromere and consisting of non-α-satellite DNA. Nat. Genet. 16, 144–153 (1997).
Black, B. E. & Cleveland, D. W. Epigenetic centromere propagation and the nature of CENP-A nucleosomes. Cell 144, 471–479 (2011).
Foltz, D. R. et al. Centromere-specific assembly of CENP-A nucleosomes is mediated by HJURP. Cell 137, 472–484 (2009).
Jansen, L. E. T., Black, B. E., Foltz, D. R. & Cleveland, D. W. Propagation of centromeric chromatin requires exit from mitosis. J. Cell Biol. 176, 795–805 (2007).
Dunleavy, E. M. et al. HJURP is a cell-cycle-dependent maintenance and deposition factor of CENP-A at centromeres. Cell 137, 485–497 (2009).
Schuh, M., Lehner, C. F. & Heidmann, S. Incorporation of Drosophila CID/CENP-A and CENP-C into centromeres during early embryonic anaphase. Curr. Biol. 17, 237–243 (2007).
Moree, B., Meyer, C. B., Fuller, C. J. & Straight, A. F. CENP-C recruits M18BP1 to centromeres to promote CENP-A chromatin assembly. J. Cell Biol. 194, 855–871 (2011).
Ravi, M. & Chan, S. W. L. Haploid plants produced by centromere-mediated genome elimination. Nature 464, 615–618 (2010).
Comai, L. & Tan, E. H. Haploid induction and genome instability. Trends Genet. 35, 791–803 (2019).
Raychaudhuri, N. et al. Transgenerational propagation and quantitative maintenance of paternal centromeres depends on Cid/Cenp-A presence in Drosophila sperm. PLoS Biol. 10, e1001434 (2012).
Gassmann, R. et al. An inverse relationship to germline transcription defines centromeric chromatin in C. elegans. Nature 484, 534–537 (2012).
Liu, H., Kim, J. M. & Aoki, F. Regulation of histone H3 lysine 9 methylation in oocytes and early pre-implantation embryos. Development 131, 2269–2280 (2004).
Burton, A. et al. Heterochromatin establishment during early mammalian development is regulated by pericentromeric RNA and characterized by non-repressive h3k9me3. Nat. Cell Biol. 22, 767–778 (2020).
Puschendorf, M. et al. PRC1 and Suv39h specify parental asymmetry at constitutive heterochromatin in early mouse embryos. Nat. Genet. 40, 411–420 (2008).
Palmer, D. K., O’Day, K. & Margolis, R. L. The centromere specific histone CENP-A is selectively retained in discrete foci in mammalian sperm nuclei. Chromosoma 100, 32–36 (1990).
Palmer, D. K., Day, K. O., Trongt Le, H., Charbonneau, H. & Margolis, R. L. Purification of the centromere-specific protein CENP-A and demonstration that it is a distinctive histone. Proc. Natl Acad. Sci. USA 88, 3734–3738 (1991).
Brinkley, B. R. et al. Arrangements of kinetochores in mouse cells during meiosis and spermiogenesis. Chromosoma 94, 309–317 (1986).
Smoak, E. M., Stein, P., Schultz, R. M., Lampson, M. A. & Black, B. E. Long-term retention of CENP-A nucleosomes in mammalian oocytes underpins transgenerational inheritance of centromere identity. Curr. Biol. 26, 1110–1116 (2016).
Richter, J. D. Cytoplasmic polyadenylation in development and beyond. Microbiol. Mol. Biol. Rev. 63, 446–456 (1999).
Zeng, F., Baldwin, D. A. & Schultz, R. M. Transcript profiling during preimplantation mouse development. Dev. Biol. 272, 483–496 (2004).
Ishiuchi, T. et al. Reprogramming of the histone H3.3 landscape in the early mouse embryo. Nat. Struct. Mol. Biol. 28, 38–49 (2021).
Barnhart, M. C. et al. HJURP is a CENP-A chromatin assembly factor sufficient to form a functional de novo kinetochore. J. Cell Biol. 194, 229–243 (2011).
Fujita, Y. et al. Priming of centromere for CENP-A recruitment by human hmis18α, hmis18β and M18BP1. Dev. Cell 12, 17–30 (2007).
Nardi, I. K., Zasadzińska, E., Stellfox, M. E., Knippler, C. M. & Foltz, D. R. Licensing of centromeric chromatin assembly through the Mis18α-Mis18β heterotetramer. Mol. Cell 61, 774–787 (2016).
Stellfox, M. E., Nardi, I. K., Knippler, C. M. & Foltz, D. R. Differential binding partners of the Mis18α/β YIPPEE domains regulate Mis18 complex recruitment to centromeres. Cell Rep. 15, 2127–2135 (2016).
Bodor, D. L. et al. The quantitative architecture of centromeric chromatin. eLife 3, e02137 (2014).
Masumoto, H., Masukata, H., Muro, Y., Nozaki, N. & Okazaki, T. A human centromere antigen (CENP-B) interacts with a short specific sequence in alphoid DNA, a human centromeric satellite. J. Cell Biol. 109, 1963–1973 (1989).
Fachinetti, D. et al. DNA sequence-specific binding of CENP-B enhances the fidelity of human centromere function. Dev. Cell 33, 314–327 (2015).
Kumon, T. et al. Parallel pathways for recruiting effector proteins determine centromere drive and suppression. Cell 184, 4904–4918 (2021).
Rossant, J. Postimplantation development of blastomeres isolated from 4 and 8 cell mouse eggs. J. Embryol. Exp. Morphol. 36, 283–290 (1976).
Lepikhov, K. & Walter, J. Differential dynamics of histone H3 methylation at positions K4 and K9 in the mouse zygote. BMC Dev. Biol. 4, 12 (2004).
Lepikhov, K. et al. Evidence for conserved DNA and histone H3 methylation reprogramming in mouse, bovine and rabbit zygotes. Epigenetics Chromatin 1, 8 (2008).
Xu, Q. & Xie, W. Epigenome in early mammalian development: inheritance, reprogramming and establishment. Trends Cell Biol. 28, 237–253 (2018).
Xie, B. et al. Histone H3 lysine 27 trimethylation acts as an epigenetic barrier in porcine nuclear reprogramming. Reproduction 151, 9–16 (2016).
Van Der Heijden, G. W. et al. Asymmetry in histone H3 variants and lysine methylation between paternal and maternal chromatin of the early mouse zygote. Mech. Dev. 122, 1008–1022 (2005).
Hou, H. et al. Centromeres are dismantled by foundational meiotic proteins Spo11 and Rec8. Nature 591, 671–676 (2021).
Monen, J., Maddox, P. S., Hyndman, F., Oegema, K. & Desai, A. Differential role of CENP-A in the segregation of holocentric C. Elegans chromosomes during meiosis and mitosis. Nat. Cell Biol. 7, 1248–1255 (2005).
Prosée, R. F. et al. Trans-generational inheritance of centromere identity requires the CENP-A N-terminal tail in the C. elegans maternal germ line. PLoS Biol. 19, e3000968 (2021).
Malik, H. S. & Henikoff, S. Major evolutionary transitions in centromere complexity. Cell 138, 1067–1082 (2009).
Maheshwari, S. et al. Naturally occurring differences in CENH3 affect chromosome segregation in zygotic mitosis of hybrids. PLoS Genet. 11, e1004970 (2015).
Bao, J. & Bedford, M. T. Epigenetic regulation of the histone-protamine transiiton during spermiogenesis. Reproduction 151, R55–R70 (2016).
Rathke, C., Baarends, W. M., Awe, S. & Renkawitz-Pohl, R. Chromatin dynamics during spermiogenesis. Biochim. Biophys. Acta 1839, 155–168 (2014).
Ameijeiras-Alonso, J., Crujeiras, R. M. & Rodríguez-Casal, A. Mode testing, critical bandwidth and excess mass. Test 28, 900–919 (2019).
Stein, P. & Schindler, K. Mouse oocyte microinjection, maturation and ploidy assessment. J. Vis. Exp. 53, 2851 (2011).
Chatot, C. L., Ziomek, C. A., Bavister, B. D., Lewis, J. L. & Torres, I. An improved culture medium supports development of random-bred 1-cell mouse embryos in vitro. J. Reprod. Fertil. 86, 679–688 (1989).
Dia, F., Strange, T., Liang, J., Hamilton, J. & Berkowitz, K. M. Preparation of meiotic chromosome spreads from mouse spermatocytes. J. Vis. Exp. 129, 55378 (2017).
Taft, R. In vitro fertilization in mice. Cold Spring Harb. Protoc. https://doi.org/10.1101/pdb.prot094508 (2017).
R: a Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2017).
Ameijeiras-Alonso, J., Crujeiras, R. M. & Rodriguez-Casal, A. multimode: An R Package for Mode Assessment. J. Stat. Soft. 97, 1–32 (2021).
Acknowledgements
We thank D. P. Dudka, V. Fu and M. Barmada for assistance with genotyping, G. Logsdon for cloning a protein expression vector, M. Gerace for antigen preparation, D. P. Dudka for help with multiple sequence alignments and R. M. Schultz, M. S. Bartolomei and M. T. Levine for comments and discussion. This work was supported by the NIH (HD058730 to B.E.B. and M.A.L).
Author information
Authors and Affiliations
Contributions
A. Das contributed to experiments, quantifications, data analysis and statistical analysis, animal husbandry and genotyping. A.I.-O. carried out experiments and quantification for some of Fig. 3g. J.D.-M. prepared and characterized new reagents and assisted with statistical analysis. A. Destouni performed the initial experimentation in zygotes and early embryos. K.G.B. carried out animal husbandry and genotyping. A. Das, B.E.B. and M.A.L. contributed to experimental design, data interpretation and writing. B.E.B. and M.A.L. provided supervision and sourced funding.
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing interests.
Peer review
Peer review information
Nature Cell Biology thanks Hiroshi Kimura and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Extended data
Extended Data Fig. 1 CENP-A chromatin is reduced in the soma of Cenpa+/− heterozygous animals in the P0 generation.
a, Bone marrow metaphase spreads: each pair of CENP-A foci represents sister centromeres in mitosis. Scale bars: 5 μm (main panel), 1μm (inset). b, Quantification of CENP-A foci intensities in control (grey) and P0 (yellow) generation in soma. N = 166, 170 centromeres (top to bottom). ** P < 0.0001, Mann–Whitney U test (two-tailed). Error bars: median ± 95% CI. Source numerical data are available in source data.
Extended Data Fig. 2 Weakened centromeres in the male germline are independent of meiotic stage.
. Because oocytes were analysed at metaphase I and spermatocytes at prophase I (Fig. 1), we confirmed that F1 spermatocytes also show weakened centromeres at metaphase I. Images (a) and quantification (b) of F1 spermatocytes show CENP-A reduced to a similar level at metaphase I (70.54 ± 7.1% of control) as prophase I. Each of the CENP-A foci represents four centromeres (a pair of homologous chromosomes, each with two sisters). N = 330 (control), 284 (F1 progeny). Scale bars: 5 μm (main panel), 1μm (inset). Quantification of SYCP3 foci from the same cells (c) shows no decrease (114.90 ± 5.6% of control). N = 235 (control), 259 (F1 progeny). ** P < 0.001, Mann–Whitney U Test (two-tailed). Error bars: median ± 95% CI. Source numerical data are available in source data.
Extended Data Fig. 3 Littermate analysis showing that weakened centromeres persist in the male but not female germline.
a, Data from Fig. 1c replotted as CENP-A levels per animal, averaged over all centromeres in each animal and normalized to controls (dashed line). N = 10,10,10, 9, 7 animals. The F1 male but not the female germline and the male and female soma are significantly lower than the controls **P < 0.001, *P < 0.05 n.s.: P > 0.05, Wilcoxon signed sum rank test (two-tailed). b, CENP-A quantifications in spermatocytes and oocytes from littermates from one set of parents. N = 121, 431, 60, 259, 246, 105 centromeres (top to bottom). Female germline levels are significantly elevated compared to littermate male germline levels. **P < 0.0001, Mann–Whitney U Test (two-tailed). Error bars: median ± 95% CI. Source numerical data are available in source data.
Extended Data Fig. 4 CENP-A nucleosomes are retained through the replacement of canonical nucleosomes with protamines during spermiogenesis.
a, Quantification and b, images showing CENP-A levels are reduced to 42.7 ± 1.5% in spermatids from Cenpa+/− males compared to WT males, similar to the reduction measured in prophase spermatocytes (Fig. 1c). N = 20 (control), 32 (Cenpa+/−) spermatids. Error bars: median ± 95% CI. Scale bars: 5 μm (main panel), 1 μm (inset). Source numerical data are available in source data.
Extended Data Fig. 5 Model to explain equalization of epigenetic differences and subsequent memory.
a, Assumptions used for the modelling. b, Epigenetic inheritance of CENP-A as determined in cycling somatic cells in culture by replication coupled dilution and G1 reloading. c, Example calculation and graph for CENP-A assembly in the first two embryonic cell cycles for progeny of a WT x WT cross. For simplicity, initial CENP-A levels are set to 100 and 50 on the maternal and paternal centromeres, respectively, based on our measurements in zygotes (Fig. 3c). At each S-phase, CENP-A levels are diluted by half on each centromere, and we assume equal assembly on maternal and paternal centromeres in the following G1. Assembly in the first cell cycle depends on the maternal pool, set to 100 for a zygote from a WT female, giving an increase of 50 on both maternal and paternal centromeres. Assembly in the second cell cycle depends on the zygotic pool, which is set to 100 for a WT zygotic genotype. d, Graphs from similar calculations as b, for the designated crosses. Initial CENP-A levels are set to 50 for maternal centromeres from Cenpa+/− mothers and 40 for paternal centromeres from Cenpa+/− fathers, based on our measurements (Fig. 1c and Fig. 3c). Arrows indicate equal assembly on maternal and paternal centromeres. In the first cell cycle, assembly is from a maternal pool of 100 (black arrows) or 50 (yellow arrows) for WT or Cenpa+/− mothers, respectively. In the second cell cycle, assembly is from a zygotic pool of 100 (purple arrows), reflecting a WT zygotic genotype. Calculations show equalization by the four-cell stage in all crosses. Furthermore, crosses with reduced maternal contribution (H♀) equalize to a lower level, which is then remembered through development. Source numerical data are available in source data.
Extended Data Fig. 6 3’ UTR of Cenpa message has hallmarks of dormant maternal mRNA.
a, Polyadenylation (addition of a poly (A) tail) of mRNA is a mechanism to control gene expression. Nuclear polyadenylation is an essential part of post-transcriptional processing of most mRNAs, dictated by the ubiquitous cis-element 3’ UTR hexameric motif AATAAA (nuclear polyadenylation element, NPE). Dormant maternal mRNAs are deposited in the oocyte with short poly(A) tails and are translationally inactive. After fertilization, these maternal mRNAs undergo translation by elongation of the poly(A) tail, controlled by a cytoplasmic polyadenylation element (CPE) usually present within 100 nt upstream of the NPE28. We find conserved CPEs in the mouse, human and frog Cenpa 3’ UTRs (CPE I = TTTTAT or CPE II = TTTTAA) upstream of the NPE as expected for dormant maternal mRNAs. b, Analysis of 12 sequenced rodent species38 reveals that CPEs (CPE I in bold boxes and CPE II in dashed boxes) are present upstream of the NPE in every species as expected for a maternal effect gene.
Extended Data Fig. 8 CENP-A intensity distribution changes from bimodal to unimodal in early embryogenesis.
Graphs show locations of the modes in each distribution from Fig. 6a. a, The WT x WT and WT♀ x H♂ zygote distributions contain two modes (dashed lines) on either side of a central antimode (dip, pointed lines) characteristic of bimodal distributions52. The separation between the two modes is greater in the WT♀ x H♂ cross as expected. In addition, the ratios of the values of the two modes (x-axis) denoted under each cross agree well with the ratios of paternal to maternal centromere intensities calculated in Figs. 3c and 6f. b,c, Similar plots of four-cell embryos (b) from the same crosses show a single central mode characteristic of a unimodal population, like the F1 adult spermatocytes (c), which represents a uniform centromere population. The ratio of the modes in bimodal or the value of the mode in unimodal distribution is indicated below the graphs. Source numerical data are available in source data.
Extended Data Fig. 9 Genetic pathway for centromere equalization.
a, Quantifications of maternal (pink) and paternal (blue) CENP-A and CENP-C intensities in zygotes from a WT x WT control for the Cenpb−/− strain38, with average paternal/maternal CENP-A or CENP-C ratios above; N = 46, 42, 237, 231 centromeres (left to right). Error bars: median ± 95% CI. Although these animals are in a CF-1/C57BL/6J/DBA/2J background, CENP-A and CENP-C ratios in WT zygotes using mothers from this background are consistent with those of C57BL/6J alone (Fig. 6b,f). Source numerical data are available in source data.
Supplementary information
Supplementary Table 1
Replicate information for all relevant figures.
Source data
Source Data Fig. 1
Numerical source data.
Source Data Fig. 2
Numerical source data.
Source Data Fig. 3
Numerical source data.
Source Data Fig. 4
Numerical source data.
Source Data Fig. 5
Numerical source data.
Source Data Fig. 6
Numerical source data.
Source Data Extended Data Fig. 1
Numerical source data.
Source Data Extended Data Fig. 2
Numerical source data.
Source Data Extended Data Fig. 3
Numerical source data.
Source Data Extended Data Fig. 4
Numerical source data.
Source Data Extended Data Fig. 5
Numerical source data.
Source Data Extended Data Fig. 8
Numerical source data.
Source Data Extended Data Fig. 9
Numerical source data.
Rights and permissions
About this article
Cite this article
Das, A., Iwata-Otsubo, A., Destouni, A. et al. Epigenetic, genetic and maternal effects enable stable centromere inheritance. Nat Cell Biol 24, 748–756 (2022). https://doi.org/10.1038/s41556-022-00897-w
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41556-022-00897-w
This article is cited by
-
Prenatally detected six duplications at Xp22.33-p11.22: a case report
BMC Pregnancy and Childbirth (2023)