Abstract
Pluripotent stem cells (PSCs) are central to development as they are the precursors of all cell types in the embryo. Therefore, maintaining a stable karyotype is essential, both for their physiological role as well as for their use in regenerative medicine. Karyotype abnormalities in PSCs in culture are common but the underlying causes remain unknown. To gain insight, we explore the composition of the centromere and kinetochore in human embryonic and induced PSCs. Centromere function depends on CENP-A nucleosome-defined chromatin. We show that while PSCs maintain abundant pools of CENP-A, CENP-C and CENP-T, these essential centromere components are strongly reduced at stem cell centromeres. Outer kinetochore recruitment is also impaired to a lesser extent, indicating an overall weaker kinetochore while the inner centromere protein Aurora B remains unaffected. We further show that, similar to differentiated human cells, CENP-A chromatin assembly in PSCs requires transition into G1 phase. Finally, reprogramming experiments indicate that reduction of centromeric CENP-A levels is an early event during dedifferentiation, coinciding with global chromatin remodelling. Our characterization of centromeres in human stem cells suggests a possible link between impaired centromere function and stem cell aneuploidies.
Footnotes
References
- 1.
Thomson JA, Itskovitz-Eldor J, Shapiro SS, Waknitz MA, Swiergiel JJ, Marshall VS, Jones JM . 1998Embryonic stem cell lines derived from human blastocysts. Science 282, 1145-1147. (doi:10.1126/science.282.5391.1145) Crossref, PubMed, ISI, Google Scholar - 2.
Cheeseman IM, Desai A . 2008Molecular architecture of the kinetochore–microtubule interface. Nat. Rev. Mol. Cell Biol. 9, 33-46. (doi:10.1038/nrm2310) Crossref, PubMed, ISI, Google Scholar - 3.
Takahashi K, Yamanaka S . 2006Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663-676. (doi:10.1016/j.cell.2006.07.024) Crossref, PubMed, ISI, Google Scholar - 4.
Ghule PN 2011Reprogramming the pluripotent cell cycle: restoration of an abbreviated G1 phase in human induced pluripotent stem (iPS) cells. J. Cell. Physiol. 226, 1149-1156. (doi:10.1002/jcp.22440) Crossref, PubMed, ISI, Google Scholar - 5.
Lee D-S 2014An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator. Nat. Commun. 5, 5619. (doi:10.1038/ncomms6619) Crossref, PubMed, ISI, Google Scholar - 6.
Milagre I 2017Gender differences in global but not targeted demethylation in iPSC reprogramming. Cell Rep. 18, 1079-1089. (doi:10.1016/j.celrep.2017.01.008) Crossref, PubMed, ISI, Google Scholar - 7.
Nashun B, Hill PWS, Hajkova P . 2015Reprogramming of cell fate: epigenetic memory and the erasure of memories past. EMBO J. 34, 1296-1308. (doi:10.15252/embj.201490649) Crossref, PubMed, ISI, Google Scholar - 8. International Stem Cell Initiative et al. 2011Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage. Nat. Biotechnol. 29, 1132-1144. (doi:10.1038/nbt.2051) Crossref, PubMed, ISI, Google Scholar
- 9.
Taapken SM, Nisler BS, Newton MA, Sampsell-Barron TL, Leonhard KA, McIntire EM, Montgomery KD . 2011Karotypic abnormalities in human induced pluripotent stem cells and embryonic stem cells. Nat. Biotechnol. 29, 313-314. (doi:10.1038/nbt.1835) Crossref, PubMed, ISI, Google Scholar - 10.
Becker KA, Ghule PN, Therrien JA, Lian JB, Stein JL, van Wijnen AJ, Stein GS . 2006Self-renewal of human embryonic stem cells is supported by a shortened G1 cell cycle phase. J. Cell. Physiol. 209, 883-893. (doi:10.1002/jcp.20776) Crossref, PubMed, ISI, Google Scholar - 11.
Weissbein U, Benvenisty N, Ben-David U . 2014Quality control: genome maintenance in pluripotent stem cells. J. Cell Biol. 204, 153-163. (doi:10.1083/jcb.201310135) Crossref, PubMed, ISI, Google Scholar - 12.
Zhang M, Cheng L, Jia Y, Liu G, Li C, Song S, Bradley A, Huang Y . 2016Aneuploid embryonic stem cells exhibit impaired differentiation and increased neoplastic potential. EMBO J. 35, 2285-2300. (doi:10.15252/embj.201593103) Crossref, PubMed, ISI, Google Scholar - 13.
McKinley KL, Cheeseman IM . 2016The molecular basis for centromere identity and function. Nat. Rev. Mol. Cell Biol. 17, 16-29. (doi:10.1038/nrm.2015.5) Crossref, PubMed, ISI, Google Scholar - 14.
Mitra S, Srinivasan B, Jansen LET . 2020Stable inheritance of CENP-A chromatin: inner strength versus dynamic control. J. Cell Biol. 219, e202005099. (doi:10.1083/jcb.202005099) Crossref, PubMed, Google Scholar - 15.
Marshall OJ, Chueh AC, Wong LH, Choo KHA . 2008Neocentromeres: new insights into centromere structure, disease development, and karyotype evolution. Am. J. Hum. Genet. 82, 261-282. (doi:10.1016/j.ajhg.2007.11.009) Crossref, PubMed, ISI, Google Scholar - 16.
Murillo-Pineda M, Jansen LET . 2020Genetics, epigenetics and back again: lessons learned from neocentromeres. Exp. Cell Res. 389, 111909. (doi:10.1016/j.yexcr.2020.111909) Crossref, PubMed, ISI, Google Scholar - 17.
Hori T, Shang W-H, Takeuchi K, Fukagawa T . 2013The CCAN recruits CENP-A to the centromere and forms the structural core for kinetochore assembly. J. Cell Biol. 200, 45-60. (doi:10.1083/jcb.201210106) Crossref, PubMed, ISI, Google Scholar - 18.
Mendiburo MJ, Padeken J, Fülöp S, Schepers A, Heun P . 2011Drosophila CENH3 is sufficient for centromere formation. Science 334, 686-690. (doi:10.1126/science.1206880) Crossref, PubMed, ISI, Google Scholar - 19.
Bodor DL, Valente LP, Mata JF, Black BE, Jansen LET . 2013Assembly in G1 phase and long-term stability are unique intrinsic features of CENP-A nucleosomes. Mol. Biol. Cell 24, 923-932. (doi:10.1091/mbc.E13-01-0034) Crossref, PubMed, ISI, Google Scholar - 20.
Falk SJ 2015Chromosomes. CENP-C reshapes and stabilizes CENP-A nucleosomes at the centromere. Science 348, 699-703. (doi:10.1126/science.1259308) Crossref, PubMed, ISI, Google Scholar - 21.
Foltz DR, Jansen LET, Black BE, Bailey AO, Yates JR, Cleveland DW . 2006The human CENP-A centromeric nucleosome-associated complex. Nat. Cell Biol. 8, 458-469. (doi:10.1038/ncb1397) Crossref, PubMed, ISI, Google Scholar - 22.
Okada M, Cheeseman IM, Hori T, Okawa K, McLeod IX, Yates JR, Desai A, Fukagawa T . 2006The CENP-H-I complex is required for the efficient incorporation of newly synthesized CENP-A into centromeres. Nat. Cell Biol. 8, 446-457. (doi:10.1038/ncb1396) Crossref, PubMed, ISI, Google Scholar - 23.
Gascoigne KE, Takeuchi K, Suzuki A, Hori T, Fukagawa T, Cheeseman IM . 2011Induced ectopic kinetochore assembly bypasses the requirement for CENP-A nucleosomes. Cell 145, 410-422. (doi:10.1016/j.cell.2011.03.031) Crossref, PubMed, ISI, Google Scholar - 24.
Hori T 2008CCAN makes multiple contacts with centromeric DNA to provide distinct pathways to the outer kinetochore. Cell 135, 1039-1052. (doi:10.1016/j.cell.2008.10.019) Crossref, PubMed, ISI, Google Scholar - 25.
Silva MCC, Bodor DL, Stellfox ME, Martins NMC, Hochegger H, Foltz DR, Jansen LET . 2012Cdk activity couples epigenetic centromere inheritance to cell cycle progression. Dev. Cell 22, 52-63. (doi:10.1016/j.devcel.2011.10.014) Crossref, PubMed, ISI, Google Scholar - 26.
Stankovic A 2017A dual inhibitory mechanism sufficient to maintain cell-cycle-restricted CENP-A assembly. Mol. Cell 65, 231-246. (doi:10.1016/j.molcel.2016.11.021) Crossref, PubMed, ISI, Google Scholar - 27.
Barnhart MC, Kuich PHJL, Stellfox ME, Ward JA, Bassett EA, Black BE, Foltz DR . 2011HJURP is a CENP-A chromatin assembly factor sufficient to form a functional de novo kinetochore. J. Cell Biol. 194, 229-243. (doi:10.1083/jcb.201012017) Crossref, PubMed, ISI, Google Scholar - 28.
Dunleavy EM, Roche D, Tagami H, Lacoste N, Ray-Gallet D, Nakamura Y, Daigo Y, Nakatani Y, Almouzni-Pettinotti G . 2009HJURP is a cell-cycle-dependent maintenance and deposition factor of CENP-A at centromeres. Cell 137, 485-497. (doi:10.1016/j.cell.2009.02.040) Crossref, PubMed, ISI, Google Scholar - 29.
Foltz DR, Jansen LET, Bailey AO, Yates JR, Bassett EA, Wood S, Black BE, Cleveland DW . 2009Centromere-specific assembly of CENP-a nucleosomes is mediated by HJURP. Cell 137, 472-484. (doi:10.1016/j.cell.2009.02.039) Crossref, PubMed, ISI, Google Scholar - 30.
McKinley KL, Cheeseman IM . 2014Polo-like kinase 1 licenses CENP-A deposition at centromeres. Cell 158, 397-411. (doi:10.1016/j.cell.2014.06.016) Crossref, PubMed, ISI, Google Scholar - 31.
Bodor DL 2014The quantitative architecture of centromeric chromatin. eLife 3, e02137. (doi:10.7554/eLife.02137) Crossref, PubMed, ISI, Google Scholar - 32.
Masumoto H, Masukata H, Muro Y, Nozaki N, Okazaki T . 1989A human centromere antigen (CENP-B) interacts with a short specific sequence in alphoid DNA, a human centromeric satellite. J. Cell Biol. 109, 1963-1973. Crossref, PubMed, ISI, Google Scholar - 33.
Krenn V, Musacchio A . 2015The Aurora B kinase in chromosome bi-orientation and spindle checkpoint signaling. Front. Oncol. 5, 225. (doi:10.3389/fonc.2015.00225) Crossref, PubMed, ISI, Google Scholar - 34.
Carmena M, Wheelock M, Funabiki H, Earnshaw WC . 2012The chromosomal passenger complex (CPC): from easy rider to the godfather of mitosis. Nat. Rev. Mol. Cell Biol. 13, 789-803. (doi:10.1038/nrm3474) Crossref, PubMed, ISI, Google Scholar - 35.
Ambartsumyan G, Gill RK, Perez SD, Conway D, Vincent J, Dalal Y, Clark AT . 2010Centromere protein A dynamics in human pluripotent stem cell self-renewal, differentiation and DNA damage. Hum. Mol. Genet. 19, 3970-3982. (doi:10.1093/hmg/ddq312) Crossref, PubMed, ISI, Google Scholar - 36.
Jansen LET, Black BE, Foltz DR, Cleveland DW . 2007Propagation of centromeric chromatin requires exit from mitosis. J. Cell Biol. 176, 795-805. (doi:10.1083/jcb.200701066) Crossref, PubMed, ISI, Google Scholar - 37.
Bodor DL, Rodríguez MG, Moreno N, Jansen LET . 2012Analysis of protein turnover by quantitative SNAP-based pulse-chase imaging. Curr. Protocol. Cell Biol. 55, 8.8.1-8.8.34. (doi:10.1002/0471143030.cb0808s55) Google Scholar - 38.
Pannell D 2000Retrovirus vector silencing is de novo methylase independent and marked by a repressive histone code. EMBO J. 19, 5884-5894. (doi:10.1093/emboj/19.21.5884) Crossref, PubMed, ISI, Google Scholar - 39.
Wood KW, Sakowicz R, Goldstein LS, Cleveland DW . 1997CENP-E is a plus end-directed kinetochore motor required for metaphase chromosome alignment. Cell 91, 357-366. (doi:10.1016/s0092-8674(00)80419-5) Crossref, PubMed, ISI, Google Scholar - 40.
Cheeseman IM, Chappie JS, Wilson-Kubalek EM, Desai A . 2006The conserved KMN network constitutes the core microtubule-binding site of the kinetochore. Cell 127, 983-997. (doi:10.1016/j.cell.2006.09.039) Crossref, PubMed, ISI, Google Scholar - 41.
Chan EM 2009Live cell imaging distinguishes bona fide human iPS cells from partially reprogrammed cells. Nat. Biotechnol. 27, 1033-1037. (doi:10.1038/nbt.1580) Crossref, PubMed, ISI, Google Scholar - 42.
Fukagawa T, Earnshaw WC . 2014The centromere: chromatin foundation for the kinetochore machinery. Dev. Cell 30, 496-508. (doi:10.1016/j.devcel.2014.08.016) Crossref, PubMed, ISI, Google Scholar - 43.
García Del Arco A, Edgar BA, Erhardt S . 2018In vivo analysis of centromeric proteins reveals a stem cell-specific asymmetry and an essential role in differentiated, non-proliferating cells. Cell Rep. 22, 1982-1993. (doi:10.1016/j.celrep.2018.01.079) Crossref, PubMed, ISI, Google Scholar - 44.
Lermontova I, Schubert V, Fuchs J, Klatte S, Macas J, Schubert I . 2006Loading of Arabidopsis centromeric histone CENH3 occurs mainly during G2 and requires the presence of the histone fold domain. Plant Cell 18, 2443-2451. (doi:10.1105/tpc.106.043174) Crossref, PubMed, ISI, Google Scholar - 45.
Ranjan R, Snedeker J, Chen X . 2018Stem cell mitotic drive ensures asymmetric epigenetic inheritance. BioRxiv (doi:10.1101/416446) Google Scholar - 46.
Drpic D, Almeida AC, Aguiar P, Renda F, Damas J, Lewin HA, Larkin DM, Khodjakov A, Maiato H . 2018Chromosome segregation is biased by kinetochore size. Curr. Biol. 28, 1344-1356.e5. (doi:10.1016/j.cub.2018.03.023) Crossref, PubMed, ISI, Google Scholar - 47.
Dunleavy EM, Beier NL, Gorgescu W, Tang J, Costes SV, Karpen GH . 2012The cell cycle timing of centromeric chromatin assembly in Drosophila meiosis is distinct from mitosis yet requires CAL1 and CENP-C. PLoS Biol. 10, e1001460. (doi:10.1371/journal.pbio.1001460) Crossref, PubMed, ISI, Google Scholar - 48.
Fachinetti D, Han JS, McMahon MA, Ly P, Abdullah A, Wong AJ, Cleveland DW . 2015DNA sequence-specific binding of CENP-B enhances the fidelity of human centromere function. Dev. Cell 33, 314-327. (doi:10.1016/j.devcel.2015.03.020) Crossref, PubMed, ISI, Google Scholar - 49.
Liu L, Michowski W, Kolodziejczyk A, Sicinski P . 2019The cell cycle in stem cell proliferation, pluripotency and differentiation. Nat. Cell Biol. 21, 1060-1067. (doi:10.1038/s41556-019-0384-4) Crossref, PubMed, ISI, Google Scholar - 50.
Cacchiarelli D 2015Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency. Cell 162, 412-424. (doi:10.1016/j.cell.2015.06.016) Crossref, PubMed, ISI, Google Scholar - 51.
Koche RP, Smith ZD, Adli M, Gu H, Ku M, Gnirke A, Bernstein BE, Meissner A . 2011Reprogramming factor expression initiates widespread targeted chromatin remodeling. Cell Stem Cell 8, 96-105. (doi:10.1016/j.stem.2010.12.001) Crossref, PubMed, ISI, Google Scholar - 52.
Ang Y-S 2011Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell 145, 183-197. (doi:10.1016/j.cell.2011.03.003) Crossref, PubMed, ISI, Google Scholar - 53.
Bergmann JH, Rodríguez MG, Martins NMC, Kimura H, Kelly DA, Masumoto H, Larionov V, Jansen LET, Earnshaw WC . 2011Epigenetic engineering shows H3K4me2 is required for HJURP targeting and CENP-A assembly on a synthetic human kinetochore. EMBO J. 30, 328-340. (doi:10.1038/emboj.2010.329) Crossref, PubMed, ISI, Google Scholar - 54.
Miga KH, Newton Y, Jain M, Altemose N, Willard HF, Kent WJ . 2014Centromere reference models for human chromosomes X and Y satellite arrays. Genome Res. 24, 697-707. (doi:10.1101/gr.159624.113) Crossref, PubMed, ISI, Google Scholar - 55.
Voullaire LE, Slater HR, Petrovic V, Choo KH . 1993A functional marker centromere with no detectable alpha-satellite, satellite III, or CENP-B protein: activation of a latent centromere?Am. J. Hum. Genet. 52, 1153-1163. PubMed, ISI, Google Scholar


