Abstract
In female mammals, each cell silences one X chromosome by converting it into transcriptionally inert heterochromatin. The inactivation is concomitant with epigenetic changes including methylation of specific histone residues and incorporation of macroH2A. Such epigenetic changes may exert influence on the positioning of the inactive X chromosome (Xi) within the nucleus beyond the level of chromatin structure. However, the dynamic positioning of the inactive X chromosome during cell cycle remains unclear. Here, we show that H3K27me3 is a cell-cycle-independent marker for the inactivated X chromosomes in WI38 cells. By utilizing this marker, three types of Xi locations in the nuclei are classified, which are envelope position (associated with envelope), mid-position (between the envelope and nucleolus), and nucleolus position (associated with the nucleolus). Moreover, serial-section analysis revealed that the inactive X chromosomes in the mid-position appear to be sparser and less condensed than those associated with the nuclear envelope or nucleolus. During the transition from G0 to G1 phase, the inactive X chromosomes tend to move from the envelope position to the nucleolus position in WI38 cells. Our results imply a role of chromosome positioning in maintaining the organization of the inactive X chromosomes in different cell phases.
Similar content being viewed by others
Abbreviations
- CC:
-
clear-cut
- U/DC:
-
unclear/decondensed chromatin
- U/CC:
-
unclear/condensed chromatin
- DAPI:
-
4′,6-diamidino-2-phenylindole dihydrochloride
- H3K9me2:
-
histone H3 lysine 9 dimethylation
- H3K27me3:
-
histone H3 lysine 27 trimethylation
- Xi:
-
inactivated X chromosome
- Xa:
-
activated X chromosome
- Xist:
-
X-inactivation specific transcript
- BrdU:
-
5′-bromodeoxyuridine
References
Bacher CP, Guggiari M, Brors B, Augui S, Clerc P, Avner P, Eils R, Heard E (2006) Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation. Nat Cell Biol 8:293–299
Barr ML, Bertram EG (1949) A morphological distinction between neurones of the male and female, and the behaviour of the nucleolar satellite during accelerated nucleoprotein synthesis. Nature 163:676–677
Boumil RM, Lee JT (2001) Forty years of decoding the silence in X-chromosome inactivation. Hum Mol Genet 10:2225–2232
Chadwick BP, Willard HF (2002) Cell cycle-dependent localization of macroH2A in chromatin of the inactive X chromosome. J Cell Biol 157:1113–1123
Chadwick BP, Willard HF (2004) Multiple spatially distinct types of facultative heterochromatin on the human inactive X chromosome. Proc Natl Acad Sci U S A 101:17450–17455
Clemson CM, Hall LL, Byron M, McNeil J, Lawrence JB (2006) The X chromosome is organized into a gene-rich outer rim and an internal core containing silenced nongenic sequences. Proc Natl Acad Sci U S A 103:7688–7693
Conway E, Healy E, Bracken AP (2015) PRC2 mediated H3K27 methylations in cellular identity and cancer. Curr Opin Cell Biol 37:42–48
Costanzi C, Pehrson JR (1998) Histone macroH2A1 is concentrated in the inactive X chromosome of female mammals. Nature 393:599–601
Costanzi C, Stein P, Worrad DM, Schultz RM, Pehrson JR (2000) Histone macroH2A1 is concentrated in the inactive X chromosome of female preimplantation mouse embryos. Development 127:2283–2289
Cremer T, Cremer M, Dietzel S, Muller S, Solovei I, Fakan S (2006) Chromosome territories—a functional nuclear landscape. Curr Opin Cell Biol 18:307–316
Csankovszki G, Nagy A, Jaenisch R (2001) Synergism of Xist RNA, DNA methylation, and histone hypoacetylation in maintaining X chromosome inactivation. J Cell Biol 153:773–784
Eils R, Dietzel S, Bertin E, Schrock E, Speicher MR, Ried T, Robert-Nicoud M, Cremer C, Cremer T (1996) Three-dimensional reconstruction of painted human interphase chromosomes: active and inactive X chromosome territories have similar volumes but differ in shape and surface structure. J Cell Biol 135:1427–1440
Heard E, Rougeulle C, Arnaud D, Avner P, Allis CD, Spector DL (2001) Methylation of histone H3 at Lys-9 is an early mark on the X chromosome during X inactivation. Cell 107:727–738
Heride C, Ricoul M, Kieu K, von Hase J, Guillemot V, Cremer C, Dubrana K, Sabatier L (2010) Distance between homologous chromosomes results from chromosome positioning constraints. J Cell Sci 123:4063–4075
Li Y, Liang Q, Tao W (2007) The methylation modification accompanying X chromosome inactivation. Chin High Tech Lett 17:1307–1311
Li Y, Tan T, Zong L, He D, Tao W, Liang Q (2012) Study of methylation of histone H3 lysine 9 and H3 lysine 27 during X chromosome inactivation in three types of cells. Chromosome Res 20:769–778
Lyon MF (1972) X-chromosome inactivation and developmental patterns in mammals. Biol Rev Camb Philos Soc 47:1–35
Lyon MF (2002) X-chromosome inactivation and human genetic disease. Acta Paediatr Suppl 91:107–112
Mermoud JE, Popova B, Peters AH, Jenuwein T, Brockdorff N (2002) Histone H3 lysine 9 methylation occurs rapidly at the onset of random X chromosome inactivation. Curr Biol 12:247–251
Pinheiro I, Heard E (2017) X chromosome inactivation: new players in the initiation of gene silencing. F1000Res 6(F1000 Faculty Rev):344
Plath K, Fang J, Mlynarczyk-Evans SK, Cao R, Worringer KA, Wang H, de la Cruz CC, Otte AP, Panning B, Zhang Y (2003) Role of histone H3 lysine 27 methylation in X inactivation. Science 300:131–135
Rasmussen TP, Mastrangelo MA, Eden A, Pehrson JR, Jaenisch R (2000) Dynamic relocalization of histone MacroH2A1 from centrosomes to inactive X chromosomes during X inactivation. J Cell Biol 150:1189–1198
Rego A, Sinclair PB, Tao W, Kireev I, Belmont AS (2008) The facultative heterochromatin of the inactive X chromosome has a distinctive condensed ultrastructure. J Cell Sci 121:1119–1127
Robert Finestra T, Gribnau J (2017) X chromosome inactivation: silencing, topology and reactivation. Curr Opin Cell Biol 46:54–61
Rougeulle C, Chaumeil J, Sarma K, Allis CD, Reinberg D, Avner P, Heard E (2004) Differential histone H3 Lys-9 and Lys-27 methylation profiles on the X chromosome. Mol Cell Biol 24:5475–5484
Silva J, Mak W, Zvetkova I, Appanah R, Nesterova TB, Webster Z, Peters AH, Jenuwein T, Otte AP, Brockdorff N (2003) Establishment of histone h3 methylation on the inactive X chromosome requires transient recruitment of Eed-Enx1 polycomb group complexes. Dev Cell 4:481–495
Smeets D, Markaki Y, Schmid VJ, Kraus F, Tattermusch A, Cerase A, Sterr M, Fiedler S, Demmerle J, Popken J, Leonhardt H, Brockdorff N, Cremer T, Schermelleh L, Cremer M (2014) Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci. Epigenetics Chromatin 7:8
Xu N, Tsai CL, Lee JT (2006) Transient homologous chromosome pairing marks the onset of X inactivation. Science 311:1149–1152
Yang F, Deng X, Ma W, Berletch JB, Rabaia N, Wei G, Moore JM, Filippova GN, Xu J, Liu Y, Noble WS, Shendure J, Disteche CM (2015) The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation. Genome Biol 16:52
Zhang LF, Huynh KD, Lee JT (2007) Perinucleolar targeting of the inactive X during S phase: evidence for a role in the maintenance of silencing. Cell 129:693–706
Acknowledgements
We are very grateful to Prof. Andrew Belmont. The initial work has been done in his laboratory.
Funding
This work was supported by the National Natural Science Foundation of China (No. 91219101, 31471205 and 31571394), the National Basic Research Program of China (973 Program, No. 2013CB530700), a fund granted by Beijing Key Laboratory of Gene Resource and Molecular Development, a fund granted by Key Laboratory for Cell Proliferation and Regulation Biology, Ministry of Education of China, and a fund granted by Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study (No. 0223-0002-0002000-56).
Author information
Authors and Affiliations
Contributions
W.T. and Q.L. conceived, designed and supervised the project, and modified the manuscript. T.T. and Q.L. analyzed the data and wrote the paper. G.L. Y.G. L.S. W.T. designed and performed most of the experiments and contributed to the interpretation of results.
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Ethical approval
This article does not contain any studies with human participants or animals performed by any of the authors.
Additional information
Responsible Editor: Dean A. Jackson
Electronic supplementary material
ESM 1
(GIF 102 kb).
Rights and permissions
About this article
Cite this article
Lyu, G., Tan, T., Guan, Y. et al. Changes in the position and volume of inactive X chromosomes during the G0/G1 transition. Chromosome Res 26, 179–189 (2018). https://doi.org/10.1007/s10577-018-9577-0
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10577-018-9577-0