Copy number variation in human embryonic stem cells with skewed X chromosome inactivation

doi:10.3969/j.issn.2095-4344.2013.10.007

Abstract

Abstract:

BACKGROUND: Human embryonic stem cells have two different X chromosome inactivation patterns: skewed X chromosome inactivation and random X chromosome inactivation. Whether there is any difference in copy number variation between those cells is not clear.
OBJECTIVE: To analyze the copy number variation in human embryonic stem cells with skewed X chromosome inactivation at whole genome level, and to analyze the effect of copy number variation on the function of human embryonic stem cells with skewed X chromosome inactivation.
METHODS: Three skewed X chromosome inactivation cell strains were included in the research group, and two random skewed X chromosome inactivation cell strains were included in the control group. The copy number variation was analyzed with Cytogenetics Whole-Genome 2.7M array produced by Affymetrix, USA. The data were analyzed using ChAS software and OMIM software. The same copy number variation regions and genes were found in the three skewed X chromosome inactivation cell strains.
RESULTS AND CONCLUSION: More than 130 copy number variation (> 50 kb) were found in the research group, which was higher than that of 36 copy number variation in the control group, the changes of copy number variation in the two groups were mainly repeated (> 70%). Nine gain copy number variation regions were found in the research group, distributed on 1q22, 1p34.1, 6q16.3, 7q31.32, 11q13.1, 16q12.2, 19p13.12, Xp22.33 and Xq26.2, respectively, all were repeated for three copy number variation. Nineteen genes were found within those copy number variation. All of those above copy number variation regions and genes in the control group were normal two copies. Genes within the copy number variation were closely related to the function of binding of DNA and nucleotide. GPC3 gene mutation on the Xq26.2 was found to be correlated with the skewed X chromosome inactivation. Micro-genomic variation in human embryonic stem cells with skewed X chromosome inactivation was higher than that in the random skewed X chromosome inactivation human embryonic stem cells. Key genes within copy number variation may have disadvantage to the function of human embryonic stem cells.

Key words: stem cells, embryo-derived stem cells, copy number variation, array, skewed X chromosome inactivation, gene, National Natural Science Foundation of China, stem cell photographs-containing paper

CLC Number:

R394.2

Liu Wei-qiang, He Wen-zhi, Cao Ding-ya, Li Jie-liang, Guo Li-yuan, Li Qing, Sun Xiao-fang. Copy number variation in human embryonic stem cells with skewed X chromosome inactivation[J]. Chinese Journal of Tissue Engineering Research, 2013, 17(10): 1748-1752.

Figures/Tables 5

References

[1] Baker DE, Harrison NJ, Maltby E,et al. Adaptation to culture of human embryonic stem cells and oncogenesis in vivo. Nat Biotechnol. 2007;25(2):207-215.

[2] Närvä E, Autio R, Rahkonen N,et al. High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity. Nat Biotechnol. 2010;28(4):371-377.

[3] Shen Y, Matsuno Y, Fouse SD,et al. X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations.Proc Natl Acad Sci U S A. 2008;105(12):4709-4714.

[4] Silva SS, Rowntree RK, Mekhoubad S,et al. X-chromosome inactivation and epigenetic fluidity in human embryonic stem cells. Proc Natl Acad Sci U S A. 2008;105(12):4820-4825.

[5] Liu W, Sun X. Skewed X chromosome inactivation in diploid and triploid female human embryonic stem cells. Hum Reprod. 2009;24(8):1834-1843.

[6] Sun X, Long X, Yin Y,et al. Similar biological characteristics of human embryonic stem cell lines with normal and abnormal karyotypes. Hum Reprod. 2008;23(10):2185-2193.

[7] Yano S, Baskin B, Bagheri A,et al. Familial Simpson-Golabi-Behmel syndrome: studies of X-chromosome inactivation and clinical phenotypes in two female individuals with GPC3 mutations. Clin Genet. 2011; 80(5):466-471.

[8] Minks J, Robinson WP, Brown CJ. A skewed view of X chromosome inactivation. J Clin Invest. 2008;118(1):20-23.

[9] Kristiansen M, Langerød A, Knudsen GP,et al. High frequency of skewed X inactivation in young breast cancer patients. J Med Genet. 2002;39(1):30-33.

[10] Ozbalkan Z, Bagi?lar S, Kiraz S,et al. Skewed X chromosome inactivation in blood cells of women with scleroderma. Arthritis Rheum. 2005;52(5):1564-1570.

[11] Dvash T, Lavon N, Fan G. Variations of X chromosome inactivation occur in early passages of female human embryonic stem cells. PLoS One. 2010;5(6):e11330.

[12] Maitra A, Arking DE, Shivapurkar N,et al. Genomic alterations in cultured human embryonic stem cells. Nat Genet. 2005; 37(10):1099-1103.

[13] Hussein SM, Batada NN, Vuoristo S,et al. Copy number variation and selection during reprogramming to pluripotency.Nature. 2011;471(7336):58-62.

[14] Diaz Perez SV, Kim R, Li Z,et al. Derivation of new human embryonic stem cell lines reveals rapid epigenetic progression in vitro that can be prevented by chemical modification of chromatin. Hum Mol Genet. 2012;21(4): 751-764.

[15] Redon R, Ishikawa S, Fitch KR,et al. Global variation in copy number in the human genome. Nature. 2006;444(7118): 444-454.

[16] Stankiewicz P, Lupski JR. Structural variation in the human genome and its role in disease. Annu Rev Med. 2010;61: 437-455.

[17] Sebat J, Lakshmi B, Malhotra D,et al. Strong association of de novo copy number mutations with autism. Science. 2007; 316(5823):445-449.

[18] Coe BP, Girirajan S, Eichler EE. The genetic variability and commonality of neurodevelopmental disease. Am J Med Genet C Semin Med Genet. 2012;160C(2):118-29.

[19] Jobanputra V, Levy B, Kinney A,et al. Copy Number Changes on the X Chromosome in Women with and without Highly Skewed X-Chromosome Inactivation.Cytogenet Genome Res. 2012;136(4):264-269.