High-resolution chromosomal microarray analysis of early-stage human embryonic stem cells reveals an association between X chromosome instability and skewed X inactivation.

Yumei Luo,Xiaofang Sun,Jieliang Li,Yong Fan,Shaoying Li,Detu Zhu

doi:10.1186/2045-3701-4-74

Abstract

X chromosome inactivation (XCI) is a dosage compensation mechanism that silences the majority of genes on one X chromosome in each female cell via a random process. Skewed XCI is relevant to many diseases, but the mechanism leading to it remains unclear. Human embryonic stem cells (hESCs) derived from the inner cell mass (ICM) of blastocyst-stage embryos have provided an excellent model system for understanding XCI initiation and maintenance. Here, we derived hESC lines with random or skewed XCI patterns from poor-quality embryos and investigated the genome-wide copy number variation (CNV) and loss of heterozygosity (LOH) patterns at the early passages of these two groups of hESC lines. It was found that the average size of CNVs on the X chromosomes in the skewed group is twice as much as that in the random group. Moreover, the LOH regions of the skewed group covered the gene locus of either XIST or XACT, which are master long non-coding RNA (lncRNA) effectors of XCI in human pluripotent stem cells. In conclusion, our work has established an experimentally tractable hESC model for study of skewed XCI and revealed an association between X chromosome instability and skewed XCI.Electronic supplementary materialThe online version of this article (doi:10.1186/2045-3701-4-74) contains supplementary material, which is available to authorized users.

Highlights

X chromosome inactivation (XCI) is the mechanism by which dosage compensation of the sex chromosome is achieved in females
The most important effector is XIST (X-inactive specific transcript), whose gene is mapped on Xq13 (73,040,48673,072,588 bp) and composes of the X inactivation center (XIC) along with another two RNA genes, JPX and FTX
XACT (X-active coating transcript), whose gene is located on chromosome Xq23 (112,983,323-113,235,148 bp) in an unusually large intergenic domain of 1.7 Mb, has been identified as the first long non-coding RNA (lncRNA) that coats the active X chromosome in human pluripotent stem cells, indicating a role in the specific kinetics of XCI in humans [8]

Summary

Introduction

X chromosome inactivation (XCI) is the mechanism by which dosage compensation of the sex chromosome is achieved in females. The XIST gene is active on only one of X chromosomes, expressing a large (17 kb), non-coding transcript that coats and silences the chromosome in cis [8]. XIST is expressed from both paternal and maternal X chromosomes but does not lead to chromosome-wide silencing, indicating a role in XCI initiation [9]. XACT (X-active coating transcript), whose gene is located on chromosome Xq23 (112,983,323-113,235,148 bp) in an unusually large intergenic domain of 1.7 Mb (only 1% of intergenic regions in humans are >1.5 Mb), has been identified as the first lncRNA that coats the active X chromosome in human pluripotent stem cells, indicating a role in the specific kinetics of XCI in humans [8]. Epigenetic mechanism that is causing or associated with skewed XCI remains unclear

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