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. 2017 Nov 5;372(1733):20160359.
doi: 10.1098/rstb.2016.0359.

X chromosome inactivation in a female carrier of a 1.28 Mb deletion encompassing the human X inactivation centre

B de Hoon  1 , Erik Splinter  2 , B Eussen  3 , J C W Douben  3 , E Rentmeester  1 , M van de Heijning  2 , J S E Laven  4 , J E M M de Klein  3 , J Liebelt  5 , J Gribnau  6
Affiliations

X chromosome inactivation in a female carrier of a 1.28 Mb deletion encompassing the human X inactivation centre

B de Hoon et al. Philos Trans R Soc Lond B Biol Sci. .

Abstract

X chromosome inactivation (XCI) is a mechanism specifically initiated in female cells to silence one X chromosome, thereby equalizing the dose of X-linked gene products between male and female cells. XCI is regulated by a locus on the X chromosome termed the X-inactivation centre (XIC). Located within the XIC is XIST, which acts as a master regulator of XCI. During XCI, XIST is upregulated on the inactive X chromosome and chromosome-wide cis spreading of XIST leads to inactivation. In mouse, the Xic comprises Xist and all cis-regulatory elements and genes involved in Xist regulation. The activity of the XIC is regulated by trans-acting factors located elsewhere in the genome: X-encoded XCI activators positively regulating XCI, and autosomally encoded XCI inhibitors providing the threshold for XCI initiation. Whether human XCI is regulated through a similar mechanism, involving trans-regulatory factors acting on the XIC has remained elusive so far. Here, we describe a female individual with ovarian dysgenesis and a small X chromosomal deletion of the XIC. SNP-array and targeted locus amplification (TLA) analysis defined the deletion to a 1.28 megabase region, including XIST and all elements and genes that perform cis-regulatory functions in mouse XCI. Cells carrying this deletion still initiate XCI on the unaffected X chromosome, indicating that XCI can be initiated in the presence of only one XIC. Our results indicate that the trans-acting factors required for XCI initiation are located outside the deletion, providing evidence that the regulatory mechanisms of XCI are conserved between mouse and human.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'.

Keywords: X chromosome inactivation; XIC; XIST; deletion.

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Conflict of interest statement

We do not have any competing interests.

Figures

Figure 1.
Figure 1.
XIC deletion identified by SNP array analysis. (a) SNP array analysis showing chromosome X with the XIC deletion. At the top a schematic representation of the X chromosome is shown with the deletion indicated in red. Below the results of the SNP array analysis are shown. Every dot is representing a probe along the X chromosome. The upper panel shows the deleted area in red. The lower panel shows SNP array data revealing loss of heterozygosity for several regions on the X, of which one overlaps with the deleted sequence (areas marked in yellow, with B allele frequency (BAF) of 100% or 0%). (b) A magnification of the region encompassing the XIC. At the top a schematic representation of the region is shown, with the genes located in this region below. The deletion is indicated in red. Panels are similar to those in (a).
Figure 2.
Figure 2.
XIC deletion identified PCR. (a) The XIC deletion as identified by comparative genomic hybridization (CGH). A schematic representation of the X-chromosome is shown, with the deleted region marked in red. (b) Comparison of qPCR results to CGH. A magnification is shown of the regions containing the breakpoints. The top panel shows qPCR results along the breakpoint regions, with copy number plotted against chromosomal position. In the map of the chromosomal region below, the inverted duplication in the centromeric breakpoint region is marked in blue.
Figure 3.
Figure 3.
XIC deletion identified by TLA. (a) TLA coverage is plotted against chromosomal position. Arrow indicates the location of the primer sets. Star indicates the increase in coverage on the other side of the deleted region. A genetic map of the region is shown below, with the inverted duplication in blue. (b) Magnification of the centromeric breakpoint region. (c) The break-spanning read, with the sequence centromeric of the breakpoint marked in blue and the sequence telomeric of the breakpoint marked in green.
Figure 4.
Figure 4.
The X-chromosome carrying the deletion is preferentially active. (a) At the top, a map of the X-chromosome is shown with the location of the BAC probes that were used indicated in blue. The location of the deletion as identified by CGH and TLA is marked in red. Below, representative images of DNA-FISH for regions located inside or outside the deleted region are shown. BAC CTD-2310H21, containing PHKA2, and BAC CTD 2530H13, containing RNF12, are located outside the deleted region. BAC CTD-2183M22, containing XIST, and BAC RP13-36G14, containing JPX, are located within the deleted region. Results from analysing at least 30 metaphases are shown in the tables to the right. (b) Representative pictures of sequential RNA-DNA-FISH. Two representative nuclei are shown with RNA-FISH results for XIST RNA in green, and DNA-FISH results for BAC RP13-36G14 in yellow and BAC CTD-2310H21 in red. The table to the right shows the percentage of nuclei with overlapping signals of XIST RNA and BAC RP13-36G14 DNA.
Figure 5.
Figure 5.
Deletions delineating the human XIC. (a) Graph of the chromosomal abnormalities studied to define the XIC. Black bars indicate the sequence present on the abnormal X-chromosome. From top to bottom: the rea(X) of female S.A., the idic(Xp) of female A.G., the X;14 translocation chromosome from a 47XXY male, the XIC deletion reported here. Below a map of the X-chromosomal region Xq13, containing the XIC is shown. (b) The topological domain structure of the XIC as identified in female IMR90 fibroblasts and male H1 human ES cells.
Figure 6.
Figure 6.
In-cis deletion of the cis-XIC and DMRTC1 results in DMRTC1 dose deficiency. (a) Normal situation: a schematic representation of two X chromosomes after X-inactivation is shown. Two copies of DMRTC1 remain active. (b) In-cis deletion of the XIC and DMRTC1: as a result of the deletion the unaffected X chromosome is preferentially inactivated, and only one copy of DMRTC1 remains active.
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  • Preface.
    Heard E, Brockdorff N. Heard E, et al. Philos Trans R Soc Lond B Biol Sci. 2017 Nov 5;372(1733):20160353. doi: 10.1098/rstb.2016.0353. Philos Trans R Soc Lond B Biol Sci. 2017. PMID: 28947653 Free PMC article. No abstract available.

References

    1. Lyon MF. 1961. Gene action in the X-chromosome of the mouse (Mus musculus L.). Nature 190, 372–373. (10.1038/190372a0) - DOI - PubMed
    1. Amos-Landgraf JM, Cottle A, Plenge RM, Friez M, Schwartz CE, Longshore J, Willard HF. 2006. X chromosome-inactivation patterns of 1,005 phenotypically unaffected females. Am. J. Hum. Genet. 79, 493–499. (10.1086/507565) - DOI - PMC - PubMed
    1. De Hoon B, Monkhorst K, Riegman P, Laven JSE, Gribnau J. 2015. Buccal swab as a reliable predictor for X inactivation ratio in inaccessible tissues. J. Med. Genet. 52, 784–790. (10.1136/jmedgenet-2015-103194) - DOI - PMC - PubMed
    1. Allderdice PW, et al. 1978. Spreading of inactivation in an (X;14) translocation. Am. J. Med. Genet. 2, 233–240. (10.1002/ajmg.1320020304) - DOI - PubMed
    1. Lafreniere RG, Brown CJ, Rider S, Chelly J, Taillon-Miller P, Chinault AC, Monaco AP, Willard HF. 1993. 2.6 Mb YAC contig of the human X inactivation center region in Xq13: physical linkage of the RPS4X, PHKA1, XIST and DXS128E genes. Hum. Mol. Genet. 2, 1105–1115. (10.1093/hmg/2.8.1105) - DOI - PubMed

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