DNA Methylation Status of SHOX-Flanking CpG Islands in Healthy Individuals and Short Stature Patients with Pseudoautosomal Copy Number Variations

Kenichiro Ogushi, Atsushi Hattori, Erina Suzuki, Hirohito Shima, Masako Izawa, Hideaki Yagasaki, Reiko Horikawa, Kimiaki Uetake, Akihiro Umezawa, Tomohiro Ishii, Koji Muroya, Noriyuki Namba, Toshiaki Tanaka, Yasuhiro Hirano, Hitoshi Yamamoto, Shun Soneda, Keiko Matsubara, Masayo Kagami, Mami Miyado, Maki Fukami

Research output: Contribution to journalArticle

Abstract

SHOX resides in the short arm pseudoautosomal region (PAR1) of the sex chromosomes and escapes X inactivation. SHOX haploinsufficiency underlies idiopathic short stature (ISS) and Leri-Weill dyschondrosteosis (LWD). A substantial percentage of cases with SHOX haploinsufficiency arise from pseudoautosomal copy number variations (CNVs) involving putative enhancer regions of SHOX. Our previous study using peripheral blood samples showed that some CpG dinucleotides adjacent to SHOX exon 1 were hypomethylated in a healthy woman and methylated in a woman with gross X chromosomal rearrangements. However, it remains unknown whether submicroscopic pseudoautosomal CNVs cause aberrant DNA methylation of SHOX-flanking CpG islands. In this study, we examined the DNA methylation status of SHOX-flanking CpG islands in 50 healthy individuals and 10 ISS/LWD patients with pseudoautosomal CNVs. In silico analysis detected 3 CpG islands within the 20-kb region from the translation start site of SHOX. Pyrosequencing and bisulfite sequencing of genomic DNA samples revealed that these CpG islands were barely methylated in peripheral blood cells and cultured chondrocytes of healthy individuals, as well as in peripheral blood cells of ISS/LWD patients with pseudoautosomal CNVs. These results, in conjunction with our previous findings, indicate that the DNA methylation status of SHOX-flanking CpG islands can be affected by gross X-chromosomal abnormalities, but not by submicroscopic CNVs in PAR1. Such CNVs likely disturb SHOX expression through DNA methylation-independent mechanisms, which need to be determined in future studies.

Original languageEnglish
JournalCytogenetic and Genome Research
DOIs
Publication statusPublished - 2019 Jan 1
Externally publishedYes

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CpG Islands
DNA Methylation
Haploinsufficiency
Blood Cells
X Chromosome Inactivation
Sex Chromosomes
Chondrocytes
DNA Sequence Analysis
Chromosome Aberrations
Computer Simulation
Exons
Leri-Weil syndrome

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

Cite this

DNA Methylation Status of SHOX-Flanking CpG Islands in Healthy Individuals and Short Stature Patients with Pseudoautosomal Copy Number Variations. / Ogushi, Kenichiro; Hattori, Atsushi; Suzuki, Erina; Shima, Hirohito; Izawa, Masako; Yagasaki, Hideaki; Horikawa, Reiko; Uetake, Kimiaki; Umezawa, Akihiro; Ishii, Tomohiro; Muroya, Koji; Namba, Noriyuki; Tanaka, Toshiaki; Hirano, Yasuhiro; Yamamoto, Hitoshi; Soneda, Shun; Matsubara, Keiko; Kagami, Masayo; Miyado, Mami; Fukami, Maki.

In: Cytogenetic and Genome Research, 01.01.2019.

Research output: Contribution to journalArticle

Ogushi, K, Hattori, A, Suzuki, E, Shima, H, Izawa, M, Yagasaki, H, Horikawa, R, Uetake, K, Umezawa, A, Ishii, T, Muroya, K, Namba, N, Tanaka, T, Hirano, Y, Yamamoto, H, Soneda, S, Matsubara, K, Kagami, M, Miyado, M & Fukami, M 2019, 'DNA Methylation Status of SHOX-Flanking CpG Islands in Healthy Individuals and Short Stature Patients with Pseudoautosomal Copy Number Variations', Cytogenetic and Genome Research. https://doi.org/10.1159/000500468
Ogushi, Kenichiro ; Hattori, Atsushi ; Suzuki, Erina ; Shima, Hirohito ; Izawa, Masako ; Yagasaki, Hideaki ; Horikawa, Reiko ; Uetake, Kimiaki ; Umezawa, Akihiro ; Ishii, Tomohiro ; Muroya, Koji ; Namba, Noriyuki ; Tanaka, Toshiaki ; Hirano, Yasuhiro ; Yamamoto, Hitoshi ; Soneda, Shun ; Matsubara, Keiko ; Kagami, Masayo ; Miyado, Mami ; Fukami, Maki. / DNA Methylation Status of SHOX-Flanking CpG Islands in Healthy Individuals and Short Stature Patients with Pseudoautosomal Copy Number Variations. In: Cytogenetic and Genome Research. 2019.
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abstract = "SHOX resides in the short arm pseudoautosomal region (PAR1) of the sex chromosomes and escapes X inactivation. SHOX haploinsufficiency underlies idiopathic short stature (ISS) and Leri-Weill dyschondrosteosis (LWD). A substantial percentage of cases with SHOX haploinsufficiency arise from pseudoautosomal copy number variations (CNVs) involving putative enhancer regions of SHOX. Our previous study using peripheral blood samples showed that some CpG dinucleotides adjacent to SHOX exon 1 were hypomethylated in a healthy woman and methylated in a woman with gross X chromosomal rearrangements. However, it remains unknown whether submicroscopic pseudoautosomal CNVs cause aberrant DNA methylation of SHOX-flanking CpG islands. In this study, we examined the DNA methylation status of SHOX-flanking CpG islands in 50 healthy individuals and 10 ISS/LWD patients with pseudoautosomal CNVs. In silico analysis detected 3 CpG islands within the 20-kb region from the translation start site of SHOX. Pyrosequencing and bisulfite sequencing of genomic DNA samples revealed that these CpG islands were barely methylated in peripheral blood cells and cultured chondrocytes of healthy individuals, as well as in peripheral blood cells of ISS/LWD patients with pseudoautosomal CNVs. These results, in conjunction with our previous findings, indicate that the DNA methylation status of SHOX-flanking CpG islands can be affected by gross X-chromosomal abnormalities, but not by submicroscopic CNVs in PAR1. Such CNVs likely disturb SHOX expression through DNA methylation-independent mechanisms, which need to be determined in future studies.",
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AU - Ogushi, Kenichiro

AU - Hattori, Atsushi

AU - Suzuki, Erina

AU - Shima, Hirohito

AU - Izawa, Masako

AU - Yagasaki, Hideaki

AU - Horikawa, Reiko

AU - Uetake, Kimiaki

AU - Umezawa, Akihiro

AU - Ishii, Tomohiro

AU - Muroya, Koji

AU - Namba, Noriyuki

AU - Tanaka, Toshiaki

AU - Hirano, Yasuhiro

AU - Yamamoto, Hitoshi

AU - Soneda, Shun

AU - Matsubara, Keiko

AU - Kagami, Masayo

AU - Miyado, Mami

AU - Fukami, Maki

PY - 2019/1/1

Y1 - 2019/1/1

N2 - SHOX resides in the short arm pseudoautosomal region (PAR1) of the sex chromosomes and escapes X inactivation. SHOX haploinsufficiency underlies idiopathic short stature (ISS) and Leri-Weill dyschondrosteosis (LWD). A substantial percentage of cases with SHOX haploinsufficiency arise from pseudoautosomal copy number variations (CNVs) involving putative enhancer regions of SHOX. Our previous study using peripheral blood samples showed that some CpG dinucleotides adjacent to SHOX exon 1 were hypomethylated in a healthy woman and methylated in a woman with gross X chromosomal rearrangements. However, it remains unknown whether submicroscopic pseudoautosomal CNVs cause aberrant DNA methylation of SHOX-flanking CpG islands. In this study, we examined the DNA methylation status of SHOX-flanking CpG islands in 50 healthy individuals and 10 ISS/LWD patients with pseudoautosomal CNVs. In silico analysis detected 3 CpG islands within the 20-kb region from the translation start site of SHOX. Pyrosequencing and bisulfite sequencing of genomic DNA samples revealed that these CpG islands were barely methylated in peripheral blood cells and cultured chondrocytes of healthy individuals, as well as in peripheral blood cells of ISS/LWD patients with pseudoautosomal CNVs. These results, in conjunction with our previous findings, indicate that the DNA methylation status of SHOX-flanking CpG islands can be affected by gross X-chromosomal abnormalities, but not by submicroscopic CNVs in PAR1. Such CNVs likely disturb SHOX expression through DNA methylation-independent mechanisms, which need to be determined in future studies.

AB - SHOX resides in the short arm pseudoautosomal region (PAR1) of the sex chromosomes and escapes X inactivation. SHOX haploinsufficiency underlies idiopathic short stature (ISS) and Leri-Weill dyschondrosteosis (LWD). A substantial percentage of cases with SHOX haploinsufficiency arise from pseudoautosomal copy number variations (CNVs) involving putative enhancer regions of SHOX. Our previous study using peripheral blood samples showed that some CpG dinucleotides adjacent to SHOX exon 1 were hypomethylated in a healthy woman and methylated in a woman with gross X chromosomal rearrangements. However, it remains unknown whether submicroscopic pseudoautosomal CNVs cause aberrant DNA methylation of SHOX-flanking CpG islands. In this study, we examined the DNA methylation status of SHOX-flanking CpG islands in 50 healthy individuals and 10 ISS/LWD patients with pseudoautosomal CNVs. In silico analysis detected 3 CpG islands within the 20-kb region from the translation start site of SHOX. Pyrosequencing and bisulfite sequencing of genomic DNA samples revealed that these CpG islands were barely methylated in peripheral blood cells and cultured chondrocytes of healthy individuals, as well as in peripheral blood cells of ISS/LWD patients with pseudoautosomal CNVs. These results, in conjunction with our previous findings, indicate that the DNA methylation status of SHOX-flanking CpG islands can be affected by gross X-chromosomal abnormalities, but not by submicroscopic CNVs in PAR1. Such CNVs likely disturb SHOX expression through DNA methylation-independent mechanisms, which need to be determined in future studies.

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