1. DNA Methylation Status of SHOX-Flanking CpG Islands in Healthy Individuals and Short Stature Patients with Pseudoautosomal Copy Number Variations
- Author
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Atsushi Hattori, Masako Izawa, Hitoshi Yamamoto, Hirohito Shima, Kenichiro Ogushi, Shun Soneda, Akihiro Umezawa, Reiko Horikawa, Hideaki Yagasaki, Erina Suzuki, Tomohiro Ishii, Noriyuki Namba, Mami Miyado, Toshiaki Tanaka, Koji Muroya, Yasuhiro Hirano, Keiko Matsubara, Masayo Kagami, Kimiaki Uetake, and Maki Fukami
- Subjects
Genetics ,0303 health sciences ,030305 genetics & heredity ,Pseudoautosomal region ,Bisulfite sequencing ,Biology ,medicine.disease ,X-inactivation ,03 medical and health sciences ,CpG site ,DNA methylation ,medicine ,Copy-number variation ,Haploinsufficiency ,Molecular Biology ,Léri–Weill dyschondrosteosis ,Genetics (clinical) ,030304 developmental biology - 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.
- Published
- 2019