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Stem Cell Res Ther. 2019 Aug 27;10(1):273. doi: 10.1186/s13287-019-1381-z.

Frequent retrotransposition of endogenous genes in ERCC2-deficient cells derived from a patient with xeroderma pigmentosum.

Author information

1
Medical Genome Center, National Center for Child Health and Development Research Institute, Setagaya, Tokyo, Japan.
2
Department of Biology, Faculty of Science, Ochanomizu University, Bunkyo, Tokyo, Japan.
3
Present address: Division of Embryology, National Institute for Basic Biology, Okazaki, Aichi, Japan.
4
Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.
5
Human Phenome Institute, Fudan University, Shanghai, China.
6
NIHR Oxford BRC, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
7
Department of Reproductive Biology, National Center for Child Health and Development Research Institute, Setagaya, Tokyo, Japan.
8
Research team for Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, Setagaya, Tokyo, Japan.
9
Department of Reproductive Biology, National Center for Child Health and Development Research Institute, Setagaya, Tokyo, Japan. umezawa@1985.jukuin.keio.ac.jp.
10
Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan. umezawa@1985.jukuin.keio.ac.jp.
11
Department of Systems BioMedicine, National Center for Child Health and Development Research Institute, Tokyo, Japan.

Abstract

BACKGROUND:

Retrotransposition of protein-coding genes is thought to occur due to the existence of numerous processed pseudogenes in both animals and plants. Unlike retrotransposons including Alu and LINE-1, direct evidence of such retrotransposition events has not been reported to date. Even if such an event occurs in a somatic cell, it is almost impossible to detect it using bulk of cells as a sample. Single-cell analyses or other techniques are needed.

METHODS:

In order to examine genetic stability of stem cells, we have established induced pluripotent stem cell (iPSC) lines from several patients with DNA repair-deficiency disorders, such as ataxia telangiectasia and xeroderma pigmentosum, along with healthy controls. Performing whole-exome sequencing analyses of these parental and iPSC lines, we compiled somatic mutations accumulated by the deficiency of DNA repair mechanisms. Whereas most somatic mutations cannot be detected in bulk, cell reprogramming enabled us to observe all the somatic mutations which had occurred in the cell line. Patterns of somatic mutations should be distinctive depending on which DNA repair gene is impaired.

RESULTS:

The comparison revealed that deficiency of ATM and XPA preferentially gives rise to indels and single-nucleotide substitutions, respectively. On the other hand, deficiency of ERCC2 caused not only single-nucleotide mutations but also many retrotranspositions of endogenous genes, which were readily identified by examining removal of introns in whole-exome sequencing. Although the number was limited, those events were also detected in healthy control samples.

CONCLUSIONS:

The present study exploits clonality of iPSCs to unveil somatic mutation sets that are usually hidden in bulk cell analysis. Whole-exome sequencing analysis facilitated the detection of retrotransposition mutations. The results suggest that retrotranspositions of human endogenous genes are more frequent than expected in somatic cells and that ERCC2 plays a defensive role against transposition of endogenous and exogenous DNA fragments.

KEYWORDS:

DNA repair; ERCC2; Retrotransposition; Somatic mutation; XPA; Xeroderma pigmentosum; iPSC

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