Chimeric chromosome landscapes of human somatic cell cultures show dependence on stress and regulation of genomic repeats by CGGBP1

Subhamoy Datta,Umashankar Singh,Divyesh Patel,Sukesh Kashyap,Manthan Patel

doi:10.18632/oncotarget.28174

Abstract

Genomes of somatic cells in culture are prone to spontaneous mutations due to errors in replication and DNA repair. Some of these errors, such as chromosomal fusions, are not rectifiable and subject to selection or elimination in growing cultures. Somatic cell cultures are thus expected to generate background levels of potentially stable chromosomal chimeras. A description of the landscape of such spontaneously generated chromosomal chimeras in cultured cells will help understand the factors affecting somatic mosaicism. Here we show that short homology-associated non-homologous chromosomal chimeras occur in normal human fibroblasts and HEK293T cells at genomic repeats. The occurrence of chromosomal chimeras is enhanced by heat stress and depletion of a repeat regulatory protein CGGBP1. We also present evidence of homologous chromosomal chimeras between allelic copies in repeat-rich DNA obtained by methylcytosine immunoprecipitation. The formation of homologous chromosomal chimeras at Alu and L1 repeats increases upon depletion of CGGBP1. Our data are derived from de novo sequencing from three different cell lines under different experimental conditions and our chromosomal chimera detection pipeline is applicable to long as well as short read sequencing platforms. These findings present significant information about the generation, sensitivity and regulation of somatic mosaicism in human cell cultures.

Highlights

In somatic cells the randomly occurring mutations create mosaic patterns of different cell clusters representative of different genotypes, including some deleterious ones [1]
By applying a similar strategy based on variant calls in the published as well as newly generated cytosine methylation-enriched DNA sequence datasets, we show that CGGBP1 depletion increases interallelic chimeras as well
Widespread occurrence of non-homologous chromosomal chimeras in cultured human fibroblasts is enhanced by heat stress

Summary

Introduction

In somatic cells the randomly occurring mutations create mosaic patterns of different cell clusters representative of different genotypes, including some deleterious ones [1]. The mosaically occurring genomic variants arise out of errors in DNA metabolism, most likely due to the errors in replication and DNA repair. Mutagens and stressors that affect the fidelity of DNA replication and repair accelerate the emergence of genomic variants and add to the mosaicism. This process generates alternative genotypes stochastically and at low frequency. The mosaically occurring sequence variants can be segregated from the inherited genotypes by applying different statistical models [5, 6]. The confidence in segregating inherited genotypes from mosaically occurring sequence variants can be enhanced by analysing the parental genotypes alongside the offspring’s genotypes. The somatic mosaicism www.oncotarget.com in cultured cells, especially transformed or cancer-derived cell lines, is very difficult to decipher

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Conclusion