Production of Extrachromosomal MicroDNAs Is Linked to Mismatch Repair Pathways and Transcriptional Activity.

Laura W Dillon,Shunichi Takeda,Jack D Griffith,Smaranda Willcox,Yuh-Hwa Wang,Yoshiyuki Shibata,Yves Pommier,Anindya Dutta,Pankaj Kumar

doi:10.1016/j.celrep.2015.05.020

Abstract

MicroDNAs are <400-base extrachromosomal circles found in mammalian cells. Tens of thousands of microDNAs have been found in all tissue types, including sperm. MicroDNAs arise preferentially from areas with high gene density, GC content, and exon density from promoters with activating chromatin modifications and in sperm from the 5'-UTR of full-length LINE-1 elements, but are depleted from lamin-associated heterochromatin. Analysis of microDNAs from a set of human cancer cell lines revealed lineage-specific patterns of microDNA origins. A survey of microDNAs from chicken cells defective in various DNA repair proteins reveals that homologous recombination and non-homologous end joining repair pathways are not required for microDNA production. Deletion of the MSH3 DNA mismatch repair protein results in a significant decrease in microDNA abundance, specifically from non-CpG genomic regions. Thus, microDNAs arise as part of normal cellular physiology—either from DNA breaks associated with RNA metabolism or from replication slippage followed by mismatch repair.

Highlights

For a long time, eukaryotic genomes were considered to be stable and relatively conserved, but advances in genome technology have revealed genetic diversity between individuals, such as SNPs and copy-number variations (Beckmann et al, 2007; Flores et al, 2007; Frazer et al, 2009; Lupski, 2010; Stankiewicz and Lupski, 2010)
We find that microDNAs are present in all tissue types examined, including germ cells, and there is very little correlation with the extent of cell proliferation
To determine whether there is any normal tissue that is bereft of microDNAs, microDNA was isolated from a battery of tissues by first purifying extrachromosomal DNA from the nuclei of homogenized tissues from normal adult C57BL/6 mice followed by removal of linear DNA

Summary

Introduction

Eukaryotic genomes were considered to be stable and relatively conserved, but advances in genome technology have revealed genetic diversity between individuals, such as SNPs and copy-number variations (Beckmann et al, 2007; Flores et al, 2007; Frazer et al, 2009; Lupski, 2010; Stankiewicz and Lupski, 2010). Evolution of an organism’s genome occurs during its lifespan, resulting in genetic mosaicism among somatic cells. One such example of genomic variation is extrachromosomal circular DNA (eccDNA) (Cohen and Segal, 2009). Previous studies of eccDNA revealed them to be several hundred to millions of bases in length and to originate from viral genomes, intermediates of mobile elements, or repetitive chromosomal sequences (Cohen and Segal, 2009). MicroDNAs are short (100–400 bp long), circular DNAs derived mostly from unique non-repetitive genomic sequences

Results

Discussion

Conclusion