Aberrant methylation and associated transcriptional mobilization of Alu elements contributes to genomic instability in hypoxia

Abstract

Hypoxia is an integral part of tumorigenesis and contributes extensively to the neoplastic phenotype including drug resistance and genomic instability. It has also been reported that hypoxia results in global demethylation. Because a majority of the cytosine-phosphate-guanine (CpG) islands are found within the repeat elements of DNA, and are usually methylated under normoxic conditions, we suggested that retrotransposable Alu or short interspersed nuclear elements (SINEs) which show altered methylation and associated changes of gene expression during hypoxia, could be associated with genomic instability. U87MG glioblastoma cells were cultured in 0.1% O2 for 6 weeks and compared with cells cultured in 21% O2 for the same duration. Real-time PCR analysis showed a significant increase in SINE and reverse transcriptase coding long interspersed nuclear element (LINE) transcripts during hypoxia. Sequencing of bisulphite treated DNA as well as the Combined Bisulfite Restriction Analysis (COBRA) assay showed that the SINE loci studied underwent significant hypomethylation though there was patchy hypermethylation at a few sites. The inter-alu PCR profile of DNA from cells cultured under 6-week hypoxia, its 4-week revert back to normoxia and 6-week normoxia showed several changes in the band pattern indicating increased alu mediated genomic alteration. Our results show that aberrant methylation leading to increased transcription of SINE and reverse transcriptase associated LINE elements could lead to increased genomic instability in hypoxia. This might be a cause of genetic heterogeneity in tumours especially in variegated hypoxic environment and lead to a development of foci of more aggressive tumour cells.

Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax

“…In particular, we found that the B1 SINE repeat showed high upregulation (see below) under severe hypoxia in the BMR brain. A similar mode of regulation was reported for human Alu SINEs that were shown to be transcriptionally upregulated under hypoxic conditions, presumably contributing to genomic instability in tumours 48 .…”

Real-time dynamics of methyl-CpG-binding domain protein 3 and its role in DNA demethylation by fluorescence correlation spectroscopy

“…[42][43][44] In other words, hypoxia is highly related to hypomethylation and may necessarily be active in maintaining low levels of DNA modifications required for stemness or tumorigenesis.…”

The Role of the Microenvironment in Mammary Gland Development and Cancer

“…ROS (reactive oxygen species) generated by infiltrating leukocytes (macrophages and neutrophils) and resulting from intermittent hypoxia induced by tissue damage, might also lead to increased mutation rates and alter the epigenetic profiles of epithelial and stromal cells. Indeed, a recent report described alterations in DNA methylation in hypoxic conditions (Pal et al 2009).…”