Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a long noncoding RNA overexpressed in various cancers that promotes cell growth and metastasis. Although hypoxia has been shown to up-regulate MALAT1, only hypoxiainducible factors (HIFs) have been implicated in activation of theMALAT1promoter in specific cell types and other molecular mechanisms associated with hypoxia-mediated MALAT1 upregulation remain largely unknown. Here, we demonstrate that hypoxia induces cancer cell-specific chromatin-chromatin interactions between newly identified enhancer-like cis-regulatory elements present at the MALAT1 locus. We show that hypoxia-mediated up-regulation of MALAT1 as well as its antisense strand TALAM1 occurs in breast cancer cells, but not in nontumorigenic mammary epithelial cells. Our analyses on the MALAT1 genomic locus discovered three novel putative enhancers that are located upstream and downstream of the MALAT1 gene body. We found that parts of these putative enhancers are epigenetically modified to a more open chromatin state under hypoxia in breast cancer cells. Furthermore, our chromosome conformation capture experiment demonstrated that noncancerous cells and breast cancer cells exhibit different interaction profiles under both normoxia and hypoxia, and only breast cancer cells gain specific chromatin interactions under hypoxia. Although the HIF-2α protein can enhance the interaction between the promoter and the putative 3′ enhancer, the gain of chromatin interactions associated with other upstream elements, such as putative-7 and-20 kb enhancers, were HIFindependent events. Collectively, our study demonstrates that cancer cell-specific chromatin-chromatin interactions are formed at theMALAT1locus under hypoxia, implicating a novel mechanism of MALAT1 regulation in cancer.
