Biochemical Studies of a Long Noncoding RNA Involved in Breast Cancer Biology

Abstract

Long non-coding RNAs, a significant fraction of the transcriptome in higher eukaryotes, are emerging as key players in many rapidly growing areas of biology, including embryonic stem cell differentiation, brain function, subcellular compartmentalization, chromatin remodeling and cancer biology. We report one of the first biochemical characterizations of a long ncRNA, which coactivates sex hormone nuclear receptors and is strongly associated with breast cancer. This was the first RNA proven to act as a regulatory non-coding RNA and to code for a protein. To date, eleven variant transcripts of the long ncRNA have been identified. We study three: 1) a noncoding isoform, 2) a coding isoform, and 3) an intron-comprising noncoding transcript, which is alternatively spliced and possesses a partial intron insertion. To assess the secondary structures of the selected RNAs and map their overall structural organization, we employ chemical probing tools at select experimental conditions.