The Khps1 lncRNA facilitates expression of SPHK1 via chromatin remodeling and E2F1 recruitment.
Major finding: The Khps1 lncRNA facilitates expression of SPHK1 via chromatin remodeling and E2F1 recruitment.
Mechanism: Khps1 forms a DNA–RNA triplex structure at a homopurine stretch in the SPHK1 promoter.
Impact: LncRNAs can promote tumorigenesis through upregulation of proto-oncogenes such as SPHK1.
Thousands of long noncoding RNAs (lncRNA) have been identified; however, little is known about their functions. It has been proposed that lncRNAs can form DNA–RNA triplexes at homopurine stretches in gene regulatory elements, which might direct targeted recruitment of epigenetic regulators and thereby alter gene expression. To test the hypothesis that lncRNAs mediate epigenetic gene regulation through DNA–RNA triplex structures, Postepska-Igielska and colleagues studied the sphingosine kinase 1 (SPHK1) gene, a proto-oncogene with multiple triplex-forming regions upstream of the transcription start site. RNA sequencing identified a lncRNA, Khps1, transcribed in the antisense orientation from the SPHK1 locus. The Khps1 promoter contained putative E2F transcription factor binding sites, which were confirmed by chromatin immunoprecipitation. SPHK1 transcription required Khps1 expression, which correlated with E2F1 occupancy at the SPHK1 promoter, and E2F1 promoted transcription of both the sense and antisense transcripts, with a more rapid increase in Khps1 expression. Knockdown of Khps1 resulted in reduced E2F1 occupancy at the SPHK1 promoter, but not a control promoter, and prevented E2F1-mediated induction of SPHK1, suggesting that Khps1 promotes SPHK1 transcription by facilitating E2F1 binding to the SPHK1 promoter. Consistent with this idea, Khps1 produced an active chromatin structure at the SPHK1 promoter through recruitment of the histone acetyltransferase p300/CBP, which resulted in an increase in activating histone marks and reduced nucleosome density that facilitated E2F1 binding. Khps1 interacted directly with the SPHK1 promoter, forming a DNA–RNA triplex requiring Hoogsteen base pairing at a homopurine stretch upstream of the SPHK1 transcription start site. Expression of both Khps1 and SPHK1 was highest during the G1/S transition of the cell cycle, promoting cell growth and lessening the proapoptotic effects of E2F1. Together, these results illustrate that the lncRNA Khps1 promotes expression of the proto-oncogene SPHK1 via DNA–RNA triplex formation and chromatin remodeling.
Postepska-Igielska A, Giwojna A, Gasri-Plotnitsky L, Schmitt N, Dold A, Ginsberg D, et al. LncRNA Khps1 regulates expression of the proto-oncogene SPHK1 via triplex-mediated changes in chromatin structure. Mol Cell 2015;60:626–36.
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