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Background  Mounting evidence suggests a major role for epigenetic feedback in  Plasmodium falciparum  transcriptional regulation. Long non-coding RNAs (lncRNAs) have recently emerged as a new paradigm in epigenetic remodeling. We therefore set out to investigate putative roles for lncRNAs in  P. falciparum  transcriptional regulation.    Results  We used a high-resolution DNA tiling microarray to survey transcriptional activity across 22.6% of the  P. falciparum  strain 3D7 genome. We identified 872 protein-coding genes and 60 putative  P. falciparum  lncRNAs under developmental regulation during the parasite's pathogenic human blood stage. Further characterization of lncRNA candidates led to the discovery of an intriguing family of lncRNA telomere-associated repetitive element transcripts, termed lncRNA-TARE. We have quantified lncRNA-TARE expression at 15 distinct chromosome ends and mapped putative transcriptional start and termination sites of lncRNA-TARE loci. Remarkably, we observed coordinated and stage-specific expression of lncRNA-TARE on all chromosome ends tested, and two dominant transcripts of approximately 1.5 kb and 3.1 kb transcribed towards the telomere.    Conclusions  We have characterized a family of 22 telomere-associated lncRNAs in  P. falciparum . Homologous lncRNA-TARE loci are coordinately expressed after parasite DNA replication, and are poised to play an important role in  P. falciparum  telomere maintenance, virulence gene regulation, and potentially other processes of parasite chromosome end biology. Further study of lncRNA-TARE and other promising lncRNA candidates may provide mechanistic insight into  P. falciparum  transcriptional regulation.

A global transcriptional analysis of Plasmodium falciparum malaria reveals a novel family of telomere-associated lncRNAs