A recent study by Koerner et al. cites the use of Epicentre's most popular products: the Ribo-Zero™ Kit (Human/Mouse/Rat) to deplete rRNA, and the ScriptSeq™ Kit to prepare RNA-Seq libraries. The authors explored the presence of CpG islands at the 5' end of the Airn noncoding RNA (ncRNA). This region contains some unusual features, such as a GC-rich region just downstream from the promoter, and tandem direct repeats (TDR) in its second half.
The authors used homologous recombination to generate embryonic stem cells that carry deletions at the endogenous locus of the entire CpG island or only the TDRs. The TDRs were shown to play a small part in the Airn transcription elongation process, but a much larger part in methylation of the Airn promoter that comes from the maternal allele. Further, the CpG island is essential for transcription initiation of Airn, and in maintaining the unmethylated state of the Airn promoter. The research provides insight into how the imprinted Airn ncRNA CpG island (normally methylated on the maternal and unmethylated on the paternal chromosome) regulates its associated promoter, suggesting that a class of CpG islands can exhibit regulatory effects on upstream transcriptional elements.
Koerner, M. et al. (2012). A Downstream CpG Island Controls Transcript Initiation and Elongation and the Methylation State of the Imprinted Airn Macro ncRNA Promoter PLoS Genetics, 8 (3) DOI: 10.1371/journal.pgen.1002540