Friday, October 21, 2011

RNA-Seq using Ribo-Zero-treated RNA aids study of chromatin-associated RNA

The structural organization of actively transcribed regions of chromatin (euchromatin) is an area of intense interest. A recent report by Caudron-Herger et al. identified a new class of RNA that is associated with transcriptionally active chromatin. The authors termed these transcripts “chromatin-interlinking” RNAs or ciRNAs.

By combining fluorescence microscopy and microinjection of substrate-specific RNases, such as RNase A, RNase III, and RNase H, the authors conclude that ciRNA is single-stranded.  They further characterized ciRNA by RNA-Seq using purified nuclear RNA fractions treated with the Ribo-Zero™ rRNA Removal Kit. ciRNA was found to compromise  long (>500 nt) RNA polymerase II transcripts that were “spliced, depleted of polyadenylation and enriched with long 3'-untranslated regions (3’-UTRs) above ~800 nt."

Based on their results, the authors conclude that ciRNA “plays an important role in maintaining a decondensed and biologically active inter-phase chromatin conformation in human and mouse cell lines” and propose that ciRNA “could act as genome-organizing architectural factors of actively transcribed chromatin compartments.”
ResearchBlogging.orgCaudron-Herger M et al. (2011). Coding RNAs with a non-coding function: Maintenance of open chromatin structure. Nucleus (Austin, Tex.), 2 (5) PMID: 21983088

Tuesday, October 11, 2011

Illumina launches Nextera DNA Sample Prep Kit

Illumina today announced the availability of the Nextera™ DNA Sample Prep Kit. The new kit offers several advantages over the current Epicentre Nextera kits:
  • Fastest time to results: Go from DNA to data in less than 8 hours with Illumina’s MiSeq™ system.
  • Highest throughput: Index up to 96 samples and use master-mixed reagents to manually process > 500 samples per week.
  • Optimized PCR: Improved formulations with fewer cycles deliver reduced GC bias and lower error rates; PCR reagents are now bundled into reagent kits.
  • Improved insert size distribution: Support long paired-end 2x150 reads on MiSeq.
  • Increased process efficiency: Automation-friendly plate-based protocol.
Epicentre's Ilumina-compatible Nextera kits will be discontinued effective December 31, 2011.

Update: The Nextera DNA Sample Prep Kits (Roche 454-Compatible) will continue to be available for sale through Epicentre Customer Service until May 31, 2012, with delivery of final shipments required by June 30, 2012. We apologize for any inconvenience and hope this transition period will allow you to complete any ongoing projects.