In a work just published at Nature, Churchman and Weissman (2011) describe a new method for directly capturing and sequencing elongating, or nascent, RNA transcripts. The authors then use this method to provide a detailed look at the transcriptional process in action, revealing a histone modification-dependent mechanism that constrains genome-wide antisense transcription, and pervasive transcriptional pausing and backtracking throughout genes.
The work adds to a rapidly expanding functional genomics toolkit that allows researchers to dissect evermore precise steps in the Central Dogma — the DNA to RNA to protein cascade that transforms genomic information into cellular function. See also the recent work by Cramer and colleagues that describes a method for quantifying genome-wide mRNA synthesis and decay rates (Miller et al, 2011), and the ribosome profiling technique, also developed in the Weissman lab, which can provide genome-wide views of protein translation (Ingolia et al, 2009).
Churchman LS & Weissman JS (2011) Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 469: 368–373
Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324:218-23
Miller C, Schwalb B, Maier K, Schulz D, Dümcke S, Zacher B, Mayer A, Sydow J, Marcinowski L, Dölken L, Martin DE, Tresch A, Cramer P (2011) Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol 7:458