Chromatin meets RNA polymerase II

It is becoming increasingly clear that the mechanisms governing eukaryotic transcription are as diverse and complex as the organisms in which they are studied. The recent Cold Spring Harbor Laboratory meeting on mechanisms of eukaryotic transcription covered various topics, including epigenetics, the architecture and regulation of the chromatin landscape through histone modifications, and the mechanisms of transcription initiation and elongation by RNA polymerase II (Pol II). Here we report on the latter two topics, attempting to integrate chromatin and Pol II regulatory mechanisms.How nucleosomes are organized throughout a genome sets the stage on which the transcription machinery engages each and every gene. Complete high-resolution maps of nucleosome locations and their modifications are now coming to light through high-resolution and data-intensive technologies such as chromatin immunoprecipitation followed by sequencing or microarray identification of the pulled-down DNA (ChIP-seq or ChIP-chip, respectively).Keji Zhao (National Heart, Lung, and Blood Institute, NIH, Bethesda, USA) reported work on the genome-wide distributions of numerous histone modifications and the histone variant H2A.Z in human cells. Using ChIP-seq, he found that monomethylation of H3 lysine 9 (K9), H3K27, H3K79, H4K20, and H2BK5 is associated with gene activation, whereas trimethylation of H3K9, H3K27, and H3K79 is linked to repression. He also found that H2A.Z was preferentially found in promoter regions, consistent with previous reports in yeast. One of us (B.F.P.) reported genome-wide maps of nucleosome locations in Saccharomyces cerevisiae and Drosophila melanogaster obtained using ChIP-seq. Their nucleosome organization was found to be remarkably similar in many respects, including nucleosome-free regions at the beginning and end of genes. However, flies place their +1 nucleosome (the first nucleosome downstream of the transcription start site) a bit further downstream than in yeast,