Eukaryotic cytosine methylation represses transcription but also occurs in the bodies of active genes, and the extent of methylation biology conservation is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons is not. We show that methylation of plant transposons in the CHG context extends to green algae and that exclusion of histone H2A.Z from methylated DNA is conserved between plants and animals, and we present evidence for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes.

The expression of many metazoan genes is regulated through controlled release of RNA polymerase II (Pol II) that has paused during early transcription elongation. Pausing is highly enriched at genes in stimulus-responsive pathways, where it has been proposed to poise downstream targets for rapid gene activation. However, whether this represents the major function of pausing in these pathways remains to be determined. To address this question, we analyzed pausing within several stimulus-responsive networks in Drosophila and discovered that paused Pol II is much more prevalent at genes encoding components and regulators of signal transduction cascades than at inducible downstream targets. Within immune-responsive pathways, we found that pausing maintains basal expression of critical network hubs, including the key NF-kB transcription factor that triggers gene activation. Accordingly, loss of pausing through knockdown of the pause-inducing factor NELF leads to broadly attenuated immune gene activation. Investigation of murine embryonic stem cells revealed that pausing is similarly widespread at genes encoding signaling components that regulate self-renewal, particularly within the MAPK/ERK pathway. We conclude that the role of pausing goes well beyond poising-inducible genes for activation and propose that the primary function of paused Pol II is to establish basal activity of signal-responsive networks. All organisms have evolved strategies to facilitate rapid and balanced responses to environmental and developmental cues. One mechanism for achieving robust upregulation of transcription in response to the external environment is exemplified by the Drosophila heatshock (Hsp) genes, which possess preloaded RNA polymerase II (Pol II) on their promoters prior to induction (Lis 1998). This Pol II is engaged in early elongation and remains paused promoter-proximally, associated with a 20-to 60-nucleotide (nt) nascent RNA. Heat shock triggers nearly immediate release of paused Pol II into the Hsp genes, permitting the scaffold of general transcription factors left at the promoter to be reused by additional Pol II molecules that generate a dramatic induction of RNA levels within minutes of heat shock (Lis 1998;Zobeck et al. 2010).Pol II pausing has recently been identified as a widespread mechanism of transcriptional regulation in higher eukaryotes. Genome-wide localization of Pol II in Drosophila, mouse, and human cells showed that thousands of genes display an accumulation of Pol II just downstream from their promoters (Guenther et al. 2007;Muse et al. 2007;Zeitlinger et al. 2007;Core et al. 2008;Lee et al. 2008;Gilchrist et al. 2010; Rahl et al. 2010), and analyses of RNA confirm that this polymerase is predominantly in a transcriptionally engaged, but paused, state (Core et al. 2008;Nechaev et al. 2010;Min et al. 2011). Notably, in all cell types investigated, pausing is found to be highly enriched among genes in stimulusresponsive networks, such as those that sense environmental and developmental cues (Muse et al. 20...

In this report we describe chd1 mutant alleles and show that the CHD1 chromatin-remodeling factor is important for wing development and fertility. While CHD1 colocalizes with elongating RNA polymerase II (Pol II) on polytene chromosomes, elongating Pol II can persist on chromatin in the absence of CHD1. These results clarify the roles of chromatin remodelers in transcription and provide novel insights into CHD1 function.