Natural genetic variation can cause significant differences in gene expression, but little is known about the polymorphisms that affect gene regulation. We analyzed regulatory variation in a cross between laboratory and wild strains of Saccharomyces cerevisiae. Clustering and linkage analysis defined groups of coregulated genes and the loci involved in their regulation. Most expression differences mapped to trans-acting loci. Positional cloning and functional assays showed that polymorphisms in GPA1 and AMN1 affect expression of genes involved in pheromone response and daughter cell separation, respectively. We also asked whether particular classes of genes were more likely to contain trans-regulatory polymorphisms. Notably, transcription factors showed no enrichment, and trans-regulatory variation seems to be broadly dispersed across classes of genes with different molecular functions.

Permafrost contains an estimated 1672 Pg carbon (C),metagenomes converged to be more similar to each other than while they were frozen. We found that multiple genes involved in cycling of C and nitrogen shifted rapidly during thaw. We also constructed the first draft genome from a complex soil metagenome, which corresponded to a novel methanogen. Methane previously accumulated in permafrost was released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost.We collected three intact frozen permafrost soil cores with their overlying seasonally thawed active layers from Hess Creek (HC), Alaska. This is a black spruce forest site containing many meters of frozen peat and the C was dated to 1200 ybp 10 .Other soil properties and microbial respiration rates were previously characterized 10 .Frozen active layer and permafrost layer samples from each core were thawed and incubated for 7 days at 5°C under a He headspace. During the incubations, CH 4 ( Fig. 1a) and CO 2 ( Supplementary Fig 1) concentrations were monitored in the headspace and DNA was extracted for 16S ribosomal RNA (rRNA) and metagenome sequencing.There was a burst of CH 4 from the permafrost within 48 h of thaw, followed by a significant (P = 0.05) decrease in concentration from day 2 to day 7 (Fig. 1a). To determine (a) if methane release was due to post-thaw production or from trapped gas, (b)whether the methane was consumed by methanotrophs or anaerobic methane oxidizers, and (c) the CH 4 oxidation potential over time, we treated additional samples with 1500 3 ppm CH 4 and 2-bromoethane sulphonic acid (BES) and measured CH 4 levels daily. BES is an inhibitor of archaeal methanogenesis and methyl-coenzyme M reductase (MCR)-dependent anaerobic methane oxidation. Rapid release of CH 4 from samples treated with BES suggested that the CH 4 primarily originated from gas present in the permafrost prior to thaw ( Supplementary Fig. 2), as previously reported 11 . Subsequent CH 4 consumption in both BES and non-BES-treated samples was indicative of CH 4 oxidation by methanotrophic bacteria (Fig. 1b). The oxygen utilized for methane oxidation presumably originated from permafrost water or aerobic microsites in the samples 12 . Together these data indicate CH 4 levels are dynamic in thawing permafrost.To determine the phylogenetic and functional gene repertoire before and after thaw, we performed deep metagenome sequencing of samples from two of the three replicate cores (cores 1 and 2). DNA was extracted from frozen active layer and permafrost samples and from samples thawed at 5°C for 2 and 7 days. This resulted in 12 samples for metagenome sequencing.Due to low DNA yield we used emulsion PCR (emPCR) to generate random shotgun short insert libraries with minimum amplification bias 13 . Sequencing yielded a total of 176 million reads and 39.8 Gb of raw sequence. The individual metagenome reads were annotated by comparison to protein-coding...