Genome-wide DNA rearrangements occur in many eukaryotes but are most exaggerated in ciliates, making them ideal model systems for epigenetic phenomena. During development of the somatic macronucleus, Oxytricha trifallax destroys 95% of its germ line, severely fragmenting its chromosomes, and then unscrambles hundreds of thousands of remaining fragments by permutation or inversion. Here we demonstrate that DNA or RNA templates can orchestrate these genome rearrangements in Oxytricha, supporting an epigenetic model for sequence-dependent comparison between germline and somatic genomes. A complete RNA cache of the maternal somatic genome may be available at a specific stage during development to provide a template for correct and precise DNA rearrangement. We show the existence of maternal RNA templates that could guide DNA assembly, and that disruption of specific RNA molecules disables rearrangement of the corresponding gene. Injection of artificial templates reprogrammes the DNA rearrangement pathway, suggesting that RNA molecules guide genome rearrangement.Parental RNA transcripts and microRNAs are critical for programming development in metazoa 1-4 , raising the possibility that altered RNA molecules can reprogramme patterning on a developmental or evolutionary timescale 5 . Despite the suggestion of template-directed events involving "an ancestral RNA-sequence cache" 6 there has been limited evidence for a direct role of RNA as a template of information across generations 7,8 . Information transfer from RNA to DNA usually involves polymerization 9 . Here we show that RNA molecules can also organize DNA rearrangements, expanding the epigenetic influence of RNA beyond gene expression and priming or directing DNA and RNA synthesis, editing, modification or repair 9-11 .O. trifallax is a unicellular eukaryote harbouring two kinds of nuclei: germline micronuclei and somatic macronuclei. Diploid micronuclei are transcriptionally inert during vegetative growth but they transmit the germline genome through subsequent generations. Effectively polyploid macronuclei provide all vegetative gene expression, but degrade after fertilization, when new micronuclei and macronuclei develop. DNA differentiation in ciliates such as Oxytricha (also called Sterkiella) involves massive chromosome fragmentation and deletion of transposons and internally eliminated sequences (IESs), accomplishing 95% genome Author Information TEBPα and TEBPβ macronucleus and micronucleus sequences have been submitted to GenBank under accession numbers EU047938-EU047941. Reprints and permissions information is available at www.nature.com/reprints. Correspondence and requests for materials should be addressed to L. RNAi against putative templates disrupts rearrangementTo test the hypothesis that putative maternal RNA templates influence rearrangement, we induced RNA interference (RNAi) to target homologous RNA degradation. Oxytricha cells, before and during conjugation, were fed Escherichia coli producing double stranded RNA fragments of two m...

The cyanobacterium Synechococcus elongatus PCC 7942 exhibits oscillations in mRNA transcript abundance with 24-h periodicity under continuous light conditions. The mechanism underlying these oscillations remains elusive-neither cis nor trans-factors controlling circadian gene expression phase have been identified. Here, we show that the topological status of the chromosome is highly correlated with circadian gene expression state. We also demonstrate that DNA sequence characteristics of genes that appear monotonically activated and monotonically repressed by chromosomal relaxation during the circadian cycle are similar to those of supercoiling-responsive genes in Escherichia coli. Furthermore, perturbation of superhelical status within the physiological range elicits global changes in gene expression similar to those that occur during the normal circadian cycle.circadian clock ͉ gene expression ͉ supercoiling ͉ cyanobacteria C ircadian rhythms in gene expression have been identified in many organisms. In general, 5-15% of an organism's transcriptome oscillates with 24-h periodicity in the absence of external cues such as light to dark or dark to light transitions (1). These transcriptional rhythms are controlled by an endogenous biological clock and allow organisms to schedule processes at appropriate times during the day and night cycle. The cyanobacterium Synechococcus elongatus PCC 7942 (hereafter, S. elongatus) is particularly striking because the majority of its gene expression is under circadian control in continuous light conditions. A ''promoter trap'' analysis using a bacterial luciferase reporter integrated at approximately 30,000 random loci showed circadian oscillations in bioluminescence at all 800 locations where bioluminescence signal was detected (2). A recent measurement of mRNA levels by microarray analysis demonstrated that at least 30% of transcript levels oscillated in circadian fashion (3). The discrepancy between promoter trap and microarray analysis is not surprising and is at least partially attributable to a combination of: (i) the limited time-resolution of microarrays and; (ii) the time-averaging of transcript levels observed in the bioluminescence output of promoter trap studies due to finite luciferase protein lifetime. The actual percentage of circadian transcripts in S. elongatus is likely between 30 and 100%; here we observe that 64% of transcripts oscillate with circadian periodicity (Fig. 1A).In S. elongatus, circadian oscillations in transcriptional activity require three genes, kaiA, kaiB, and kaiC, whose products comprise the core circadian oscillator. The proteins encoded by the kai genes interact with one another to generate circadian rhythms in KaiC phosphorylation at serine and threonine residues (4). Amazingly, an in vitro mixture of the Kai proteins and ATP reproduces in vivo oscillations in the phosphorylation state of KaiC (5). Inactivation of any kai gene abolishes circadian oscillations in both transcription and phosphorylation, and when kaiC is mutated such that p...

Goal-directed navigation is thought to rely on the activity of head-direction cells, but how this activity guides moment-to-moment action remains poorly understood. Here we characterize how heading neurons in the Drosophila central complex guide moment-to-moment actions. We establish an innate, heading-neuron dependent, tethered navigational behavior where walking flies maintain a straight trajectory along a specific angular bearing for hundreds of body lengths. While flies perform this task, we use chemogenetics to transiently rotate their neural heading estimate and observe that the flies slow down and turn in a direction that aims to return the heading estimate to the angle it occupied prior to stimulation. These results support a working model in which the fly brain quantitatively compares an internal estimate of current heading with an internal goal heading and uses the sign and magnitude of the difference to determine which way to turn, how hard to turn, and how fast to walk forward.