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Long intergenic non-coding RNAs (lincRNAs) are transcripts longer than 200 nucleotides that are transcribed from non-coding loci yet undergo biosynthesis similar to coding mRNAs. The disproportional number of lincRNAs expressed in testes suggests that lincRNAs are important during gametogenesis, but experimental evidence has implicated very few lincRNAs in this process. We took advantage of the relatively limited number of lincRNAs in the genome of the nematode Caenorhabditis elegans to systematically analyse the functions of lincRNAs during meiosis. We deleted six lincRNA genes that are highly and dynamically expressed in the C. elegans gonad and tested the effects on central meiotic processes. Surprisingly, whereas the lincRNA deletions did not strongly impact fertility, germline apoptosis, crossovers, or synapsis, linc-4 was required for somatic growth. Slower growth was observed in linc-4-deletion mutants and in worms depleted of linc-4 using RNAi, indicating that linc-4 transcripts are required for this post-embryonic process. Unexpectedly, analysis of worms depleted of linc-4 in soma versus germline showed that the somatic role stems from linc-4 expression in germline cells. This unique feature suggests that some lincRNAs, like some small non-coding RNAs, are required for germ-soma interactions.

C. elegans worms exhibit a natural chemotaxis towards food cues. This provides a potential platform to study the interactions between stimulus valence and innate behavioral preferences. Here we perform a comprehensive set of choice assays to measure worms’ relative preference towards various attractants. Surprisingly, we find that when facing a combination of choices, worms’ preferences do not always follow value-based hierarchy. In fact, the innate chemotaxis behavior in worms robustly violates key rationality paradigms of transitivity, independence of irrelevant alternatives and regularity. These violations arise due to asymmetric modulatory effects between the presented options. Functional analysis of the entire chemosensory system at a single-neuron resolution, coupled with analyses of mutants, defective in individual neurons, reveals that these asymmetric effects originate in specific sensory neurons.

Underwater divers are susceptible to neurological risks due to their exposure to increased pressure. Absorption of elevated partial pressure of inert gases such as helium and nitrogen may lead to nitrogen narcosis. Although the symptoms of nitrogen narcosis are known, the molecular mechanisms underlying these symptoms have not been elucidated. Here, we examined the behaviour of the soil nematode Caenorhabditis elegans under scuba diving conditions. We analysed wild-type animals and mutants in the dopamine pathway under hyperbaric conditions, using several gas compositions and under varying pressure levels. We found that the animals changed their speed on a flat bacterial surface in response to pressure in a biphasic mode that depended on dopamine. Dopamine-deficient cat-2 mutant animals did not exhibit a biphasic response in high pressure, while the extracellular accumulation of dopamine in dat-1 mutant animals mildly influenced this response. Our data demonstrate that in C. elegans , similarly to mammalian systems, dopamine signalling is involved in the response to high pressure. This study establishes C. elegans as a powerful system to elucidate the molecular mechanisms that underly nitrogen toxicity in response to high pressure.

Efficient navigation based on chemical cues is an essential feature shared by all animals. These cues may be encountered in complex spatio-temporal patterns and with orders of magnitude varying intensities. Nevertheless, sensory neurons accurately extract the relevant information from such perplexing signals. Here, we show how a single sensory neuron inC. elegansworms can cell-autonomously encode complex stimulus patterns composed of instantaneous sharp changes and of slowly-changing continuous gradients. This encoding relies on a simple negative feedback in the GPCR signaling pathway in which TAX-6/Calcineurin plays a key role in mediating the feedback inhibition. Crucially, this negative feedback pathway supports several important coding features that underlie an efficient navigation strategy, including exact adaptation and adaptation to the magnitude of the gradient’s first derivative. A simple mathematical model accurately captured the fine neural dynamics of both wt andtax-6mutant animals, further highlighting how the calcium-dependent activity of TAX-6/Calcineurin dictates GPCR inhibition and response dynamics. As GPCRs are ubiquitously expressed in all sensory neurons, this mechanism may be a universal solution for efficient cell-autonomous coding of external stimuli.

SummaryThe notion that associative memories may be transmitted across generations is intriguing, yet controversial. Here, we trainedC. elegansnematodes to associate an odorant with stressful starvation conditions, and surprisingly, this associative memory was evident two generations down of the trained animals. The inherited memory endowed the progeny with a fitness advantage, as memory reactivation induced rapid protective stress responses that allowed the animals to prepare in advance for an impending adversity. Sperm, but not oocytes, transmitted the associative memory, and the inheritance required H3K9 and H3K36 methylations, the small RNA-binding Argonaute NRDE-3, and intact neuropeptide secretion. Remarkably, activation of a single chemosensory neuron sufficed to induce a serotonin-mediated systemic stress response in both the parental trained generation and in its progeny. These findings challenge long-held concepts by establishing that associative memories may indeed be transferred across generations.

Long intergenic non-coding RNAs (lincRNAs) are transcripts longer than 200 nucleotides that are transcribed from non-coding loci yet undergo biosynthesis similar to coding mRNAs. The disproportional number of lincRNAs expressed in testes suggests that lincRNAs are important during gametogenesis, but experimental evidence has implicated very few lincRNAs in this process. We took advantage of the relatively limited number of lincRNAs in the genome of the nematode Caenorhabditis elegans to systematically analyse the functions of lincRNAs during meiosis. We deleted six lincRNA genes that are highly and dynamically expressed in the C. elegans gonad and tested the effects on central meiotic processes. Surprisingly, whereas the lincRNA deletions did not strongly impact fertility, germline apoptosis, crossovers, or synapsis, linc-4 was required for somatic growth. Slower growth was observed in linc-4-deletion mutants and in worms depleted of linc-4 using RNAi, indicating that linc-4 transcripts are required for this post-embryonic process. Unexpectedly, analysis of worms depleted of linc-4 in soma versus germline showed that the somatic role stems from linc-4 expression in germline cells. This unique feature suggests that some lincRNAs, like some small non-coding RNAs, are required for germ-soma interactions.

A major goal in neuroscience is to elucidate the principles by which memories are stored in a neural network. Here, we have systematically studied how four types of associative memories (short- and long-term memories, each as positive and negative associations) are encoded within the compact neural network of Caenorhabditis elegans worms. Interestingly, sensory neurons were primarily involved in coding short-term, but not long-term, memories, and individual sensory neurons could be assigned to coding either the conditioned stimulus or the experience valence (or both). Moreover, when considering the collective activity of the sensory neurons, the specific training experiences could be decoded. Interneurons integrated the modulated sensory inputs and a simple linear combination model identified the experience-specific modulated communication routes. The widely distributed memory suggests that integrated network plasticity, rather than changes to individual neurons, underlies the fine behavioral plasticity. This comprehensive study reveals basic memory-coding principles and highlights the central roles of sensory neurons in memory formation.

SummaryInducible transcription is essential for consolidation of salient experiences into long-term memory. However, the question of whether inducible transcription relays information representing the identity of the experience being encoded, has not been explored. To this end, we have analyzed transcription across multiple brain regions, induced by a variety of rewarding and aversive experiences. Our results define robust transcriptional signatures uniquely characterizing individual salient experiences. A subset of these induced transcriptional markers suffice for near-perfect decoding of the identity of recent experiences at the level of individual mice. Furthermore, experiences with shared attributes display commonalities in their transcriptional representation, exemplified in the representation of valence, habituation and reinforcement. Taken together, our results demonstrate the existence of a neural transcriptional code that represents the encoding of experiences in the mouse brain. This code is comprised of distinct transcriptional signatures that correlate to the affective attributes of the experiences that are being encoded.

Can we tell what important event a mouse – or even a person – has recently experienced? The current experience of an individual can be inferred from brain imaging experiments. However, along with changing brain activity, such an experience also switches on gene activity throughout the brain. This enables neurons to produce the proteins required to form a long-term memory of the experience. Do distinct, memorable experiences trigger unique signatures of gene activity? To answer this question, Mukherjee, Ignatowska-Jankowska, Itskovits et al. exposed mice to a variety of experiences. Some were unpleasant and induced aversion; for example, the mouse may have felt nauseous or experienced brief pain and fear. Other experiences, such as when the mouse drank sugary water, received food or was injected with cocaine, were rewarding. Each of the experiences led to the activation of unique combinations of genes in different regions of the brain. Analysing a subset of the activated genes in various brain regions led to the identification of unique and reliable gene expression signatures of experience. These signatures allowed the recent experience of mice to be decoded with nearly 100% accuracy. While these unique signatures can distinguish between recent experiences, experiences that share common features do trigger overlapping patterns of gene activation. For example, negative experiences – but not positive or neutral ones – activated similar patterns of genes in a brain region called the amygdala. In contrast, repeated rewarding experiences induced a distinct gene activity pattern that was most pronounced as increased activity in part of the brain called the frontal cortex. These findings increase our understanding of how the brain represents information. The approach described in the paper provides a strategy to measure the changes in the brain that occur when information is encoded for long-term storage. This measure could also be useful during drug development, revealing how new drug compounds affect the brain, as well as providing an objective measure of the subjective experience of an individual. For example, substances that trigger similar patterns of gene activation to addictive drugs may themselves be addictive. On the other hand, substances that induce similar activity patterns to known medications could also have similar therapeutic properties.

A major goal of systems neuroscience is to decipher the structure-function relationship in neural networks. Here we study network functionality in light of the common-neighbor-rule (CNR) in which a pair of neurons is more likely to be connected the more common neighbors it shares. Focusing on the fully-mapped neural network of C. elegans worms, we establish that the CNR is an emerging property in this connectome. Moreover, sets of common neighbors form homogenous structures that appear in defined layers of the network. Simulations of signal propagation reveal their potential functional roles: signal amplification and short-term memory at the sensory/inter-neuron layer, and synchronized activity at the motoneuron layer supporting coordinated movement. A coarse-grained view of the neural network based on homogenous connected sets alone reveals a simple modular network architecture that is intuitive to understand. These findings provide a novel framework for analyzing larger, more complex, connectomes once these become available., Author Summary How can we understand the function of gigantic complex networks (e.g. the brain) based on connectivity data alone? We use the available full connectome of a nematode and apply new approaches to find that the neural network is made of structurally homogeneous neural circuits. These sets of neurons also appear in defined regions of the network where they may provide valuable functional roles such as signal integration and synchronization. Moreover, if we redraw the network considering these homogeneous sets alone, we reveal a simplified network layout that is intuitive to understand. As connectome data of higher brain systems are soon to be released our novel approaches can be immediately applied to studying these complex systems.

The packaging of eukaryotic genomes into nucleosomes plays critical roles in all DNA-templated processes, and chromatin structure has been implicated as a key factor in the evolution of gene regulatory programs. While the functions of many histone modifications appear to be highly conserved throughout evolution, some well-studied modifications such as H3K9 and H3K27 methylation are not found in major model organisms such asSaccharomyces cerevisiae, while other modifications gain/lose regulatory functions during evolution. To study such a transition we focused on H3K9 methylation, a heterochromatin mark found in metazoans and in the fission yeastS. pombe, but which has been lost in the lineage leading to the model budding yeastS. cerevisiae. We show that this mark is present in the relatively understudied yeastKluyveromyces lactis, a Hemiascomycete that diverged fromS. cerevisiaeprior to the whole-genome duplication event that played a key role in the evolution of a primarily fermentative lifestyle. We mapped genome-wide patterns of H3K9 methylation as well as several conserved modifications. We find that well-studied modifications such as H3K4me3, H3K36me3, and H3S10ph exhibit generally conserved localization patterns. Interestingly, we show H3K9 methylation inK. lactisprimarily occurs over highly-transcribed regions, including both Pol2 and Pol3 transcription units. We identified the H3K9 methylase as the ortholog ofSet6, whose function inS. cerevisiaeis obscure. Functionally, we show that deletion ofKlSet6does not affect highly H3K9me3-marked genes, providing another example of a major disconnect between histone mark localization and function. Together, these results shed light on surprising plasticity in the function of a widespread chromatin mark.