AP-2 transcription factors, which control sleep in flies and worms, are confirmed to do the same in mammals.

Humans are not alone in their deep need for sleep. Almost all animals, even tiny nematode worms and fruit flies, suffer when deprived of their Z’s, but little is known about how sleep is controlled. New work published in GENETICS advances our understanding of this mysterious physiological state by pinpointing a key gene family that affects sleep architecture.

Two research groups independently conducted parallel studies on neural crest-derived AP-2 transcription factors in mice. Their work demonstrates that the associated genes play a conserved role in mammalian sleep, though there is some evolutionary divergence and added complexity in mammals compared to invertebrates.

From Worms to Mice

Henrik Bringmann leads the Max Planck Research Group on Sleeping and Waking. In 2013, his laboratory screened C. elegans worms for mutations affecting sleep. AP-2 deletion mutants showed no detectable sleep, suggesting these transcription factors are important regulators of the process. In 2016, Bringmann led another study showing that AP-2 transcription factors are also needed for sleep in Drosophila. 

“Sleep appears to have evolved at least 600 million years ago and has been conserved since then, which suggests that many fundamental principles of sleep regulation are conserved,” said Bringmann. “This said, sleep is more complex in humans than in worms or flies, so we need mammalian models to understand additional levels of complexity.”

The researchers’ next step was to establish whether a similar sleep-regulating role is played by related genes in mammals, the TFAP2 genes. In their most recent study, the team generated mice that were heterozygous knockouts for either Tfap2a or Tfap2b and compared each mutant to wild-type littermates. In addition to analyzing sleep duration and brain waves, they examined symptoms of sleep deprivation such as memory loss and stress resistance.

Since the AP-2 transcription factors promote sleep in invertebrates, researchers initially expected that the equivalent genes would also promote sleep in mice. They were therefore surprised to find that while losing Tfap2bfunction reduced both sleep quality and quantity, Tfap2a mutants slept for the typical amount of time and the quality of their sleep was actually higher than wild-type. This result suggests that the function of AP-2 transcription factors has diverged over the course of evolution, perhaps to allow sleep quality to be fine-tuned in either direction.

Working Backwards from Human Disorders

Meanwhile, another research group also published an article in the same issue of GENETICS examining the effects of two specific TFAP2B mutations in mice. Yu Hayashi of Kyoto University  and University of Tsukuba said his lab was inspired to pursue this avenue of research by a paper in PNAS. That study described multiple human families with mutations in TFAP2B that are associated with a rare disorder known as Char syndrome. Two of these families exhibited symptoms of disordered sleep, including sleepwalking and extremely shortened sleep.

“We were astonished to read about a family that slept just two to three hours per night and had no signs of fatigue. We thought that maybe analyzing this gene can help us understand what sleep is for in the first place,” said Hayashi. “We even thought that maybe this mutation might somehow substitute for the function of sleep. Could there be a way to help humans need less sleep?”

To answer these questions, Hayashi’s team set out to replicate those families’ specific TFAP2B point mutations in mouse models. They measured both how long the mice stayed awake and the duration of different sleep phases compared to wild-type mice and heterozygous knockouts. The results showed that TFAP2B helps determine the amount of nonrapid eye movement sleep (NREMS). However, the effects of the point mutations in mice did not match the symptoms observed in humans—the mice did not sleepwalk or show dramatically shortened sleep.

In the mice that carried the same mutation as the human family with short sleep, female mice showed fragmented sleep, while male mice did not. This result was unforeseen because there was no reported gender difference in the human family. “It was surprising for me to see the gender difference,” said lead author Ayaka Nakai, a graduate student in the Hayashi lab. It is possible that future research may uncover sex differences in sleep regulation.

In terms of generating a model of fatigue-free short sleep, the results did not match their initial hopes—sleep was reduced overall in heterozygous mutant mice, but it was generally fragmented rather than shortened. However, the results clearly established TFAP2B’s important role in sleep architecture and laid the groundwork for learning more about how sleep works.

Next Steps

Ultimately, said Bringmann, “it was satisfying to hear that both approaches converged on the same conclusions regarding TFAP2B’s role in sleep.” Together, these two papers establish that AP-2 transcription factors contribute to sleep control in mammals—just as they do in flies and worms.

The gene’s evolutionary conservation is a key lesson from the study, said Nakai.

For Nakai and Yu, the next research step is creating knockdown mice that have Tfap2b downregulated only in the nervous system. This will allow them to observe the neural effect of a homozygous loss-of-function mutation, which is developmentally lethal if the knockout is genome-wide. Studying a homozygous knockdown may offer clearer insights into how the gene affects neuron specification and activity.

Next, Bringmann is interested in examining other mammalian AP-2 paralogs, but he says invertebrates will continue to be important for identifying other genes that contribute to sleep regulation. “Going back and forth between different models will be the future of sleep research for the next years, and this will be facilitated by looking at homologous genes and conserved principles.”

CITATION:

Functional Divergence of Mammalian TFAP2a and TFAP2b Transcription Factors for Bidirectional Sleep Control

Yang Hu, Alejandra Korovaichuk,  Mariana Astiz, Henning Schroeder, Rezaul Islam, Jon Barrenetxea, Andre Fischer, Henrik Oster and Henrik Bringmann

GENETICS 2020 216: 735-752. 

https://doi.org/10.1534/genetics.120.303533

Sleep Architecture in Mice Is Shaped by the Transcription Factor AP-2β

Ayaka Nakai, Tomoyuki Fujiyama, Nanae Nagata, Mitsuaki Kashiwagi, Aya Ikkyu, Marina Takagi, Chika Tatsuzawa, Kaeko Tanaka, Miyo Kakizaki, Mika Kanuka, Taizo Kawano, Seiya Mizuno, Fumihiro Sugiyama, Satoru Takahashi, Hiromasa Funato, Takeshi Sakurai, Masashi Yanagisawa and Yu Hayashi

GENETICS 2020 216:753-764

https://doi.org/10.1534/genetics.120.303435

New Faculty Profiles allow GSA members who are establishing their first labs to introduce themselves to our wider community. If you’d like to submit your profile, please complete this form.

Aakanksha Singhvi

Assistant Member
Division of Basic Sciences
Fred Hutchinson Cancer Research Center
Lab website

Briefly describe the ongoing and expected research projects as your lab gets up and running.

In a nutshell, “Glia-Neuron interactions,” in health and disease. My laboratory wants to decode the molecular conversations between glia and neurons, the two major cell types of our nervous system. We know that disrupted interactions between glia and neurons are an underlying factor in many neurological disorders of development (e.g. Autism), function (e.g. sensory or cognitive impairments) and aging (e.g. Alzheimer’s). However, mechanisms underlying these interactions are still not well-defined at molecular resolution. We are excited to explore how glia regulate sensory perception, neuronal physiology, neural circuit activity, memory formation, and animal behavior. We use C. elegans as a genetic model because its nervous system has some unique features that make it an especially powerful system to address these questions in vivo.

How has being a member of GSA helped you advance in your career? Why do you think societies like GSA are important? 

My association with GSA started as a graduate student and has helped me grow as a scientist throughout my career, including now in setting up as a new PI. My first C. elegans paper was in GENETICS, and my professional networks have grown through GSA-sponsored worm meetings. As a postdoc, I served as the first Trainee Representative on the GSA publication committee and the TAGC 2016 organizing committee. I have also known of GSA’s support for trainees and advocacy for basic research. As I start a lab, I realize that these experiences have influenced my perspectives on many facets of science—research, administration, mentoring, publishing, and career paths. As a new PI, I am now organizing a Glia workshop at the 2019 C. elegans meeting, and I look forward to continued association with GSA members and trainees.

Are you looking to recruit students and/or postdocs? If so, please describe and be sure to also post the opportunity to GeneticsCareers.org. 
I am always excited to meet students and postdocs who share our wonder for glia-neuron interactions in the nervous system. My lab accepts graduate students from the fantastic inter-departmental programs between Fred Hutch and the University of Washington. Anyone who is interested, please email me! By the way, Seattle is a gorgeous city with an awesome and diverse scientific community.

What is your favorite thing about science or about your work? 
Everything about biology is so cool! As experiences, the thrill of thinking, creating, and exploring this wonder freely with fellow scientists, as well as the “aha” moment when a puzzle clicks into place, are perhaps my favorite things about this job. Every new data point or mutant analysis is a dopamine fix.
As a biological question, I cannot stop being in awe of the nervous system! How do we sense the world around us, make memories of this rich and complex information? How do cells molecularly talk to each other; what do they say? What goes wrong in neural disease or aging? There are so many awesome puzzles to solve that one lifetime feels too little. So, for now, we are focused on finding everything we can about the most mysterious of cells in our brain—glia.

What do you like to do when you’re not at work? 
My other passion is dancing, lindy-hop to dandiya! Throughout my postdoc I actively performed Bharatanatyam, an Indian classical dance form I have trained in, with a dance group in NYC. In a way, I find it parallels biology research. One spends long years passionately mastering the technique, the beauty of its structure and rules, and existing knowledge. Then, you start thinking outside the box, pushing boundaries with your creativity and unique thinking. Each performance takes practice and has a presentation structure and a story to tell. And it is pure joy when audiences engage with your story or findings!

Previous training experiences:

• BS, Gujarat University, India
• MS Fellow, National Center for Biological Sciences, India
• PhD, University of California Berkeley (with Dr. Gian Garriga)
• Postdoctorate, The Rockefeller University (with Dr. Shai Shaham)

Analysis of insulin-like signaling in C. elegans reveals extensive positive and negative feedback regulation.

The insulin-like signaling system of nematode worms is comparable to that of more complex organisms; it helps regulate a wide range of the animal’s biology, including metabolism, growth, and development. This system is remarkably flexible, with the ability to maintain a physiological steady-state (homeostasis) while also controlling switches between quite different developmental fates (developmental plasticity). A report published in GENETICS reveals the pervasive involvement of both positive and negative feedback in regulating this master pathway in the model nematode Caenorhabditis elegans.

The C. elegans genome encodes one insulin-like receptor and 40 insulin-like signaling proteins. The activity of insulin-like peptides can, in turn, affect the expression of these peptides themselves, yet exactly how this signaling network is regulated remains ambiguous. Kaplan et al. explored the extent of the feedback mechanisms of insulin-like signaling, along with their dependence on nutrient availability.

The worm insulin-like receptor, DAF-2, signals through antagonizing the activity of the transcription factor DAF-16, the nematode ortholog of mammalian FoxO. Because of these opposing functions, daf-2– and daf-16-mutant nematodes were employed to observe how changes in insulin-like signaling affect the expression of insulin-like genes.

Using these mutants under multiple conditions, such as fed vs. starved larval worms, the authors analyzed the expression of insulin-like genes, along with other genes involved in insulin-like signaling, like those in the PI3K pathway.

The authors found extensive feedback regulations within insulin-like signaling; the expression of nearly all detectable insulin-like genes was affected by altering insulin-like signaling, as were some components of the PI3K pathway. These feedback mechanisms were extensive and complex; for example, the well-studied insulin-like protein DAF-28, an agonist of DAF-2, seems to be repressed by DAF-16—thus, DAF-28 is a positive regulator of its own transcription, since activating DAF-2 represses DAF-16.

Overall, considerable evidence for both negative and positive feedback of insulin-like signaling was found; the authors write that this is likely to allow for rapid response to stimuli—like food availability—while still maintaining homeostasis. Further studies will be needed to delve into the precise molecular mechanisms of such feedback systems and to explore similar regulation in other organisms.

CITATION:

Pervasive Positive and Negative Feedback Regulation of Insulin-Like Signaling in Caenorhabditis elegans

Rebecca E. W. Kaplan, Colin S. Maxwell, Nicole Kurhanewicz Codd, L. Ryan Baugh

GENETICS  January 2019 211: 349-361; https://doi.org/10.1534/genetics.118.301702

https://www.genetics.org/content/211/1/349

Apoptotic pathway promotes asymmetric cell division during C. elegans development.

Cell division doesn’t always produce identical daughter cells; often, the demands of multicellular development require cells to split into two quite different daughters with quite different fates. These “asymmetric” divisions are needed so that cells can differentiate and specialize, and some cells are even programmed to die shortly after their creation to ensure the proper function of the organism as a whole. In GENETICS, Mishra et al. found that the apoptotic cell death pathway regulates asymmetric division in the nematode worm Caenorhabditis elegans.

C. elegans is an exceptionally useful model organism for studying development because the fate of each of its relatively few cells can be precisely mapped. Many of the cells destined for death in the worm are actually the product of unequal division into a larger cell that differentiates and a smaller cell that undergoes apoptosis. The authors of the new report had previously studied the parent of one such uneven division, a cell known as the embryonic neurosecretory motor neuron neuroblast. They found that in the parental neuroblast, there is a gradient of activated CED-3 caspase, an executioner of apoptosis. This gradient leads to more active CED-3 caspase in the smaller daughter cell, which helps facilitate its death.

The authors wondered whether this CED-3 caspase gradient might be a general phenomenon in asymmetric divisions, so in the GENETICS report they studied another cell that divides into a large cell that survives and a smaller cell that dies: the QL.p neuroblast. The authors identified a similar CED-3 caspase gradient in these cells, showing that the phenomenon is indeed somewhat general.

Then, the authors used loss-of-function mutants to explore the role of the CED-3 caspase and its related pathways in the asymmetric division of QL.p. They found that disrupting the cell death pathway impaired the ability of QL.p to divide asymmetrically and could impact the fate of the daughter cells—often giving rise to two living cells, rather than one that lives and one that dies. Mutations in other genes associated with asymmetric division, like pig-1, also affected the fate of the daughter cells but did not change the CED-3 caspase gradient.

The authors explain that, in QL.p, two molecular gradients are simultaneously created: one of “mitotic potential,” which is normally passed on to the larger daughter to facilitate its differentiation, and one of “apoptotic potential,” which is passed on to the smaller daughter and promotes its death. Although the details of these “potentials” are not yet understood, this separation within the parental cell seems crucial for ensuring that each cell reaches its proper endpoint.

Although caspases are well-known for their role in apoptosis, it is particularly noteworthy that mutations in CED-3 caspase do not only affect the ability of the small daughter cell to die. CED-3 caspase also appears to function in the division of the parental cell, suggesting a more complicated role of this molecular executioner during development.

CITATION:

Caenorhabditis elegans ced-3 Caspase Is Required for Asymmetric Divisions That Generate Cells Programmed To Die

Nikhil Mishra, Hai Wei, Barbara Conradt

GENETICS November 1, 2018 vol. 210 no. 3 983-998; https://doi.org/10.1534/genetics.118.301500

The Genetics Society of America (GSA) is pleased to announce that Anne Villeneuve, PhD, of Stanford University is the recipient of the 2019 Genetics Society of America Medal. Villeneuve is recognized for her research on the mechanisms governing chromosome inheritance during sexual reproduction.  Her research focuses on meiosis, the specialized cell division program involved in generating egg and sperm cells. Meiosis enables diploid organisms (which have two copies of each chromosome) to generate haploid gametes (which have only a single set of chromosomes). This halving of chromosome number is crucial for sexual reproduction, as it allows restoration of the diploid chromosome number in the offspring formed once the egg and sperm fuse.

As an independent fellow at Stanford, Villeneuve recognized the considerable untapped potential of the nematode Caenorhabditis elegans as an experimental system for studying chromosomes during meiosis. Trained as a geneticist, she set out to exploit this opportunity by conducting screens to identify genes important for meiosis, most famously an elegant approach nicknamed “Green eggs and Him,” which was published in GENETICS and continues to be used as an exemplar in many university genetics courses.

Research from Villeneuve’s lab and those of her former trainees has played a key role in establishing C. elegans as one of the premier experimental systems for investigating chromosome organization, genetic recombination, and genome maintenance in the context of meiosis. Villeneuve’s research integrates sophisticated genetic strategies with high-resolution and super-resolution cytological imaging of chromosomes in the context of an optically transparent gonad in which germ cells progressing through meiosis are arranged in a temporal/spatial “time course.” This approach has enabled them to identify numerous components of the machinery responsible for the key chromosomal and DNA events of meiosis and to elucidate the mechanisms underlying these events and how they are coordinated. A substantial fraction of the genetic mutants, assays, and cytological reagents used to investigate genome maintenance, recombination, and meiosis in C. elegans was developed in her laboratory.

Papers published by the Villeneuve lab during the past 15 years have had a significant impact on our understanding of most major aspects of the meiotic program, including pairing between homologous chromosomes; structure, function, assembly and dynamics of the synaptonemal complex (SC), a meiosis-specific structure located at the interface between aligned homologs; formation and repair of DNA double-strand breaks; spatial patterning and maturation of  meiotic crossovers; remodeling of chromosome structure in response to recombination; regulated release of sister chromatid cohesion; organization of chromosomes on the oocyte meiotic spindle; and quality control mechanisms that ensure a robust outcome of meiosis.

“Literally every major event in meiosis has been dissected in Anne’s lab and generated beautiful, high-profile papers,” says Barbara Meyer, a Professor at the University of California, Berkeley and one of the scientists who nominated Villeneuve for the Medal. “It is extremely rare to be able to cite a single lab with such a huge impact on a field of biology.”

A hallmark of research from the Villeneuve lab is the generation of microscopic images of meiotic chromosomes that provide a stunning visual readout of the inner workings of meiosis. This is beautifully illustrated in a recent paper from postdoctoral researcher Alex Woglar, which revealed the distinct spatial architecture of recombination proteins localized at meiotic crossover sites and showed that recombination site architecture undergoes dynamic changes during meiotic progression.

Villeneuve’s group has also provided insight into the process of crossover interference, which was originally described by Muller over 100 years ago, yet has remained largely mysterious during the intervening century. Crossover interference refers to the non-random placement of crossovers, such that a (nascent) crossover reduces the likelihood that another crossover will be formed nearby. A series of papers from the Villeneuve lab exploited genetic and cell biological tools available in the worm to implicate the SC as an important conduit of communication along the chromosomes. Their findings support a model of meiotic crossover regulation as a self-limiting system in which SC components initially promote the formation of crossover intermediates, which in turn trigger a change in the state of the SC that inhibits further crossover formation.

“Anne is a true scholar and has made a number of significant and impactful contributions to the field of genetics over the last 15 years,” says JoAnne Engebrecht, a Professor at the University of California, Davis and one of the scientists who nominated Villeneuve for the GSA Medal. “She embodies the ingenuity of the GSA membership in using genetics to investigate a fundamental biological process.”

Villeneuve’s influence on the fields of meiosis and recombination in particular, and genetics in general, extends well beyond the research conducted in her own lab.   She has an outstanding record for mentoring younger scientists, and many of her trainees have gone on to establish their own productive independent research groups. Moreover, she has fostered a collegial community among meiosis researchers and has provided mentorship for numerous scientists outside her own group. Villeneuve also has a long-standing involvement with the GSA. She first joined the GSA as a graduate student, served as its Secretary from 2013 to 2015, and was an Associate Editor for the GSA journal GENETICS from 2004 to 2010. Villeneuve’s scientific contributions and leadership in the Meiosis and Recombination fields have been recognized in recent years by a Research Professor Award from the American Cancer Society and by her election to the American Academy of Arts and Sciences in 2016 and the National Academy of Sciences of the USA in 2017.

The GSA Medal was established in 1981 to recognize members who have made outstanding contributions to the field of genetics during the past 15 years. The award will be presented to Villeneuve at the 22nd International C. elegans Conference, which will be held June 20–24, 2019 in Los Angeles, CA.

Mitochondria cell-autonomously regulate the secretion of neuropeptides in C. elegans.

Neurons are hard-working cells that need a lot of energy to do their jobs, so it’s no surprise that they are highly dependent on their mitochondria to function properly. Yet these organelles do much more for cells than simply produce energy. In GENETICS, Zhao et al. report on how mitochondria are directly involved in regulating the secretion of neuropeptides.

In a previous paper, the authors found that disruption of the gene ric-7 caused decreased neuropeptide secretion and locomotion defects in C. elegans—but the mechanism underlying these phenotypes was unclear because little was known about the function of ric-7. After another group demonstrated that ric-7 is required for the long-distance transportation of mitochondria from the neuron’s cell body into its axons, Zhao and colleagues hypothesized that disrupting mitochondrial transport might be the mechanism by which ric-7 defects cause neuronal phenotypes.

To test this, the authors expressed a chimeric kinesin construct, kin-Tom7, in ric-7 mutant axons. This chimera is a kinesin protein fused to a mitochondrial membrane protein. A prior study showed that kin-Tom7 restored transport of mitochondria to the axons of ric-7 mutants but did not affect other cellular functions. The authors showed that kin-Tom7 also rescues the ric-7 mutation-impaired neuropeptide secretion and locomotion defects, suggesting that improper mitochondrial transport was indeed the cause of neuronal defects in ric-7 mutants.

Because mitochondria are involved in so many cellular processes, the authors wondered which function(s) of axonal mitochondria might be necessary for neuropeptide secretion. Using selected mutant worms, they found that disrupting oxidative phosphorylation decreased neuropeptide secretion—but impairing mitochondrial calcium uptake didn’t.

Impaired oxidative phosphorylation can cause increased levels of reactive oxygen species (ROS) and hypoxia, so the authors suspected that these stress states might be involved in neuropeptide secretion. Indeed, they found that impairing the function of ROS detoxification enzymes—an alternative way to increase ROS—and growth in hypoxic conditions both led to decreased neuropeptide secretion.

Further investigation showed that the effects of axonal mitochondria on neuropeptide secretion were mediated by the hypoxia-inducible factor HIF-1, which is central to the response to hypoxia in C. elegans. Worms with constitutively active HIF-1 had lower secretion of neuropeptides, but this could be reversed by turning HIF-1 “off” again through other transgenic manipulations. Crucially, combining the constitutively active HIF-1 with the ric-7 defect in a double mutant had no additional phenotypic effects, suggesting the two proteins act in the same pathway. Consistent with this, hif-1 null mutations restored neuropeptide secretion in ric-7 mutants.

Together, these results support the idea that mitochondria regulate neuropeptide secretion in part by modulating ROS production and the hypoxic stress response. These findings could provide a mechanism by which the biochemical conditions within a neuron alter communication between neurons to trigger more widespread changes in the nervous system.

CITATION:

Axonal Mitochondria Modulate Neuropeptide Secretion Through the Hypoxic Stress Response in Caenorhabditis elegans

Tongtong Zhao, Yingsong Hao, Joshua M. Kaplan

Genetics September 2018 210: 275-285; https://doi.org/10.1534/genetics.118.301014

http://www.genetics.org/content/210/1/275

Food-deprivation inhibits the stress-induced sleep response in C. elegans.

For many animals, the essential physiological drives of sleep and food are intimately linked. You might have noticed this if you’ve ever stayed up far too late and found yourself craving a snack. Yet because it’s impossible for most animals to eat and sleep at the same time, these two biological necessities must compete with each other. In GENETICS, Goetting et al. report what happens when the need for sleep and the need for food come into direct conflict in the model nematode Caenorhabditis elegans.

When C. elegans is exposed to a stressful condition like high heat or UV radiation, it goes into a quiescent state called stress-induced sleep (SIS). Sleeping worms cease moving and feeding, and they barely respond to normally unpleasant stimuli—unless they are rudely awoken by a sharp poke.

In contrast, the authors found that food-deprived worms were less prone to this stress-induced snooze than their well-fed counterparts. This was true regardless of whether there was more food around to forage for; that is, the worms tended to remain active after stress whether or not they were provided with additional food after being starved.

The authors also found that starvation-induced sleep-suppression was enhanced when there were more worms on the plate. This makes sense, because higher population densities mean fewer resources, so seeking food instead of going to sleep is likely the better option. Interestingly, crowding only inhibited SIS when worms were starved; well-fed worms in crowded plates showed no change in SIS after stress treatment.

Insulin signaling and TGF-β signaling play major roles in sensing food availability in C. elegans, so the authors asked whether these pathways play a role in SIS under normal conditions. They found that worms with mutations in a TGF-β ligand, but not the insulin receptor, had impairments in SIS. Further investigation revealed that TGF-β involvement in SIS is downstream of the ALA neuron (a master neural regulator of SIS) and dependent on the gene DAF-3, which is involved in TGF-β signaling.

If this DAF-3-dependent pathway was necessary and sufficient for food-deprivation-induced inhibition of SIS, it would follow that worms lacking DAF-3 would have no trouble falling asleep after being starved and stressed—but when the authors tested this, they instead found that the DAF-3 mutants had the same response as wild-types: they stayed awake. Therefore, the authors conclude that although the TGF-β pathway plays a role in normal SIS, it is not solely responsible for the lack of SIS when worms are starved. Consistent with this notion, the authors uncovered evidence that the TOR signaling pathway, which is active when nutrients are available and promotes growth and protein synthesis, plays a role in starvation-induced sleep suppression as well.  

Since sleep deprivation can be deadly, the authors tested whether food deprivation affected how much the worms needed to sleep to stay alive. They found that worms that were deprived of food, stressed, and then kept awake survived better than worms that were just stressed and kept awake. Thus, starving the worms allowed them to stay awake, at least in part, because they needed their sleep less.

CITATION:

Food-Dependent Plasticity in Caenorhabditis elegans Stress-Induced Sleep Is Mediated by TOR–FOXA and TGF-b Signaling

Desiree L. Goetting, Rony Soto, Cheryl Van Buskirk

Genetics August 2018 209: 1183-1195; https://doi.org/10.1534/genetics.118.301204

By borrowing a system found in plants, researchers can turn off sperm production in an inducible, reversible, and non-toxic manner

Let’s say you want to study how your favorite gene affects aging. You pick Caenorhabditis elegans for your study because it is one of the most important models of aging, and you put some of the worms on a plate—but within days, they multiply, and suddenly your plate is a random mix of worms young and old! How are you supposed to study how long these nematodes live? A new system reported in G3: Genes|Genomes|Genetics provides a handy solution: a reversible way to sterilize your worms at the start of the experiment.

Kasimatis et al. set out to create a system for inducing sterility in C. elegans so that mating can be precisely controlled in the lab—whether for aging experiments or for studies in which controlling the timing of mating is beneficial, such as investigations of sexual reproduction itself. While methods like treatment with the chemotherapy agent FUdR have been used for some time, these systems are typically toxic and have off-target effects.

To create a method that was inducible, non-toxic, and reversible, the authors used the auxin-induced degradation (AID) system, which originates from Arabidopsis thaliana. In plants, the hormone auxin causes TIR1 to mark other proteins for ubiquitin-mediated degradation by adding a degron tag. The authors generated worms that express plant TIR1 and have degron tags on the gene spe-44, which is crucial for production of sperm. In these worms, auxin treatment leads TIR1 to degrade spe-44, thus preventing the worms from making sperm.

C. elegans has two sexes: hermaphrodite and male, and the authors tested the AID system in both. Auxin treatment in their model induced self-sterility in both hermaphroditic and male worms, just as expected. Self-sterile hermaphrodites were still able to mate with wild-type males, though, because egg production was unaffected. Male worms treated with auxin as larvae regained their virility after auxin withdrawal in adulthood, demonstrating that the system is reversible. The authors also compared their system to the common FUdR system; the new AID system resulted in longer lifespans, demonstrating that it’s a less toxic approach.

This new system, while an improvement over previous methods, is not without its drawbacks. Worms with degron-tagged spe-44 that were not treated with auxin still showed a detectable, though statistically insignificant, decrease in fertility, likely because the function of spe-44 was affected by the degron tag. Still, the AID system is a big advance over chemically toxic methods and is less labor-intensive than separating out adult worms by hand, leaving researchers more flexibility in designing assays to study longevity and mating.

Citation:

Auxin-Mediated Sterility Induction System for Longevity and Mating Studies in Caenorhabditis elegans

Katja R. Kasimatis, Megan J. Moerdyk-Schauwecker, Patrick C. Phillips

G3: GENES|GENOMES|GENETICS August 2018 8: 2655-2662; https://doi.org/10.1534/g3.118.200278

http://www.g3journal.org/content/8/8/2655

There’s no doubt that an extra copy of chromosome 21 is what causes Down syndrome. There’s a lot of doubt, however, over which particular gene—or combination of genes—on chromosome 21 is the actual cause of its symptoms. To flesh out our understanding, geneticists must grapple with this large chunk of the genome that includes more than 200 genes. How many of these genes contribute to the Down phenotype? Which are the most important? What are their roles? Studies in mice and other animals have uncovered clues about the function of a few of the genes on chromosome 21, but many remain understudied.

In G3: Genes|Genomes|Genetics, Nordquist et al. used Caenorhabditis elegans to systematically investigate the function of these genes and identified some that could play previously overlooked roles in nervous system function. Because C. elegans has a simple nervous system and can be genetically manipulated quickly, the authors were able to screen dozens of genes—many more than were practical in previous studies using mice.

After investigating which human chromosome 21 orthologues may be essential for C. elegans survival, they studied 27 nonessential genes using existing mutant strains. Because people with Down Syndrome experience a variety of neurological and neuromuscular symptoms, the authors evaluated the worm mutants through a battery of tests for muscular and neurological function.

Ten C. elegans orthologs, when mutated, impaired the worms’ locomotion and nervous system. Several of these are known to be important for neural development in worms—for example, the gene cle-1 is needed for axon guidance. Three of the genes the authors identified had not been previously linked to the nervous system, and little to nothing is known about these genes’ functions.

These results are just the beginning. To reveal their role—if any—in human disease, the genes identified will need to be studied further. But our best bet for understanding the complex genetics underlying Down syndrome is to use a wide variety of tools, including the lowly but powerful worm.

CITATION:

Systematic Functional Characterization of Human 21st Chromosome Orthologs in Caenorhabditis elegans

Jonathan Hodgkin

The Genetics Society of America’s Edward Novitski Prize recognizes a single experimental accomplishment or a body of work in which an exceptional level of creativity and intellectual ingenuity has been used to design and execute scientific experiments to solve a difficult problem in genetics.

The 2017 winner, Jonathan Hodgkin, used elegant genetic studies to unravel the sex determination pathway in Caenorhabditis elegans. He inferred the order of genes in the pathway and their modes of regulation using epistasis analyses, a powerful tool that was quickly adopted by other researchers. He expanded the number and use of informational suppressor mutants in C. elegans, which are able to act on many genes. He also introduced the use of collections of wild C. elegans to study naturally occurring genetic variation, paving the way for SNP mapping and QTL analysis, as well as studies of hybrid incompatibilities between worm species. His current work focuses on nematode-bacterial interactions and innate immunity.

This interview was published in the December 2017 issue of GENETICS.

What inspired you to become a scientist?

I was exposed to research from a very early age and learned a great deal from my father and grandfather. My father was Alan Hodgkin who was a physiologist and neurobiologist, and my mother’s father was Peyton Rous, who was a virologist who discovered the Rous sarcoma virus.  I had various other scientific relatives —cousins and what have you—going further back. I wouldn’t say it was inevitable that I became a scientist, but it was the easiest career option! And of course, I was inspired by the people who taught me at university, from about second-year onwards, who were enormously influential.

Why did you choose C. elegans as your research system?

Very largely because of Sydney Brenner. He gave a lecture that I heard as an undergraduate, and I thought that here was a great system for investigating the things in biology that I thought were really, really interesting. So, when I graduated I went and persuaded Brenner take me on, and he —somewhat reluctantly—did. He was inspirational and brilliant in all ways, truly extraordinary. And it was indeed a great system. It has gone off in all sorts of directions and keeps on generating new lines of research and new amazing discoveries.

What’s the most memorable moment from your career so far?

Probably when I realized the spectacular effect of a particular mutation on sex determination in C. elegans. It was a dominant mutation that caused the animal to change sex completely, and I’d previously found mutations in the same gene that caused the absolutely opposite transformation. It was just astonishing to realize that with that one gene you control everything about the animal’s sex.  This was a very satisfying and elegant result, which came together in a fairly short time.

Who have been your most important mentors?

At university, I was very lucky to be taught directly by a superb yeast geneticist, Brian Cox, whom I much admired. He did a lot of things that were underappreciated; for example, he discovered one of the systems that turned out to involve a yeast prion. He made it clear to me how immensely powerful genetics is. Then as a grad student, Sydney Brenner obviously, but also other people at the MRC Laboratory in Cambridge, like molecular biologist Mark Bretscher, who was very influential and full of good advice, and also inspirational people like Francis Crick. Francis was the only person smarter than Sydney at the MRC Lab!!

What types of questions are you fascinated by?

The big questions in development. Looking back on it now, I think what got me into research —and what I thought C. elegans was particularly powerful for—is a very difficult question that remains in many ways completely unanswered. How do you specify complicated behavior genetically? It’s obvious from all sorts of examples of instinctive behavior that they must be genetically programmed. How on earth do you do that? We have no idea whatsoever! We’ve made enormous progress in understanding development and the basis of the nervous system, but how do you do genetically specify things like the behavior of crows that can make tools out of bits of leaf? They don’t need to learn that! If you take a New Caledonian crow and allow it to hatch and grow up in isolation, after a while it will start finding bits of leaves and turning them into tools for picking up insects. I’m baffled by how such behavior can be generated, and I’d love to know the mechanism.  C. elegans has such simple behavior that we may   be able to eventually understand how it’s specified, though the more we more we learn about the worm, the fancier its behavior becomes. I don’t work in this area anymore, but the people who do are making nice progress. The most sophisticated aspects of it are still very mysterious though, and big questions remain unanswered.

What are you currently working on?

I’m working on how worms and bacteria interact with each other, and how the worms are able to fight off disease, how they recognize that they’ve got a disease, how infection happens, how some bacteria are able to infect some worms and not other worms. That involves a lot of interesting questions that still haven’t been answered, but it’s also led to lots of unexpected things along the way. For example, finding a bacterium that kills worms by causing them to stick together by their tails, but the worms can sometimes escape by dividing themselves in two. Nobody knew that nematodes s could do autotomy, so that was really surprising!

Autotomy raises questions about how they manage to do it. Unfortunately, so far, the half-worms survive but won’t regenerate. If you cut Planaria in half they will regenerate, but nematodes do not. Or at least we can’t get them to do it, which doesn’t necessarily mean it doesn’t happen.

If you hadn’t been a scientist, what would you have liked to have become?

Probably an archaeologist. I spent a lot of time hanging out with archaeologists on excavations until about the end of 1980s. Archaeology is like doing biological research in that you’re always discovering things, and it’s like genetics in that it’s open ended. The trouble with being an archeologist is there’s a factor of maybe 100 in the difference in employability between a biologist and an archaeologist.

What’s the best advice you ever received? 

Perhaps what Mark Bretscher said to me, which was: everything depends on having a good assay. I think that this is true whatever kind of experimental science you do, and it’s something I’ve always kept in mind. Avoid assays that are too arduous. Sometimes you have no choice, but if you can, try to get a stringent assay and one that’s easy to do.

What advice would you give to younger scientists?

Hang in there. It has gotten harder. It would be hard to deny, both in terms of career prospects and in terms of some of the questions that are out there, that it’s not as easy to do research as once it was.  But on the other hand, science goes on being enormously rewarding and enjoyable, and amongst other things there is a very strong community. You find yourself working with a lot of people who are interested in the same things and are all very bright, very funny, and very agreeable. That was the great thing about working at the Molecular Biology Laboratory in Cambridge: you instantly realized that it was a wonderful environment, nonhierarchical and dedicated and excited about research. Many other occupations can involve more or less going around in circles, or trying to solve incredibly difficult social problems. There aren’t many careers that go on being satisfying and fascinating in quite the same way as this one—or where you actually get to move back the frontiers of knowledge.