A new associate editor is joining GENETICS. We’re excited to welcome Bo Zhang to the editorial team.

Bo Zhang
Associate Editor

Bo Zhang is a Professor in Developmental Biology and Genetics at Peking University in China. She received her BS and PhD degrees in Cell Biology from Peking University in 1989 and 1995, respectively, and pursued her post-doctoral training in the Institute of Molecular Biology at University of Zürich, Switzerland. She has been a visiting scholar at University of Wisconsin, Madison, as well as University of California, Los Angeles. Her group is interested in dissecting molecular and cellular mechanisms of vertebrate development through genetic approaches, using zebrafish as the major model with a focus on heart development and regeneration, as well as on developing genome editing techniques in zebrafish based on engineered endonucleases, including TALEN and CRISPR/Cas9.

One of life’s great mysteries is how a single egg cell can contain all the information needed to create a fully specialized complex organism, including more egg cells.

Ruth Lehmann, director of the Whitehead Institute at MIT, has done a tremendous amount to solve that mystery. Beginning in her graduate student days, she uncovered a pathway that controls germ cell specification within the embryo. Since then, her work has continued to illuminate many unique facets of germ cell biology, providing a deep foundation from which to understand how the germline lineage carries genetic and cytoplasmic information from generation to generation.

For her achievements, Lehmann has been awarded the 2021 Thomas Hunt Morgan Medal for lifetime achievement in the field of genetics from the Genetics Society of America.

“Her work became textbook material, not just for developmental biology books, but biology books in general,” says Alexander Schier of Biozentrum, the University of Basel and Harvard University, one of the scientists who nominated Lehmann for the award. 

Embryos gain a clear polarity early on, ensuring that the animal’s head and tail develop on opposite ends. As a graduate student at the University of Tübingen, working with Christiane Nüsslein-Volhard, Lehmann went looking for Drosophila mutants that lacked proper patterning. 

Researchers had already observed that fly egg cells had a specialized cytoplasm with the instruction for germ cells located at the posterior pole. Lehmann wanted to find the germ cell determinants, those genes that told the germ plasm what to do. In her screening, she found a number of mutations that produced embryos with no abdomen, that were also missing their germ cells.

It was during these experiments that Lehmann first discovered oskar, nanos, and pumilio, genes she would continue to study throughout her career. As she characterized more and more genes with the same ‘posterior group’ phenotype, she realized that oskar acted as an important organizer of the pathway, and that all the other genes are needed downstream. Take out any individual member of the pathway, and no abdomen and in most cases no germ plasm nor germ cells.

“I had a very good genetically-based idea of how that pathway worked. Then molecular tools became available, which allowed us to study genes at the DNA, RNA, and protein level and ultimately to uncover their mechanisms of action,” she says. “I was at a crossroads. I realized I could not continue as a pure geneticist, but really had to become a molecular geneticist as well.”

She spent a year working at the MRC Laboratory of Molecular Biology in Cambridge to learn how to ‘clone’ genes with the goal to identify their DNA sequence and study their molecular function. At the end of her year at MRC, she had a position waiting for her on the faculty of the Whitehead Institute and the MIT Biology department, where she remained for eight years before moving to the Skirball Institute at NYU School of Medicine in 1996. 

Once she cloned oskar and other genes, such as nanos, pumilio and egalitarian in the pathway, she found that the RNA of some of these genes are deposited by the mother to a specific location, at the posterior pole, of the egg. Control over the distribution of the protein product comes from spatially controlled translation of these localized RNAs, rather than localized transcription, as was commonly expected.

“This idea of RNA localization and translational control, that was quite revolutionary at the time,” says Schier. “This was a whole level of control that people hadn’t anticipated at the time. She always stumbles across these strange and intriguing mechanisms.”

Her pursuit of the mechanics of germ cell migration led her into lipid biosynthesis, perhaps somewhat unusual territory for a geneticist. She discovered that flies lacking the enzyme HMG-CoA reductase, which synthesizes cholesterol in humans (But not in flies—they have to take it up from their diet.), developed germ cells that looked normal, but were scattered around the egg. Somehow the enzyme was acting as the rate-limiting step for a homing signal for germ cells, but how it did so remained a mystery. Now, it appears that HMG-CoA regulates the production of a hormone that attracts the germ cells to the correct location in the egg. 

“She sees things that others haven’t seen,” says Alex Schier. “She doesn’t follow fashion; she carves out her own niche and makes really interesting discoveries that then are followed up by many others.”

For her part, Lehmann describes her philosophy as “follow the phenotype.” Rather than focusing on a single molecule and studying it in different organisms or cell types, she’s chosen to stick with the problem and explore the entire panoply of molecules involved in the germline life cycle. So she and her group have studied how germ cells are initially set aside from the other cells in the body, how they remain “naïve” during larval stages until they eventually, in the adult, develop into gametes, egg, and sperm so that the life cycle can start anew.   

“I’ve always been lucky to make these discoveries, and I think it’s because I’m not prejudiced,” she says. “I start from the mutant phenotype, which tells me about the normal role of the gene that was hit by the mutation. And if this defective gene leads to a protein that is novel or unexpected for the process we study, I’m not afraid to study something new and learn about the function of this gene, that has allowed us to discover novel pathways or placed known pathways into a novel context.”

That strategy hasn’t been easy. Following the phenotype has meant learning to work with a wide variety of biochemical processes, from RNA transport, localization, and translation to lipid phosphorylation, hormone signaling, and transposon-mediated chromatin regulation. “It’s a hard way, it’s true,” she says. “It only works when you get really good people in your lab, because the people in my lab become the experts in a variety of fields.”

Eventually, those experts leave and start their own labs, taking their projects with them.  Attracting early career scientists who bring their own expertise in new techniques and fields is part of the process for Lehmann. “The projects grow as the technologies grow,” she says. 

These days, she’s developing new cell biology methods to understand how the cell physically brings together the molecules that make up the membraneless germ granules. Traditional biochemical methods involve grinding up the cell, and that’s no use when you’re studying condensates that only form in a tiny region of the egg. Recent innovations in visualizing liquid-liquid phase separations are enabling more research in this area. 

“I really want to understand how these molecules come together in germ granules to create activities only there, so that germ cells attain and maintain the special ability to create the next generation,” she says. “And that’s why I am still working on this.”

More than half of her postdocs have gone on to secure faculty positions, an indication of her leadership strategy, which she says emphasizes independence. “While they are in my lab, they can see whether they like being a scientist, whether they are good at being a scientist, because I’m not telling them every day what to do,” she says. “I don’t think that’s my role. I see the training in my lab as a pathway to independence.” 

Alex Schier describes her as “a generous mentor,” ready and willing to go to bat for her students, postdocs, and colleagues against administrators who might be tempted to undervalue basic research. “She really is a great defender of fundamental research of discovery,” he says, “as well as a defender of research driven by individuals with creative ideas.”

The T.H. Morgan Medal recognizes extraordinary achievement in the field of genetics. Lehmann’s work spans many disciplines, including cell biology, developmental biology, and molecular biology, and her contributions have been recognized by various professional societies. Still, she firmly considers herself a geneticist.

“People ask, ‘What are you?’ At heart, I’m really a geneticist,” she says. “The problem always starts with genetics. That’s the discovery phase.”

The Thomas Hunt Morgan Medal recognizes lifetime achievement in the field of genetics. It recognizes the full body of work of an exceptional geneticist. Lehmann accepted the award at the 62^nd Annual Drosophila Research Conference (#Dros21) and will present an Award Seminar online on April 28, 2021 from 1-2 p.m. EDT.

After giving a talk in Seattle about chromosome pairing, Chao-ting (Ting) Wu boarded the redeye flight back to Boston and settled in to read a new research paper on an odd new discovery in the human genome. “It was so exciting, I had to get up and walk around on the plane,” she says. “I could not stay in my seat.”

The paper that had Wu pacing the aisle that day was the first report describing DNA sequences called ultraconserved elements (UCEs), from Gill Bejerano in David Haussler’s group at UC Santa Cruz. UCEs are nucleotide sequences more than 200 nucleotides long that are identical in the human, rat, and mouse genomes. It’s incredibly unlikely that a sequence that long could remain unchanged over hundreds of millions of years of evolution, and yet Bejerano reported finding 481 of them.

“I remember reading it and thinking, how can that be?” Wu says. “How could we have missed this? How can something be so important and so hidden?”

Intrigued, Wu began studying UCEs in her own lab. “They are considered by some to be the longest-standing mystery of the genome era,” she says. “We don’t have an explanation for why any genome would retain even one sequence that long. The reason my lab studies it is this: pairing could be a very simple explanation.”

Wu has spent decades studying how homologous chromosomes pair up. Once considered a quirk of Drosophila’s genome, the idea that chromosomes communicate by coming into contact with each other is now being studied in mammals, fungi, and even plants. “It’s moved from being an ‘artifact’ to possibly being a universal way in which homologous chromosomes can communicate,” Wu says. “That’s been extremely exciting to see.”

Wu’s studies began when she was a graduate student with William Gelbart, who was a professor at Harvard University and a previous awardee of the George W. Beadle Award, and continued in her own laboratory with Jim Morris, a graduate student and now a professor at Brandeis University, and Pam Geyer, a professor at the University of Iowa. These studies focused on transvection, in which gene expression can be regulated by interactions between homologous alleles on different chromosomes. If the basis of UCEs is pairing, she speculates, that could explain why the sequences cannot tolerate changes.

This model aligns two otherwise incongruous observations. First, she and Adnan Derti, a graduate student and now at Auron Therapeutics, discovered that copy number variation of a UCE – a deletion or duplication – is rarely found in healthy individuals. On the other hand, other groups found that some UCEs can be deleted from both chromosomes without causing lethality in mice. The pairing model, however, predicts exactly such outcomes for UCEs whose function is to pair.

Perhaps these perfectly conserved regions act as “guardians of the genome,” she speculates, helping preserve the integrity of the full set of chromosomes. Understanding them could ultimately provide protection from disease.

“She’s always thinking about the weird and the wonderful, and what are the things we have no idea about,” says Jack Bateman, a former postdoc who studied transvection and now heads his own lab at Bowdoin College. “She’s so fun to talk to because she just has these ideas that are different.”

In addition to her work as professor of genetics at Harvard Medical School, she directs the Consortium for Space Genetics and the Personal Genetics Education Project (pgEd), a public engagement program intended to empower citizens to educate themselves about the genomic technologies that pervade our modern society. This team of scientists, social scientists, educators, and community organizers work with schools, teachers, policymakers, filmmakers, communities of faith, and other groups to prompt conversations about the benefits and ethical and social implications of genetics.

For all of these diverse contributions, Ting Wu has been awarded the 2021 George W. Beadle Award from the Genetics Society of America, which recognizes individuals who have made outstanding contributions to the community of genetics researchers beyond an exemplary research career. 

“She’s so passionate about things,” says Pamela Geyer, professor of biochemistry at the University of Iowa, one of the scientists who nominated Wu for the award. “She pushes you to think about things in a different way.”

At some point thinking becomes experimenting, and, eventually, time came to get a good look at the chromosomes, themselves. Thanks to work done in Wu’s lab, geneticists have powerful tools to visualize the 3D shapes of chromosomes and trace the dynamic system as they interact.

This story begins with Ben Williams, a graduate student and now with Helmsley Charitable Trust, whose idea for Oligopaints was demonstrated and then advanced by Brian Beliveau, a graduate student and now an assistant professor at the University of Washington,­ and Eric Joyce, a postdoctoral fellow and now an assistant professor at the University of Pennsylvania. Oligopaints are low-cost fluorescent probes that hybridize to specific locations along the chromosomes and, led by Beliveau, the Wu group and her collaborators, Peng Yin and Xiaowei Zhuang, professors at Harvard Medcial School and Harvard University, respectively, enabled Oligopaints to image chromosomes in super-resolution. “It’s been very exciting,” says Wu. “The super-resolution structures are giving us true measurements of distance, volume, and shape, and we are now looking at greater and greater expanses of the genome. We’re seeing how completely dynamic the genome can be.” 

The infectious enthusiasm that has propelled her lab into uncharted scientific waters has also spilled over into the realm of education. The advent of home genetic testing and personal genomics sparked lots of probing conversations among her lab members about communicating with the public about the social and ethical considerations around advances in genetics.

“Have we communicated enough with everybody, non-scientists, about genetics?” Wu muses. “So that when these technologies come out, they are informed enough to make decisions for themselves about whether they want to use those technologies?”

To learn what questions were percolating through the community, she and her husband, geneticist George Church, and their daughter, Marie, took a road trip across the country to talk to people who had volunteered their DNA for the Personal Genome Project. “These were people from all walks of life,” Wu says. “We came back so much more enriched by their conversations and so much more knowledgeable about the challenges that we had to address.”

That trip sparked her to co-found the Personal Genetics Education Project, or pgEd, with Bateman and Dana Waring, who is the Education Director. The program started by visiting local high schools and making presentations in biology classrooms. Realizing that they wouldn’t get too far just visiting individual schools, the team began publishing curriculum and teacher training materials to spread genetics education into more classrooms, particularly those where students might not have a strong background in genetics or biology. But Wu emphasizes that the goal isn’t to teach the nuts and bolts of DNA, or recruit students into STEM careers. Rather, she says, pgEd seeks to spark curiosity and debate, such that when students encounter genetic technology in their lives, they feel qualified to ask questions. 

“We’re not talking about what DNA bases are,” she says. “We’re talking about interesting things people might want to know to help them navigate their lives. When people are interested, they start asking questions. We’re hoping that when a physician comes along and says, ‘we’re going to do this DNA test,’ they aren’t silent, thinking, ‘oh, this person knows a lot more than I do.’ Instead, they will feel confident enough to ask questions, and I think that is the greatest protection you can give somebody. Laws are helpful, but one-on-one in a doctor’s office, you need the confidence that you can hold your own in a conversation about genetics. That’s what we’re going for.”

pgEd, whose activities are coordinated by Marnie Gelbart, Director of Programs, has spread well beyond schools into TV and film, congressional briefings, and faith communities. Recently, Gelbart, Robin Bowman (Professional Development Associate), and Nadine Vincentin (Research Fellow) worked on the public engagement programming and educational resources that accompanied the Ken Burns PBS documentary “The Gene: An Intimate History.” They have also been working closely with The Learning Center for the Deaf on lessons and curricula in American Sign Language, with Mohammed Hannan (Community Liaison) extending their engagement within communities. “It’s been amazing to see it grow,” says Bateman. “They’ve done so many things. They’ve done congressional briefings. How do these things happen? They happen because it’s Ting.”

The George W. Beadle Award honors individuals who have made outstanding contributions to the community of genetics researchers. Wu will accept the award at the 62^nd Annual Drosophila Research Conference (#Dros21) and will present an Award Seminar online on April 29^th from 1-2 pm EDT.

Interested in learning about public engagement from pgEd? GSA has partnered with pgEd for a program on inclusive public engagement for geneticists. Sign up now for the “Discussing Genetics” webinar series and join us for additional training workshops coming soon. 

NUN bodies in C. elegans offer clues about nervous system differentiation.

One of the most active areas of research today explores the differences between individual cell types and how cells become differentiated. This specialization of cell types relies on changes in gene expression, but how those changes are orchestrated remains unknown.

Now, research published in GENETICS has identified a new organelle inside the nucleus of nerve cells in the nematode worm, C. elegans. Named “nuclear nervous system-specific bodies,” or NUN bodies, these organelles only occur in the cells of the nervous system, report Pham et al. The exact function of the NUN bodies isn’t known yet, but because these bodies are highly specific to nervous system cells, they may lead researchers to a better understanding of how these important cell types differentiate.

In their quest to unravel the mechanisms behind neuronal differentiation, the team of researchers, based at Columbia University and led by Oliver Hobert, take advantage of the simplicity of the C. elegans experimental system. The developmental fate of each of the worm’s cells is known, and the total number of distinct cell types in C. elegans is small, making it ideal for investigating tissue-specific features.

During the process of differentiation, the cells of the nervous system, known as neurons and glia, develop an unusually compact nucleus with a “speckly” appearance. This so-called granular nucleoplasm intrigued the team because there are very few morphological features that are common to all nervous system cells but absent from any other cell types.

“Why is there this nervous system specificity that’s so striking?” says first author Kenneth Pham, who was a post-baccalaureate student working in Hobert’s lab at the time. “That was the diving off point.”

Neuronal nucleus with multiple NUN bodies, as visualized with differential interference contrast microscopy. Image courtesy of the Hobert lab.‌

Inside the nucleus is the “control center” of the cell, where genes are turned on and off, determining the fate of the cell. Various organelles help keep things running smoothly, and it stands to reason that cells headed for different fates might have different nuclear bodies managing their gene expression patterns. To investigate, Pham set out to characterize the granules present in the nuclei of C. elegans nervous system cells.

To start with, he tested whether the granules were indeed phase-separated membraneless organelles by showing that, chemically, they behaved the same way as nucleoli. Like these known membraneless organelles, the nuclear granules dissolved in a hypertonic salt solution, and heat caused them to grow larger and decrease in number.

To make sure they weren’t just extra nucleoli, he tagged nucleolus-specific markers with fluorescent dye, revealing that each neuron contained only one nucleolus. The newly identified bodies were not nucleoli.

Pham set to work, searching for what else the granules might be. Although none are as cell type-specific as NUN bodies, a number of nuclear bodies have been described previously, such as splicing speckles, paraspeckles, PcG bodies, PML bodies, gems, stress-induced nuclear bodies, and clastosomes. He combed through the C. elegans genome, looking for any homologs of the proteins that make up these nuclear organelles in mammalian cells. By attaching a fluorescent tag to each protein, he could track whether the tag followed the NUN bodies in worm neurons. None of the six organelle components that he found in the worm genome appeared to colocalize with NUN bodies. Pham then used loss-of-function mutations in all of the organelle constituent genes that he could find, and none of them had any effect on the NUN bodies.

So, these new structures seem to be unrelated to known nuclear bodies, and what NUN bodies are made of remains a mystery. But Pham took a stab at identifying their function. In a type of cell called “canal associated neurons,” or CANs, the NUN bodies change over the course of development. At first, there may be five or six NUN bodies in the nucleus. As the worms develop, that drops to only two or three NUN bodies per nucleus, and they are enlarged.

To find out how this was happening, Pham zeroed in on genes that play a role in CAN maturation, knocking them out and looking for changes in NUN body behavior. A mutation that reduced the activity of a transcription factor, ceh-10, stopped the rearrangement of NUN bodies normally seen during development.

Ultimately, NUN bodies offer a tantalizing hint to how nervous system cells might differentiate, with lots of possible avenues for learning more. For instance, Pham began screening a mutant library to find genes needed for making NUN bodies, but so far, nothing has turned up. He’s moved on from Columbia now, beginning an MD/PhD program at the University of Pennsylvania, but he hopes someone picks up the project where he left off. “Please work on the mystery, because I really want to know.”

CITATION
A nervous system-specific subnuclear organelle in Caenorhabditis elegans
Kenneth Pham, Neda Masoudi, Eduardo Leyva-Díaz, Oliver Hobert
GENETICS, Volume 217, Issue 1, January 2021, iyaa016,

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

Holes in the plasma membrane trigger the activation of the Torso receptor tyrosine kinase.

As a general rule, cells don’t do well when holes are poked in their plasma membranes. That’s why many immune cells use enzymes like perforin to puncture the membranes of pathogenic cells, dysregulating and often killing them. However, a new report in GENETICS by Mineo et al. suggests that creating holes in the plasma membrane might be a normal and necessary process during development.

The authors were interested in whether membrane hole-punching could play a role in activation of a receptor tyrosine kinase known as Torso. Torso is crucial for development of the fruit fly Drosophila melanogaster and is activated at both poles of the developing embryo. Torso activation depends on the polar accumulation of Torso-like (Tsl), which is the only Drosophila protein known to have a Membrane Attack Complex/Perforin domain. This domain is often present in proteins that perforate cell membranes, so the authors hypothesized that Tsl’s function might be to create membrane pores and, therefore, that simply pricking holes in the cell membrane might substitute for its function.

To test their hypothesis, Mineo et al. studied mutant embryos that either lacked the Tsl protein entirely or carried a non-functional version; both mutants exhibit several easily observable developmental defects. At this stage of development, the embryos are syncytial, which means all the dividing nuclei share a common cytoplasm and are surrounded by a single cell membrane. The researchers poked holes in the membrane at the poles of the embryo using sharpened capillaries of the type sometimes used to inject DNA for genetic engineering. Remarkably, embryos that had holes poked in them had fewer defects than their un-poked counterparts, suggesting that the mechanical formation of holes partially compensate for Tsl function.

To determine whether the rescue was due to mechanical stress on the membrane—but not necessarily the holes themselves—the authors then prodded membranes but did not puncture them. Prodded embryos showed the same developmental defects as their untreated counterparts, showing that an actual rupture in the membrane was required to rescue the developmental phenotype in Tsl-deficient fly embryos.

The authors also demonstrated that Torso signaling is required for the rescue effect of these membrane holes; fly embryos lacking Torso or its ligand, Trunk, did not show any change in developmental phenotypes when they were mechanically punctured. The location of the holes also mattered; the rescue was greatly diminished when the holes were created in the middle of the embryos, rather than at their poles.

Overall, the results suggest that Tsl spatiotemporally regulates Torso signaling by puncturing the cell membrane. These punctures are presumably needed for the exchange of a molecular signal between the interior of the embryo and its extracellular surroundings; it remains to be seen exactly how activation by Tsl works. What is clear is that, sometimes, all that’s needed to keep development on track is a sharp punch in the membrane.

CITATION:

Holes in the Plasma Membrane Mimic Torso-Like Perforin in Torso Tyrosine Kinase Receptor Activation in the Drosophila Embryo

Alessandro Mineo, Esther Fuentes, Marc Furriols, Jordi Casanova

Genetics September 2018 210: 257-262; https://doi.org/10.1534/genetics.118.301397

http://www.genetics.org/content/210/1/257

GC content alone is associated with distinct functional classes of human enhancers.

Because enhancers can be located hundreds of kilobases away from their target genes, it can be challenging to accurately predict their functions. A new report in GENETICS uses sequence composition to distinguish two enhancer classes that have distinct functions and spatial organization in humans.

Enhancers are regulatory DNA sequences that aid in transcription initiation. In some ways, enhancers are like promoters, since both are bound by transcription factors as part of transcription initiation. Unlike promoters, which are located near the transcriptional start site of the genes they regulate, enhancers are sequentially far away from their targets, typically coming into long-distance contact with gene promoters via 3D DNA looping. Since it is difficult to identify enhancers through sequence information alone, our understanding of them is somewhat primitive compared with other DNA regulatory elements.

Lecellier, Wasserman, and Mathelier were interested in classifying enhancers based on their sequences. The percentage of a given sequence that is guanine and cytosine (the GC content or %GC) can be used to classify promoters, so they investigated whether a similar approach could be useful for enhancer classification. To perform this analysis, they took advantage of the FANTOM5 project, which recently cataloged tens of thousands of enhancers across the human genome.

The enhancers were divided into two simple groups: those with higher %GC and those with lower %GC than the median overall. The authors compared the properties of the two groups, finding that different transcription factors were predicted to be associated with each group. Each group was also associated with different DNA shapes (e.g. bending) and distinct localization in chromatin loops, suggesting that the enhancer sequence composition is linked to the 3D architecture of the chromatin.

The authors then examined whether the two groups of enhancers had distinct biological functions. By consolidating previous reports, they compiled lists of thousands of genes predicted to be targets of each class of enhancer, and they analyzed these genes as proxies for the biological functions of the enhancers across different cell and tissue types. They found that enhancers with a higher %GC were associated with ubiquitous gene expression, whereas enhancers with a lower %GC were associated with specific patterns of expression in particular subsets of cells.

In particular, lower %GC enhancers were linked to immune response genes. To test this association against experimental data, the authors used data obtained from dendritic cells infected with Mycobacterium tuberculosis. This data tracked changes in chromatin accessibility, which can be mediated by enhancer activity. They found that lower %GC enhancers were significantly more activated in infected cells, providing experimental support for their observations.

CITATION:

Human enhancers harboring specific sequence composition, activity, and genome organization are linked to the immune response

Charles-Henri Lecellier, Wyeth W. Wasserman, Anthony Mathelier

Genetics August 2018, 209: 1055-1071; https://doi.org/10.1534/genetics.118.301116

http://www.genetics.org/content/209/4/1055

Recent evolution of simple germ–soma division in a green alga sheds light on the early stages of complex multicellular life.

Among evolution’s greatest innovations are germ cells. These specialized reproductive cells—familiar to us as sperm and eggs in humans—set the stage for complex multicellular life because they free up all the other cells in the body (known as somatic cells) to specialize for many other functions. Because they appeared so long ago in our evolutionary history, the way our germ cells emerged has been obscured, leaving many questions about this momentous biological turning point.

We may never know precisely how the germ–soma dichotomy arose in our lineage, but scientists are still searching for clues. In a report in G3, researchers Gavriel Matt and James Umen describe their work on the green alga Volvox carteri, an intriguing species that has recently and independently evolved a simple germ–soma division. In this alga, a spheroid composed of somatic cells and extracellular matrix surrounds germ cells called gonidia. The gonidial cells undergo embryogenesis to produce new juvenile spheroids that hatch from their mother spheroid, whereas the somatic cells that are left behind eventually senesce and die. This system offers a unique opportunity to explore the early evolution of germ cells.

By comparing the V. carteri germ and somatic cell transcriptomes, Matt and Umen found that the somatic cells had more transcripts from young, lineage-specific genes, whereas the germ cells had more transcripts from ancient genes that are similar to those expressed in stem cells from animals and land plants. The germ cells also expressed more genes overall than the somatic cells did, despite being specialized for reproduction. Although counterintuitive, this is reminiscent of the way certain pluripotent stem cells in other systems express a greater number of genes—including more ancient genes—than their somatic daughter cells do.

The duo also investigated the idea that V. carteri evolved its germ–soma division by repurposing genes initially used for the transition to a simpler form of multicellularity without a germ–soma dichotomy, but found little support for this hypothesis. Genes exclusive to V. carteri and one of its close multicellular algal relatives that does not have differentiated cell types, Gonium pectorale, were not specifically enriched in either V. carteri cell type. Instead, they discovered that each V. carteri cell type expresses orthologs of genes from different temporal phases of the light–dark cycle in a related unicellular alga, Chlamydomonas reinhardtii, with somatic cells enriched for expression of dark-phase genes, and gonidial cells enriched for expression of light-phase genes. These results suggest that V. carteri cell types may have evolved through cooption of temporal gene regulation in an ancestor whose different phases were converted into germ- and soma-specific expression programs.

Notably, the researchers also found increased expression of genes involved in anabolic pathways in gonidial cells, which contrasts with the upregulation of genes involved in catabolic pathways found in somatic cells. Specifically, somatic cells preferentially expressed genes involved in breaking down carbon stores into sugars, which are important building blocks for the extracellular matrix that surrounds gonidia and provides a structural scaffold that maintains organismal shape and integrity. These observations suggest that the somatic cells sacrifice themselves for the multicellular collective, contributing stored resources at their own expense. With such an investment in the next generation, it’s no surprise that germ–soma dichotomies have evolved repeatedly, giving researchers fertile ground to explore the rise of complex lifeforms.

CITATION:

Cell-Type Transcriptomes of the Multicellular Green Alga Volvox carteri Yield Insights into the Evolutionary Origins of Germ and Somatic Differentiation Programs
Gavriel Y. Matt and James G. Umen
G3: GENES|GENOMES|GENETICS 2018 8: 531-550; https://doi.org/10.1534/g3.117.300253
http://www.g3journal.org/content/8/2/531

In the late 1980s, Japanese biologist Yoshimori Ohsumi finally got to run a lab of his own and began casting around for a suitable topic to occupy himself and his new grad students. At 43 years old, he did not consider himself much of a scientific success; he was now hoping to corner a niche of biology to call his own and chose a relatively obscure topic in the biology of bakers’ yeast. A little less than three decades later, Ohsumi has been awarded the 2016 Nobel Prize for Physiology or Medicine for what his seemingly arcane research ultimately showed about human health, disease, and aging. Ohsumi’s story illustrates the essential role that fundamental research —science performed for the sake of understanding the natural world— plays in medical advances.

His insights revealed how our cells renew themselves. Nearly all the proteins in the human body are constantly destroyed and replaced in a carefully orchestrated garbage disposal and recycling scheme. Without this system, our cells would be quickly overwhelmed with damaged and potentially toxic junk. One of the most vital components of this cellular housekeeping is a process called autophagy, which means, in Greek, “self-eating.”

Before Ohsumi’s work, the importance of autophagy was not widely appreciated, and the mechanics of how a cell could dine on itself were unknown. In the 1950s, biologists discovered a compartment in the cell filled with degradative enzymes, an organelle they named the lysosome (for “digestive body”). The enzymes in the lysosome break down large biological molecules like proteins, carbohydrates, fats, nucleic acids, and membranes into their component parts. Through the microscope, scientists could see bubbles of doubled-up membranes—autophagosomes—delivering debris to the cell’s degradation center. But the details of how this system worked were unclear. How do the autophagosomes know which cell components should be delivered to the lysosome? How do they engulf and transport their targets? What other events in the cell depend on it? What happens when autophagy grinds to a halt?

These questions went unanswered because nobody knew the identity of genes specifically involved in autophagy. This was a roadblock because biologists rely heavily on the tools of genetic analysis when exploring new and unknown processes. Without an idea of the genes involved, they didn’t know what proteins took part in autophagy, or how to unambiguously identify autophagosomes, how to block autophagy, or how to quantify it. So for decades, the molecular details remained mysterious.

In 1988, Ohsumi decided to tackle this problem using the yeast Saccharomyces cerevisiae, the familiar fungal cells that help bakers to bake bread, brewers to brew beer, and winemakers to ferment wine. Yeast also frequently help biologists to make knowledge. They are popular in the lab because they are single cells—so they are considerably easier to study than multi-celled organisms—but they still have the complex internal organization common to plants, animals, and fungi. They are also much easier to genetically manipulate than many organisms. In effect, they provide scientists with a fast-growing, inexpensive, powerful, safe, and mostly pleasant-smelling alternative to studying our own cells.

Yeast had rescued Ohsumi from his lab struggles during an often frustrating postdoctoral stint in the United States. Defeated by an initial project on in vitro fertilization in mice, he had switched to studying how yeast cells duplicate their genome during cell division. When he moved back to Tokyo in 1977 to the lab of Yasuhiro Anraku, Ohsumi continued with his new study subject, but worked on transport systems that moved small molecules like amino acids and calcium into and out of the yeast version of the lysosome (idiosyncratically known by yeast biologists as the vacuole—which means “empty space”).

Once he became an associate professor, Ohsumi needed stake out new territory for his own lab. He decided to explore how the vacuole breaks down biomolecules. He had a simple but powerful plan to test whether autophagy occurred in yeast: he examined the vacuoles of yeast deficient in key enzymes that degrade proteins. If autophagic vesicles were being delivered to the vacuole but their degradation was blocked, they should start to build up.

When autophagy is induced, a double layer of membranes wraps around cellular debris, eventually sealing up its target inside a closed autophagosome. The autophagosome then fuses with the lysosome/vacuole, releasing a single-membrane bound package that is then degraded by enzymes (left). In vacuole degradation mutants like those used in Ohsumi’s lab (right), the autophagosome contents that are delivered to the vacuole are not degraded and instead accumulate.

Knowing that autophagy in animal cells was stimulated by starvation, he grew some of his mutant yeast in growth medium that was nutritionally deficient, and he then examined the cells under a simple light microscope. Within an hour, a few tiny wobbling blobs appeared within the vacuoles. Within three hours, the vacuoles were massively bloated and so jam-packed with the spherical blobs that they could no longer wobble. These structures were the remnants of autophagosomes that had been delivered to the vacuole. In normal cells, they would be rapidly degraded by the vacuolar enzymes, but in the mutants, they just kept arriving at the vacuole and were never broken down. The autophagy traffic was piling up.

Ohsumi and his students had not only shown that yeast cells underwent autophagy, they now had a means for finding the genes that controlled it. Grad student Miki Tsukuda embarked on a mission to find other yeast mutations that affected autophagy. She treated the protein-degradation deficient strain with a chemical that induces random mutations, then screened these mutated strains in a two-step procedure: she first isolated all the strains that had trouble surviving starvation conditions, then she examined their vacuoles under the microscope to hone in on those with autophagy defects. In these effective but labor-intensive experiments, Tsukuda found 15 different genes that disrupted autophagy when mutated. She had uncovered most of the building blocks of autophagy.

Once Ohsumi’s group and others learned the location and sequence of the mutated genes, they had the challenging job of figuring out what job each gene performed in the autophagic pathway. Intriguingly and at first unhelpfully, most of the proteins produced by these genes were new to science, which meant the scientists  could not rely much on studies of other biological pathways as a guide. In spite of this, the elegant mechanisms that drive autophagy were gradually revealed, and robust methods to study the process in other organisms were developed. It soon became clear that autophagy in yeast was very similar to the process in animals, including humans. The field exploded. The year Ohsumi and Tsukuda published their yeast screen, only a couple of dozen research papers were published on autophagy. So far in 2016 alone, nearly 4,000 have been published.

Part of the reason for the field’s growth is the importance of autophagy for health and disease. The ability to recycle nutrients and cellular components helps our cells to survive starvation. Autophagy is important during the development of embryos. It is involved in fighting infection by bacteria and viruses. When autophagy stops functioning, the buildup of toxic proteins can lead to neurodegenerative diseases. When autophagy goes into overdrive, it is associated with cancer formation. With such a key role in maintenance of the cell, many other disease links are being uncovered every year, and there is intense interest in developing drugs that can influence autophagy.

Ohsumi and his students, postdocs, and collaborators have had an outsized influence on this field, not only in identifying the genes that underlie cellular recycling, but in revealing many of the molecular details of how these players function. By seeking out unexplored territory in our understanding of the cells that make bread rise, yeast biologists provided a map for understanding ourselves.