A better way to make endogenous reporters in C. elegans

CRISPR systems for gene editing have revolutionized biological research, but the method still has limitations. While it is usually straightforward to delete parts of the genome using CRISPR, large insertions can be a challenge. This has been the case even for the nematode Caenorhabditis elegans, one of the most established model organisms. But now, work published in GENETICS by Vicencio, Martínez-Fernández, Serrat, and Cerón has produced a more effective way to use CRISPR to insert longer stretches of DNA into the nematodes’ genomes.

A method for adding long DNA fragments is essential because many genes of interest, including important fluorescent reporter genes, are too long to be effectively inserted using existing methods. In fact, the team embarked on the work after attempts to insert a gene into the nematodes using another CRISPR-based technique repeatedly failed—a problem also reported in at least one other publication. In contrast, they found that their method, called Nested CRISPR, could efficiently add segments of DNA up to 792 base pairs long. They also achieved insertions of 927 base pairs, although the efficiency was lower.

In their method, the gene is inserted in two CRISPR-based steps. First, a short fragment with nucleotides from each end of the gene is inserted into the target site. Next, this fragment is replaced by the full-length insertion via homology-directed repair.

Their results mean that when insertions of a few hundred base pairs are needed, Nested CRISPR is a viable alternative to current methods involving extrachromosomal or randomly inserted DNA. The Nested CRISPR technique may even be broadly applicable to other organisms, particularly through the authors’ one-shot approach to achieve the two editing steps in a single injection.

It’s not completely clear why this group and others have had difficulty reproducing the level of efficiency reported for an existing CRISPR-based method for inserting DNA segments of this length into C. elegans. Slight differences in reagents among labs may be partially to blame for the lack of reproducibility of some laboratory methods, including those used for genome editing, but the authors of this study believe that won’t be an issue in the case of Nested CRISPR because all the reagents are commercially available and affordable. The availability of these premade reagents may also make it easier for researchers with less experience in gene editing (or molecular cloning in general) to perform the technique, allowing them to pursue projects that they otherwise may have avoided. The group has called for the C. elegans community to come together to evaluate the utility of methods such as theirs for inserting long stretches of DNA—which may become even more important as the field continues to hurtle forward.

CITATION:

Efficient Generation of Endogenous Fluorescent Reporters by Nested CRISPR in Caenorhabditis elegans
Jeremy Vicencio, Carmen Martínez-Fernández, Xènia Serrat, Julián Cerón
GENETICS 2019 211(4): 1143-1154; https://doi.org/10.1534/genetics.119.301965
https://www.genetics.org/content/211/4/1143

An analysis of the acknowledgment sections of theoretical population genetics papers from the 1970s and 1980s reveals overlooked contributions of women to the foundation of the field.

Theoretical population genetics has a gender imbalance, and it’s easy to get the impression that it’s always been this way. After all, introductory genetics courses emphasize important concepts such as the Hardy–Weinberg principle, the Wright–Fisher model, and Haldane’s rule, all named after the men who made these critical advances in the field’s early days. But according to a Perspectives article published in GENETICS by a team of undergraduate researchers from San Francisco State University, women contributed more to population genetics during a transformative era in its history than would first appear.

Today, much research in theoretical population genetics depends on computer simulations rather than the pen-and-paper work of the field’s founders. Programmers thus became important contributors to the field as soon as computers capable of such tasks were developed, although authorship norms at the time meant their names were typically relegated to the acknowledgements. While the gender breakdown in programming now favors men—although this disparity has shrunk somewhat in recent years—the ratio of male to female programmers hasn’t always been so lopsided.

The inspiration from the project struck during a discussion between Rori Rohlfs of San Francisco State University and Emilia Huerta-Sánchez of the University of California Merced over coffee. They had noticed how often programmers in older papers were listed in the acknowledgements and thought they saw a trend: a disproportionate number of those programmers were women. “We thought, we should actually figure out how often this happened,” Rohlfs says. So the two decided to find out whether their impression would be backed by a more rigorous analysis.

Unconventionally, the study was conducted entirely by a team of seven undergraduate students working under Huerta-Sánchez’ and Rohlfs’ supervision. With little to no prior research experience, the students dove in, searching for programmers’ contributions by manually trawling the acknowledgements of every paper from 1970 through 1990 in Theoretical Population Genetics, a journal selected because of its large proportion of highly cited foundational population genetics papers involving programming. Cutting their search off at 1990 made sense because few programmers were listed in the acknowledgements after that point; instead, they were authors. The team found that although only 7.4% of authors were women within those two decades, women accounted for 43.2% of the acknowledged programmers—and the number of women acknowledged for programming decreased over time, from a peak of 58.6% in the 1970s.

In some cases, the gender assignment was simple because participants were given gendered honorifics such as Mr. or Mrs., while in others the researchers had to rely on authors’ names to infer gender, leaving some cases ambiguous. (They note that a limitation of this work is that it would not be possible to separate the contributions of individuals who do not identify as either male or female.) When contributors were acknowledged using initials, the researchers dug for other works in which they were acknowledged, including papers and books, to find their full names.

Using this method, the group also discovered that some programmers were acknowledged more than once, sometimes in very high-impact papers. For example, Margaret Wu—who went on to become a faculty member at the University of Melbourne—was not an author but was repeatedly acknowledged, including on a paper with over 3400 citations and counting. Cases like this, the finding that a disproportionately large percentage of acknowledged programmers were women, and the group’s additional finding that papers with acknowledged programmers were cited more on average than those without them were suggest that women contributed more to this critical transition in an apparently male-dominated field than it may seem.

“This is a great contribution to understanding how research has been conducted over the history of theoretical population genetics,” says Noah Rosenberg, Editor in Chief of Theoretical Population Biology. “The programmers acknowledged in early studies are people whose work continues to have a significant presence in the field. It is great that their efforts are being highlighted.”

The five undergraduate researchers who made the major contributions to the study presented their work at the Population, Evolutionary, and Quantitative Genetics Conference last year, aided by GSA Undergraduate Travel Awards. They say the reception was positive—many attendees were interested to learn about women’s hidden contributions to the field, and some gave their thoughts on further work they could do. “It was great to have a community that was very positive and gave us good feedback about our research and our work,” says study author Rochelle-Jan Reyes, for whom the conference was a first.

Presenting on their own as a team of undergraduates was a bit nerve-wracking at the beginning, says author Ricky Thu, and the amount of attention they received at the conference was a surprise to him. “Once I started talking to people at the poster presentation, they were really excited about it,” Thu says. “So I was excited to talk about it as well, and then I got more comfortable.” For their outstanding work, the presenters received special recognition in the conference poster awards.

Future studies by this group or others could involve investigating whether these findings apply to different fields or to people in other roles often mentioned in the acknowledgements section, such as lab technicians. The results could also be more powerful if the data collection process were made less laborious. Some conference attendees asked why the group didn’t collect more data by automating the process, but in this case, PDFs of the historical papers were not available on the journal’s website, so the team had to do things the old-fashioned way by going to the library and flipping through each issue by hand. Although their choice of journal makes sense given the high concentration of papers with acknowledged programmers, many journals do make scanned copies of older papers available online. That means it’s possible data collection could be automated using PDF mining and natural language processing—so programmers may be among the authors of these future studies.

Check out this fantastic video abstract produced by the researchers, including a link to an interview with acknowledged programmer Margaret Wu.

CITATION

Illuminating women’s hidden contribution to historical theoretical population genetics
Samantha Kristin Dung, Andrea López, Ezequiel Lopez Barragan, Rochelle-Jan Reyes, Ricky Thu, Edgar Castellanos, Francisca Catalan, Emilia Huerta-Sánchez, and Rori V. Rohlfs

Genetics February 2019, 211: 363-366; https://doi.org/10.1534/genetics.118.301277

http://www.genetics.org/content/211/2/363

A new genome assembly for Antarctic fur seals sheds light on their historic comeback after 19^th century hunting.

In the late 19^th century, the Antarctic fur seal was thought to be effectively extinct. After over a century of overexploitation driven by demand for the seal’s prized pelt, populations at known breeding grounds seemed to have disappeared, making further hunting impossible—and suggesting that the species may even have died out altogether. But in the 1930s, a small breeding population was discovered on South Georgia, a remote island in the southern Atlantic Ocean with no indigenous human inhabitants. Today, the Antarctic fur seal has made a comeback, with a population thought to number as many as two or three million—but a new G3 report by Humble et al. suggests this picture of the seal’s dramatic rebound is incomplete.

As a well-studied species that has undergone a remarkable recovery, the Antarctic fur seal (Arctocephalus gazella) holds great interest for conservation biologists and others seeking to understand the genomic impacts of population changes. In the report, a multinational team of authors describe an improved A. gazella genome assembly and a collection of 677,607 single nucleotide polymorphisms (SNPs), both useful tools for deeper dives into the genetics of the species. Their data also contain clues about how the Antarctic fur seal may have repopulated much of its former range.

Humble et al. found that linkage disequilibrium in A. gazella is on par with that of other vertebrates—a result that may seem strange given that such a severe population bottleneck should increase linkage disequilibrium. However, a separate analysis recently hinted that the population may not have dropped as low as once thought and could have included hundreds of individuals at its minimum. The Antarctic fur seal population also recovered within just a few generations, reducing the amount of time inbreeding and genetic drift would have had to impact linkage disequilibrium.

Although the species has a large, free-ranging population, the researchers found that some individuals were more inbred than others. This may be due in part to the fact that both males and females of the species return to the same breeding grounds each year with great precision—in one study, females were found to return to within one body length of the places they were born. Further, the species is highly polygynous, with one male often siring offspring with over a dozen females in a given season.

Information about fur seal population structure gave the team evidence that A. gazella may have persisted at a small number of the breeding grounds and thus was not limited to South Georgia, where it was first spotted after hunting ceased. Further investigation of how the seal recovered from being critically endangered, including the role of these final holdouts, could provide valuable information to guide conservation of other species facing extinction. And while A. gazella now numbers in the millions, any such insight may one day be important for its preservation, too: climate change and an increase in tourism has begun to put pressure on many Antarctic species, including the resilient fur seal.

CITATION:

RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding
Emily Humble, Kanchon K. Dasmahapatra, Alvaro Martinez-Barrio, Inês Gregório, Jaume Forcada, Ann-Christin Polikeit, Simon D. Goldsworthy, Michael E. Goebel, Jörn Kalinowski, Jochen B. W. Wolf, Joseph I. Hoffman
G3: Genes, Genomes, Genetics 2018 8: 2709-2722; https://doi.org/10.1534/g3.118.200171
http://www.g3journal.org/content/8/8/2709

Sexual reproduction is scarce in skin infection culprit.

While some people love to feel the burn during a workout, we generally seek that sensation in our muscles—not our feet. Treading barefoot in damp, communal environments like gym showers and the perimeters of pools can expose us to the fungus Trichophyton rubrum, the most common cause of athlete’s foot. Despite its name, athlete’s foot isn’t found exclusively in fitness fanatics—it affects around 15% of people worldwide. New work published in GENETICS shows that across this global range, the T. rubrum genome varies surprisingly little.

T. rubrum is widespread and comes in many varieties called morphotypes that differ in characteristics such as which parts of the body they can infect and the appearance of their colonies. In this study, the researchers found that T. rubrum samples from around the world were remarkably genetically similar to one another despite representing many different morphotypes. The data also suggest T. rubrum rarely, if ever, sexually reproduces. Mating in many fungi occurs between cells of different mating types, but of the 135 samples tested, the mating types of all but a single Mediterranean strain were identical.

The researchers found no evidence of mating when they paired the Mediterranean strain with strains of the opposite mating type, which supports the idea that the fungi reproduce clonally. This result comes with some caveats, though: the lab conditions may not have favored mating, and it’s possible that mating does occur when the Mediterranean strain comes in contact with some of the other strains in the wild. Overall, the results are consistent with one hypothesis that has been put forth about the fungi, which that is the species recently experienced a sharp decrease in sexual reproduction. The authors suggest this might have occured when T. rubrum began specializing for growth on humans.

Given that pathogens must dodge the defenses of their constantly adapting hosts, it may seem strange that T. rubrum exhibits such low genetic diversity, but it’s not alone in this trait. For reasons that haven’t been fully established, bacteria that cause tuberculosis and Hansen’s disease (leprosy) also come in a variety of types despite being highly clonal.

Although T. rubrum infections are treatable and rarely progress to serious disease, they’re common and often extremely uncomfortable. Those of us who wear sandals in the gym shower would certainly agree it’s well worth it to learn more about how this pesky fungus operates.

CITATION:

Whole-Genome Analysis Illustrates Global Clonal Population Structure of the Ubiquitous Dermatophyte Pathogen Trichophyton rubrum
Gabriela F. Persinoti, Diego A. Martinez, Wenjun Li, Aylin Döğen, R. Blake Billmyre, Anna Averette, Jonathan M. Goldberg, Terrance Shea, Sarah Young, Qiandong Zeng, Brian G. Oliver, Richard Barton, Banu Metin, Süleyha Hilmioğlu-Polat, Macit Ilkit, Yvonne Gräser, Nilce M. Martinez-Rossi, Theodore C. White, Joseph Heitman, Christina A. Cuomo
GENETICS 2018 208: 1657-1669; https://doi.org/10.1534/genetics.117.300573
http://www.genetics.org/content/208/4/1657

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An evolutionary approach outperforms a design approach in modeling protein sequence variation.

Over generations, evolution shapes proteins, leading to variation in their amino acid sequences both between and within species. Despite our ever-increasing knowledge of the physical constraints that guide protein structure, advanced modeling techniques don’t capture the site-specific variability observed in natural proteins. Bafflingly, complex models that account for physical influences on the positions of all atoms in a protein often perform worse than elementary models at recapitulating natural proteins’ variability.

In GENETICS, Jiang, Teufel, et al. provide evidence for a possible explanation: advanced modeling techniques don’t take into account the order of the steps by which protein sequences change. A popular protein-design suite called RosettaDesign, for example, deletes the amino acid side chains from a template structure, leaving only the peptide backbone, and then replaces them with new side chains all at once. After this dramatic step, additional changes are made to maximize the protein’s calculated stability.

Evolution works very differently. Sequence changes are usually made one amino acid residue at a time, meaning the effect of each alteration depends on how it fits with the existing sequence. Whether a sequence change will be fixed or lost depends on how it affects fitness, which is partly influenced by how it impacts protein stability—variations that make proteins prone to unfolding are typically not favorable.

When the group tested their new algorithm, which functions more similarly to evolution, on the same natural proteins, they found that its effects were different in several ways from those of RosettaDesign. In almost every case, their evolved sequences resembled natural ones more than designed proteins’ sequences did. This might not, at first, seem surprising, since the designed proteins started with a completely stripped peptide backbone and thus shouldn’t have been influenced as much by the natural starting sequences—but the researchers found that this wasn’t the reason. Even when they used a designed sequence as a template, the evolution-based simulation created sequences that better mimicked natural ones.

In protein design, the ability to build proteins with sequences unlike natural ones could be interpreted as a positive thing since it’s conceivable that these proteins would have a wider range of properties than those of proteins found in the wild. But despite the fact that the designed sequences had diverged more from the starting sequences, their site-specific variability was lower than that of the evolved sequences. This implies that, even though a greater number of sites were altered in the designed sequences, the changes were restricted to a smaller set of amino acid residues.

RosettaDesign and similarly sophisticated software have facilitated major advances in protein design, such as developing new enzymes and previously unseen protein folds, and Jiang, Tuefel, et al.’s findings don’t make these types of software obsolete. Different computational techniques fill different niches, and they evolve just as proteins do, with new variants continuously under development. By tweaking existing methods and studying the effects of new algorithms, we can improve how we use these techniques—and perhaps develop new ones with even better fitness than their ancestors had.

CITATION:

Beyond Thermodynamic Constraints: Evolutionary Sampling Generates Realistic Protein Sequence Variation
Qian Jiang, Ashley I. Teufel, Eleisha L. Jackson, Claus O. Wilke
GENETICS 2018 208: 1387-1395; https://doi.org/10.1534/genetics.118.300699
http://www.genetics.org/content/208/4/1387

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A suppressor screen in C. elegans uncovers previously unknown flexibility in the genetics underlying extracellular membranes.

In nearly all animal tissues, thin barriers called basement membranes anchor outward-facing layers of cells—the linings of lungs, the top layers of skin, the insides of blood vessels—to the connective tissues that support them. Mutations disrupting any major basement membrane component are often incompatible with human life, and partial loss of function can lead to diseases such as muscular dystrophy.

In the nematode C. elegans, as in humans, mutations in basement membrane components can be lethal. New work published in GENETICS by Gotenstein et al. shows that this lethality can be rescued by mutations in certain membrane structural components. Worms, like other animals, rely on enzymes called peroxidasins to crosslink basement membrane constituents and thus increase their structural integrity. This crosslinking is critical during development; disabling the peroxidasin PXN-2, for example, prevents worms from surviving beyond the embryonic or larval stage.

Unexpectedly, Gotenstein et al. discovered that gain-of-function mutations in a few proteins that make up the basement membrane itself, including perlecan and type IV collagen, can prevent the dysfunctions caused by pxn-2 mutations. Mutations that affect part of the extracellular domain of LET-805, a transmembrane protein thought to help the basement membrane adhere to the epidermis, also suppressed the mutant phenotype. Mutations that suppressed the phenotype of pxn-2 mutants also restored normal development in worms with mutations in spon-1, which is also important for basement membrane assembly.

SPON-1’s precise role in basement membrane formation isn’t fully understood, but its molecular mechanism is thought to be different from that of PXN-2, implying that the newly discovered suppressor mutations affect the basement membrane broadly, rather than being narrowly involved in individual pathways. The unanticipated flexibility in the formation of the basement membrane offers a new perspective on this vital, highly conserved structure, unlocking a new realm of possible mechanisms to explore.

CITATION:

Genetic Suppression of Basement Membrane Defects in Caenorhabditis elegans by Gain of Function in Extracellular Matrix and Cell-Matrix Attachment Genes
Jennifer R. Gotenstein, Cassidy C. Koo, Tiffany W. Ho, Andrew D. Chisholm
Genetics 2018 208: 1499-1512; https://doi.org/10.1534/genetics.118.300731
http://www.genetics.org/content/208/4/1499

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New evidence for genome instability in fly tumors suggests key similarities—and differences—from human disease processes.

Human cancers display a variety of abnormal genomic features, including increased numbers of single nucleotide variants (SNVs) and copy number variants (CNVs). However, a 2014 study on a fruit fly tumor detected no elevation of SNVs or CNVs compared to non-tumor tissues, raising questions about how well the fly tumors, which are sometimes used in cancer research, represent cancer in humans. Rossi et al. investigated whether this was generally the case in malignant neoplasms in flies by sequencing the genomes of 17 such tumors caused by mutations in four different genes.

To address this question, the researchers used a process called allografting: they dissected tumors from fly larvae, then implanted them into the abdomens of adult flies. Each time the tumors filled up the abdomens of their hosts, the tumors were removed, and some of the tumor cells were allografted again into new fly hosts. This approach allowed them to monitor which types of mutations accumulate over many rounds of cell division. Without these successive iterations of allografting, they would have been limited to studying mutations that occur over the comparatively short lifespan of the hosts.

In all of the allografted tumors, the researchers found increases in SNVs and CNVs similar in number to those seen in human cancers, and in the case of CNVs, with a similar size distribution. Also as in humans, the increases in the number of mutations varied from one tumor type to the next. However, they also found that the CNVs weren’t distributed in any discernable pattern, no two allografts had SNVs affecting the same genes, and the CNVs and SNVs often weren’t retained from one allograft to later allografts. This implies that these mutations may merely be byproducts of genome instability in the tumors and thus don’t contribute to malignancy, whereas in humans, it’s thought that the accumulation of such mutations as tumors age is a driver of malignancy.

One important consideration, though, is that studies looking for genetic variants correlated with cancer in humans often have much larger sample sizes, which might reveal associations this fly study could not identify. Still, because flies are important model organisms for cancer research, furthering our understanding of the similarities and differences between human and fly tumors, as Rossi et al. have done, is essential.

CITATION:

Drosophila Larval Brain Neoplasms Present Tumour-Type Dependent Genome Instability
Fabrizio Rossi, Camille Stephan-Otto Attolini, Jose Luis Mosquera, Cayetano Gonzalez
G3: Genes|Genomes|Genetics 2018 8: 1205-1214; https://doi.org/10.1534/g3.117.300489
http://www.g3journal.org/content/8/4/1205

Offshoot of the modENCODE project provides crucial data and strains for understanding gene regulation.

Following a multidisciplinary effort spanning six institutions, researchers working on the modERN (model organism Encyclopedia of Regulatory Networks) project have released a powerful resource for biologists studying the fruit fly Drosophila melanogaster and the nematode worm Caenorhabditis elegans. So far, report Kudron, Victorsen, et al., the project has yielded information about the interactions of 262 transcription factors (TFs) with 1.23 million binding sites in flies, along with 219 TFs with 670,000 binding sites in worms—all of which can be found in a searchable database organized by gene and developmental stage.

Along with announcing the availability of this resource, the group shared findings made during its construction. One such observation is that genomic regions with a large number of TF binding sites are often associated with broadly expressed genes, whereas regions with fewer TF binding sites are more often found near genes that are expressed mainly in specific tissues.

The collection includes 403 worm strains and 427 fly strains, each of which has a different TF tagged with green fluorescent protein. Researchers can obtain stocks through existing resources, the Caenorhabditis Genetics Center and the Bloomington Drosophila Stock Center. The strains have a variety of possible uses—for example, determining expression patterns of TF genes of interest.

Choosing flies and worms for the modERN project was a logical choice for multiple reasons, not least of which being that so much is known about these important model organisms. The authors also note that a major advantage of working with flies and worms for this project is that they can be studied as whole, living organisms at all developmental stages, which is not possible with human subjects. And since many fly and worm TFs are homologous to human TFs, it’s likely that research fueled by modERN data will provide a treasure trove of useful leads for biologists studying humans as well.

CITATION:

The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors
Michelle M. Kudron, Alec Victorsen, Louis Gevirtzman, LaDeana W. Hillier, William W. Fisher, Dionne Vafeados, Matt Kirkey, Ann S. Hammonds, Jeffery Gersch, Haneen Ammouri, Martha L. Wall, Jennifer Moran, David Steffen, Matt Szynkarek, Samantha Seabrook-Sturgis, Nader Jameel, Madhura Kadaba, Jaeda Patton, Robert Terrell, Mitch Corson, Timothy J. Durham, Soo Park, Swapna Samanta, Mei Han, Jinrui Xu, Koon-Kiu Yan, Susan E. Celniker, Kevin P. White, Lijia Ma, Mark Gerstein, Valerie Reinke, Robert H. Waterston
Genetics 2018 208: 937-949; https://doi.org/10.1534/genetics.117.300657
http://www.genetics.org/content/208/3/937

A new fruit fly model of Leigh syndrome reveals the importance of mtDNA variation.

Inherited mitochondrial disorders pose a perplexing problem to researchers and clinicians: people with the same condition can have vastly different clinical manifestations, even if they share the same mutation. For example, a neurodegenerative disorder called Leigh syndrome, which can be caused by many different mutations in genes encoding mitochondrial proteins, is usually first noticed in infancy and causes death within a couple years. Some affected individuals, however, don’t experience any apparent problems related to the mutations until they’re teens or adults.

Researchers Carin Loewen and Barry Ganetzky recently reported in GENETICS that they identified a fly strain exhibiting a Leigh syndrome-like phenotype, including mitochondrial abnormalities, decreased lifespan, and neurodegeneration. They found that the flies had a mutation in the gene ND23, an ortholog of a human gene (NDUFS8) that is mutated in some cases of Leigh syndrome. The gene encodes a core subunit of mitochondrial complex 1, part of the cellular machinery that makes energy.

In characterizing the ND23-mutant flies, Loewen and Ganetzky found that a maternally inherited factor mediated the severity of the Leigh syndrome-like phenotype. The pair hypothesized that the factor was a variant encoded in the mitochondrial genome because mitochondria are inherited only from the mother. In support of this hypothesis, they showed that the onset of the Leigh syndrome-like phenotype could be modified by mitochondria from different fly strains. By sequencing all the protein- and tRNA-coding genes in the mitochondrial genomes of these various strains, Loewen and Ganetzky determined that the mitochondrial genomes of strains in which the ND23-mutant phenotype was delayed shared polymorphisms that were not seen in the mitochondrial genomes of strains with earlier disease onset. None of these polymorphisms had any effect on flies in the absence of the ND23 nuclear mutation, showing how otherwise benign mitochondrial backgrounds can interact with mutations in nuclear genes to mediate the severity of mitochondrial disorders.

Not only did this work provide evidence for one explanation of the tremendous phenotypic variation observed in mitochondrial disorders, it also introduced a new model system for studying Leigh syndrome and its phenotypic variability. Although the prognosis varies, it is uniformly poor, and there is no cure—so further research on Leigh syndrome is desperately needed.

CITATION:
Mito-Nuclear Interactions Affecting Lifespan and Neurodegeneration in a Drosophila Model of Leigh Syndrome
Carin A. Loewen, Barry Ganetzky
Genetics 2018 208: 1535-1552; https://doi.org/10.1534/genetics.118.300818
http://www.genetics.org/content/208/4/1535

Photosensitive alternative splicing of a malt fly circadian clock gene varies between northern and southern populations.

Over the course of a day, most organisms undergo profound changes. Over the course of a season, the changes can be even more dramatic. For example, insects’ responses to the brisk nights and cooler days of fall and winter often involve transformations of both physiology and behavior, including reproduction, activity level, and metabolism. Whether in insects or humans, these daily and seasonal transitions are in part controlled by the internal circadian clock, with the expression of circadian genes responding to rhythmic environmental fluctuations.

Tapanainen et al. wondered how alternative splicing—a common gene regulatory mechanism—of the core circadian gene timeless might be linked to light and temperature in the fly Drosophila montana, a much more cold-tolerant relative of the familiar lab model D. melanogaster. They discovered that in D. montana, timeless splicing is regulated only by the amount of daily light exposure, not by temperature—in contrast to the thermal regulation seen in D. melanogaster. There was also no evidence that northern or southern D. montana had a particular timeless splice variant found in many cold-adapted D. melanogaster populations.

The group also made a peculiar observation: the way timeless splicing was regulated in D. montana differed depending on where the flies originated. For any given number of hours of light per day, if a splice variant was more abundant in flies from northern populations in North America and Europe, it was less abundant in flies from southern populations of the same continents, and vice versa. That the regulation of critical genes can be completely reversed even in two populations of the same species is a reminder of the importance of studying individuals from different populations and regions—perhaps especially in research on something as complex as the circadian clock.

CITATION:
Photosensitive Alternative Splicing of the Circadian Clock Gene timeless Is Population Specific in a Cold-Adapted Fly, Drosophila montana
Riikka Tapanainen, Darren J. Parker, Maaria Kankare
G3: Genes|Genomes|Genetics 2018 8: 1291-1297; https://doi.org/10.1534/g3.118.200050
http://www.g3journal.org/content/8/4/1291