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[
International Worm Meeting,
2015]
In C. elegans, dosage compensation reduces the expression of X-linked genes by half in hermaphrodites (XX) to equal their expression level in males (X0). During dosage compensation, a condensin-like dosage compensation complex (DCC) actively remodels X chromosomes of hermaphrodites into a unique, sex-specific spatial conformation, distinct from that of autosomes, using its highest-affinity recruitment sites on X (rex) to facilitate long-range interactions across X. The dosage-compensated X chromosome consists of self-interacting domains resembling mammalian topologically associating domains (TADs). TADs are found in all metazoans examined, but neither the mechanism by which they are formed nor their functional significance for transcriptional regulation is well understood. Because dosage compensation involves global changes in chromosome structure accompanied by chromosome-wide gene repression, we can use this system to investigate the mechanisms of TAD boundary establishment and the relationship between TAD structure and transcription. Each DCC-dependent TAD boundary contains a strong rex site. To test the model that rex interactions establish TAD boundaries, we are deleting rex sites from X and inserting new rex sites on X and autosomes. We deleted three strong rex sites that interact with each other and are located at adjacent DCC-dependent TAD boundaries using CRISPR/Cas9-mediated homology-directed repair. For one of these sites, we have shown that the deletion causes a loss of DCC binding and significantly diminishes the TAD boundary. We are assessing the impact on TAD structure and gene expression caused by deleting all three pivotal rex sites.
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[
International Worm Meeting,
2017]
Interphase chromosome structure is regulated at multiple length scales, and each level of organization controls nuclear functions such as transcription, replication, and recombination. To learn how these structures are formed, we dissected the mechanism by which a condensin complex imposes a distinct, higher-order structure across X chromosomes of C. elegans hermaphrodites. Here our deletion analysis of the endogenous X revealed that architectural proteins can remodel chromosome-wide topology by binding to a small number of sites. The dosage compensation complex (DCC), a specialized condensin complex, is recruited to dozens of specific sites (rex sites) on both hermaphrodite X chromosomes and represses X-linked gene expression by half. The DCC establishes a higher-order structure composed of megabase-scale topologically associating domains (TADs) that is distinct from the structure of autosomes and male X chromosomes. The DCC-dependent TAD boundaries all contain a strong rex site, and the DCC promotes long-range interactions both between rex sites at TAD boundaries and between rex sites within TADs. To discern the contributions of these different rex-site interactions to TAD boundary formation, we deleted the eight rex sites at DCC-dependent TAD boundaries and examined X structure using an updated in-nucleus Hi-C protocol that detects distant interactions efficiently. In the rex-delete strain, the specific loops between adjacent DCC-dependent TAD boundaries were eliminated. All eight DCC-dependent boundaries were lost or significantly weakened, producing a structure that recapitulates the X structure of a DCC mutant. Therefore, though the DCC binds dozens of sites on X, the TAD boundaries are established by binding to these eight high-affinity sites. Disruption of TAD structure by deleting a series of cis elements uniquely allows us to assess the effects of TAD boundaries on gene expression. The rex-deleted worms lack strong dosage compensation phenotypes, indicating that TAD boundaries alone are insufficient to enact full repression of X gene expression. Ongoing sensitive gene expression assays are determining whether TAD boundary disruption causes local or subtle transcriptional changes. Intra-TAD interactions present in wild-type and rex-delete animals but absent in DCC mutants likely underlie mechanisms that control X gene expression. Furthermore, Hi-C results showed that in C. briggsae, which also uses a condensin DCC, X chromosomes have a unique TAD structure compared to that of autosomes, even though the rex sites are in different locations relative to C. elegans' sites. Hi-C also revealed errors in C. briggsae's genome assembly, which are now being corrected based on Hi-C data. This improved genome assembly facilitates studies of how condensin's role in shaping higher-order chromosome structure is maintained as its binding sites evolve.
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[
Development,
2021]
Swathi Arur is an Associate Professor for the Department of Genetics at the MD Anderson Cancer Center, USA, where she uses multidisciplinary approaches to understand female germline development and fertility. She has received numerous accolades, including the MD Anderson Distinguished Research Faculty Mentor Award in 2017. In 2020, she was elected to the American Association for the Advancement of Science (AAAS). Swathi joined the team at Development as an Academic Editor in 2020, and we met with her over Zoom to hear more about her life, her career and her love for <i>C. elegans</i>.
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[
Dev Cell,
2019]
In this issue of Developmental Cell, Anderson etal. (2019) show that chromatin domain structure on the X chromosome in C.elegans is dispensable for dosage compensation but regulates longevity and thermotolerance. This study sheds light on the mechanisms of domain formation in C.elegans and how these features affect physiology.
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Meyer, Barbara J., Frokjaer-Jensen, Christian, Bian, Qian, Anderson, Erika, Jorgensen, Erik, Wheeler, Bayly
[
International Worm Meeting,
2015]
The relationship between chromosome structure, nuclear positioning, and long-range gene regulation is poorly understood. To explore this relationship, we dissected X-chromosome-wide gene regulation enacted by a dosage compensation complex (DCC), which represses X transcription in hermaphrodites to balance gene expression between sexes. We inserted transgenes throughout the genome and queried their expression to determine whether different transcriptional environments exist on X and autosomes. Transgenes integrated on X were dosage compensated regardless of position, meaning their expression was equal in wild-type males and hermaphrodites but elevated in dosage-compensation-defective hermaphrodites. This result indicates the X chromosome is broadly permissive for repression, and endogenous genes that escape have special features enabling them to overcome this repression. In contrast, we found no chromosome-wide mechanism to balance X expression with that of autosomes, given that transgenes on X were expressed at half the level of transgenes on autosomes. Repression of X transgenes was independent of their proximity to DCC recruitment sites (rex), highlighting the long-range mechanism of regulation employed by the DCC. We already showed that changes in higher order X-chromosome structure accompany repression of X-linked genes, so we next explored whether spatial positioning of X influences dosage compensation. We first addressed a model of others that rex sites target X to the nuclear periphery in males to increase gene expression, and DCC binding to rex sites in hermaphrodites helps relocate X to the interior, thereby repressing X. Using FISH, we found for both sexes that neither endogenous rex sites on X nor ectopically inserted rex sites on autosomes were preferentially located at the nuclear periphery. Furthermore, though rex insertions on autosomes recruit the DCC, the expression of adjacent genes was not elevated in DCC-depleted animals. These observations disfavor the proposed model. Instead, we found that pairs of distant rex sites interact in a DCC-dependent manner, and interacting rex sites are preferentially located at the nuclear periphery compared to non-interacting sites. Interacting rex pairs associate with nuclear pores, not the lamina. We propose the nuclear pore might act as a scaffold to promote rex site interactions, which in turn influence gene expression by remodeling higher order chromosome structure.
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Pickle, Catherine, Anderson, Erika, Lo, Te-Wen, Gurling, Mark, Schartner, Caitlin, Meyer, Barbara J., Ralston, Ed
[
International Worm Meeting,
2013]
We have achieved targeted genome editing across nematode species diverged by 300 million years. These methods have proven to be invaluable for evolutionary studies across species that lack reverse genetic tools but have sequenced genomes. Our editing protocols work in parasitic nematodes (P. pacificus), male/female species (C. sp.9), and hermaphroditic species (C. elegans and C. briggsae). Our approach uses engineered nucleases made of fusions between the DNA cleavage domain of FokI and a custom-designed DNA-binding domain of transcription activator-like effector (TALE) repeats. Our protocols permit not only the isolation of "knock-out" mutations, but also the recovery of multiple different custom-designed "knock-in" mutations in the genomic location of choice. The various "knock-in" and "knock-out" modifications can be recovered from the progeny of a single injected animal. The entire process from TALEN design to isolation of DNA-sequence-verified homozygous mutants can be completed in three weeks, and the cost is minimal.
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[
MicroPubl Biol,
2022]
Caenorhabditis elegans is a model species, increasingly used in experimental evolution studies to investigate such major topics as: maintenance of genetic variation, host-pathogen interaction and coevolution, mutations, life history, evolution of reproductive systems, sexual selection (Gray and Cutter, 2014; Teotnio, Estes, Phillips, and Baer, 2017). Its reproductive system in the wild, known as androdioecy, involves mostly self-fertilization of hermaphrodites and occasionally outcrossing with males, which are generally rare (Stewart and Phillips, 2002). This system can be experimentally changed to dioecy, i.e., obligatory outcrossing, through genetic manipulations (see Table I in Anderson, Morran, and Phillips, 2010; Gray and Cutter, 2014).
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[
Nematologica,
1969]
Several investigators have reported that nutritional or environmental factors induce morphological variations in the "so-called' bacteriophagous nematodes. For example, Nigon & Dougherty described a morphological mutant of the free-living, self-fertilizing, hermaphroditic nematode Rhabditis (Caenorhabditis) briggsae that ensued following heat-treatment of progeny cultured on bacteria. Also Anderson reported that certain diagnostic features of an Acrobeloides sp., specifically the shape of the labial probolae and tail, varied significantly when the nematodes were grown on bacterial cultures as compared to those grown in soil. The current paper describes a consistent morphological variation in Caenorhabditis briggsae grown axenically on a meridic medium containing a growth factor from a bacterium as compared with nematodes reared on a growth factor from liver extract.
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[
Fundamental and Applied Nematology,
1997]
The effects of structural heterogeneity on both chemical diffusion and nematode movement are examined with the development of a theoretical model. The model considers three factors affecting nematode movement: soil structure, nematode foraging strategy and chemotaxis. Using a continuous model, we develop a discrete system which allows nematode trails to be simulated in any of the four experimental conditions given by Anderson et al (1997). We show that structural heterogeneity causes mixed levels of attractant concentration over small areas as well as "fingering" of the attractant. Soil structural heterogeneity also restricts the foraging strategy of the nematode which then becomes a strategy to avoid structural "traps". The effect of localised increases in structural density is shown to increase significantly "fingering" of the attractant.
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[
Worm Breeder's Gazette,
1988]
As previously reported (WBG 10-1: 112, 10-2: 30, etc.) mutations at six different loci act as allele-specific suppressors of mutations in a variety of genes:
tra-2,
unc-54, etc. These mutations also have characteristic morphological effects on the anatomy of the adult male tail and, to a lesser extent, of the hermaphrodite vulva. For this reason they have hitherto been assigned to the mab (male abnormal) gene category:
mab-1, ed) and
mab-12 through
mab-16 (unpublished). However, they exhibit such a distinctive set of common properties that it has been decided (with the agreement of Andy Papp, Victor Ambros, Rock Pulak and Phil Anderson, who have been responsible for isolating most of these suppressor mutations) to assign them to a new gene