The meiotic phosphatase GSP-2/PP1 promotes germline immortality and small RNA-mediated genome silencing

Verdugo C, Wu CW. Differential effect of ubiquitous and germline depletion of Integrator complex function on C. elegans physiology

The Integrator is a metazoan-conserved protein complex with endonuclease activity that functions to cleave various RNA substrates to shape transcriptome homeostasis by coordinating small nuclear RNA biogenesis to premature transcription termination. Depletion of Integrator results in developmental defects across different model systems and has emerged as a causative factor in human neurodevelopmental syndromes. Here, we used the model system Caenorhabditis elegans to enable study of the temporal effects of Integrator depletion on various physiological parameters with the auxin-inducible degron system that permitted depletion of INTS-4 (Integrator subunit) catalytic subunit of the protein complex. We found that Integrator activity is critical and required for C. elegans development within the L1 larval stage but becomes dispensable for development and lifespan after the animals have reached the L2/L3 stage. Depletion of INTS-4 only shortened lifespan if auxin was introduced at the L1 stage, suggesting that the previously described lifespan reduction by Integrator inhibition is linked to developmental growth defects. We also found that while germline-specific degradation of Integrator results in the accumulation of misprocessed snRNA transcript, it did not impair the development or lifespan but surprisingly increased progeny production. Together, our study illustrates a temporal, and a potentially tissue-specific requirement of the Integrator complex function in shaping whole organism development, aging, and reproduction.

HIM-17 regulates the position of recombination events and GSP-1/2 localization to establish short arm identity on bivalents in meiosis

The position of recombination events established along chromosomes in early prophase I and the chromosome remodeling that takes place in late prophase I are intrinsically linked steps of meiosis that need to be tightly regulated to ensure accurate chromosome segregation and haploid gamete formation. Here, we show that RAD-51 foci, which form at the sites of programmed meiotic DNA double-strand breaks (DSBs), exhibit a biased distribution toward off-centered positions along the chromosomes in wild-type Caenorhabditis elegans, and we identify two meiotic roles for chromatin-associated protein HIM-17 that ensure normal chromosome remodeling in late prophase I. During early prophase I, HIM-17 regulates the distribution of DSB-dependent RAD-51 foci and crossovers on chromosomes, which is critical for the formation of distinct chromosome subdomains (short and long arms of the bivalents) later during chromosome remodeling. During late prophase I, HIM-17 promotes the normal expression and localization of protein phosphatases GSP-1/2 to the surface of the bivalent chromosomes and may promote GSP-1 phosphorylation, thereby antagonizing Aurora B kinase AIR-2 loading on the long arms and preventing premature loss of sister chromatid cohesion. We propose that HIM-17 plays distinct roles at different stages during meiotic progression that converge to promote normal chromosome remodeling and accurate chromosome segregation.

Germ granule dysfunction is a hallmark and mirror of Piwi mutant sterility

In several species, Piwi/piRNA genome silencing defects cause immediate sterility that correlates with transposon expression and transposon-induced genomic instability. In C. elegans, mutations in the Piwi-related gene (prg-1) and other piRNA deficient mutants cause a transgenerational decline in fertility over a period of several generations. Here we show that the sterility of late generation piRNA mutants correlates poorly with increases in DNA damage signaling. Instead, sterile individuals consistently exhibit altered perinuclear germ granules. We show that disruption of germ granules does not activate transposon expression but induces multiple phenotypes found in sterile prg-1 pathway mutants. Furthermore, loss of the germ granule component pgl-1 enhances prg-1 mutant infertility. Environmental restoration of germ granule function for sterile pgl-1 mutants restores their fertility. We propose that Piwi mutant sterility is a reproductive arrest phenotype that is characterized by perturbed germ granule structure and is phenocopied by germ granule dysfunction, independent of genomic instability.

Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields

Background

De Bruijn graphs are key data structures for the analysis of next-generation sequencing data. They efficiently represent the overlap between reads and hence, also the underlying genome sequence. However, sequencing errors and repeated subsequences render the identification of the true underlying sequence difficult. A key step in this process is the inference of the multiplicities of nodes and arcs in the graph. These multiplicities correspond to the number of times each k-mer (resp. k+1-mer) implied by a node (resp. arc) is present in the genomic sequence. Determining multiplicities thus reveals the repeat structure and presence of sequencing errors. Multiplicities of nodes/arcs in the de Bruijn graph are reflected in their coverage, however, coverage variability and coverage biases render their determination ambiguous. Current methods to determine node/arc multiplicities base their decisions solely on the information in nodes and arcs individually, under-utilising the information present in the sequencing data.

Results

To improve the accuracy with which node and arc multiplicities in a de Bruijn graph are inferred, we developed a conditional random field (CRF) model to efficiently combine the coverage information within each node/arc individually with the information of surrounding nodes and arcs. Multiplicities are thus collectively assigned in a more consistent manner.

Conclusions

We demonstrate that the CRF model yields significant improvements in accuracy and a more robust expectation-maximisation parameter estimation. True k-mers can be distinguished from erroneous k-mers with a higher F₁ score than existing methods. A C++11 implementation is available at https://github.com/biointec/detoxunder the GNU AGPL v3.0 license.

Transcriptional adaptation in Caenorhabditis elegans

Transcriptional adaptation is a recently described phenomenon by which a mutation in one gene leads to the transcriptional modulation of related genes, termed adapting genes. At the molecular level, it has been proposed that the mutant mRNA, rather than the loss of protein function, activates this response. While several examples of transcriptional adaptation have been reported in zebrafish embryos and in mouse cell lines, it is not known whether this phenomenon is observed across metazoans. Here we report transcriptional adaptation in C. elegans, and find that this process requires factors involved in mutant mRNA decay, as in zebrafish and mouse. We further uncover a requirement for Argonaute proteins and Dicer, factors involved in small RNA maturation and transport into the nucleus. Altogether, these results provide evidence for transcriptional adaptation in C. elegans, a powerful model to further investigate underlying molecular mechanisms.