The Nucleolus of<i>Caenorhabditis elegans</i>

Lee, Li‐Wei; Lee, Chi-Chang; Huang, Chih-Cheng; Lo, Szecheng J.

doi:10.1155/2012/601274

Cited by 32 publications

(25 citation statements)

References 78 publications

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“…In the majority of cells, we observed one or two distinct fluorescent foci per cell (Figure 4) (an average of 1.76 foci per cell over all samples), consistent with reported nucleolar marker fibrillarin localization during embryogenesis (Lee et al 2012). For each strain, we imaged at least 100 cells (Table S12) and quantified the FISH foci in each cell.…”

Section: Molecular Inversion Probe-based Copy Number Estimation Yieldsupporting

confidence: 83%

Challenges and Approaches to Genotyping Repetitive DNA

Morton¹,

Hall

Kwan³

et al. 2020

G3 Genes|Genomes|Genetics

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Individuals within a species can exhibit vast variation in copy number of repetitive DNA elements. This variation may contribute to complex traits such as lifespan and disease, yet it is only infrequently considered in genotype-phenotype associations. Although the possible importance of copy number variation is widely recognized, accurate copy number quantification remains challenging. Here, we assess the technical reproducibility of several major methods for copy number estimation as they apply to the large repetitive ribosomal DNA array (rDNA). rDNA encodes the ribosomal RNAs and exists as a tandem gene array in all eukaryotes. Repeat units of rDNA are kilobases in size, often with several hundred units comprising the array, making rDNA particularly intractable to common quantification techniques. We evaluate pulsed-field gel electrophoresis, droplet digital PCR, and Nextera-based whole genome sequencing as approaches to copy number estimation, comparing techniques across model organisms and spanning wide ranges of copy numbers. Nextera-based whole genome sequencing, though commonly used in recent literature, produced high error. We explore possible causes for this error and provide recommendations for best practices in rDNA copy number estimation. We present a resource of high-confidence rDNA copy number estimates for a set of S. cerevisiae and C. elegans strains for future use. We furthermore explore the possibility for FISH-based copy number estimation, an alternative that could potentially characterize copy number on a cellular level.

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Section: Molecular Inversion Probe-based Copy Number Estimation Yieldsupporting

confidence: 83%

Challenges and Approaches to Genotyping Repetitive DNA

Morton¹,

Hall

Kwan³

et al. 2020

G3 Genes|Genomes|Genetics

View full text Add to dashboard Cite

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“…FIB-1 encodes the C. elegans ortholog of human fibrillarin and Saccharomyces cerevisiae Nop1p (21). FIB-1 localizes to the nucleolus in embryos.…”

Section: Significancementioning

confidence: 99%

Erroneous ribosomal RNAs promote the generation of antisense ribosomal siRNA

Zhu

Weng

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

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Ribosome biogenesis is a multistep process, during which mistakes can occur at any step of pre-rRNA processing, modification, and ribosome assembly. Misprocessed rRNAs are usually detected and degraded by surveillance machineries. Recently, we identified a class of antisense ribosomal siRNAs (risiRNAs) that down-regulate pre-rRNAs through the nuclear RNAi pathway. To further understand the biological roles of risiRNAs, we conducted both forward and reverse genetic screens to search for more suppressor of siRNA () mutants. We isolated a number of genes that are broadly conserved from yeast to humans and are involved in pre-rRNA modification and processing. Among them, SUSI-2(ceRRP8) is homologous to human RRP8 and engages in m1A methylation of the 26S rRNA. C27F2.4(ceBUD23) is an m7G-methyltransferase of the 18S rRNA. E02H1.1(ceDIMT1L) is a predicted m6(2)Am6(2)A-methyltransferase of the 18S rRNA. Mutation of these genes led to a deficiency in modification of rRNAs and elicited accumulation of risiRNAs, which further triggered the cytoplasmic-to-nuclear and cytoplasmic-to-nucleolar translocations of the Argonaute protein NRDE-3. The rRNA processing deficiency also resulted in accumulation of risiRNAs. We also isolated SUSI-3(RIOK-1), which is similar to human RIOK1, that cleaves the 20S rRNA to 18S. We further utilized RNAi and CRISPR-Cas9 technologies to perform candidate-based reverse genetic screens and identified additional pre-rRNA processing factors that suppressed risiRNA production. Therefore, we concluded that erroneous rRNAs can trigger risiRNA generation and subsequently, turn on the nuclear RNAi-mediated gene silencing pathway to inhibit pre-rRNA expression, which may provide a quality control mechanism to maintain homeostasis of rRNAs.

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“…In the presence of risiRNA, NRDE-3 accumulated in the nucleoli of cde-1 mutants (Figure 2D). FIB-1 in C. elegans is encoded by an ortholog of the genes encoding human fibrillarin and Saccharomyces cerevisiae Nop1p (Lee, Lee et al, 2012, Yi, Ma et al, 2015). FIB-1 localizes to the nucleolus in embryos.…”

Section: Resultsmentioning

confidence: 99%

CDE-1 suppresses the production of risiRNA by coupling polyuridylation and degradation of 26S rRNA

Wang

Weng

Chen

et al. 2019

Preprint

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22Antisense ribosomal siRNAs (risiRNAs) downregulate pre-rRNAs through the 23 nuclear RNAi pathway in Caenorhabditis elegans. However, the biogenesis and 24 regulation of risiRNAs remain obscure. Previously, we showed that 26S rRNAs are 25 uridylated at the 3'-ends by an unknown terminal polyuridylation polymerase before 26 the rRNAs are degraded by a 3' to 5' exoribonuclease SUSI-1(ceDIS3L2). There are 27 three polyuridylation polymerases, CDE-1, PUP-2, and PUP-3, in C. elegans. Here, we 28 found that CDE-1 is specifically involved in suppressing risiRNA production. CDE-1 29 localizes to perinuclear granules in the germline and uridylates both Argonaute-30 associated 22G-RNAs and 26S rRNAs at the 3'-ends. Immunoprecipitation followed by 31 mass spectrometry (IP-MS) revealed that CDE-1 interacts with SUSI-1(ceDIS3L2). 32Consistent with those results, both CDE-1 and SUSI-1(ceDIS3L2) are required for the 33 inheritance of RNAi. Therefore, this work identified a rRNA surveillance machinery of 34 rRNAs that couples terminal polyuridylation and degradation. 35 36 37 38 3

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The Nucleolus ofCaenorhabditis elegans

Cited by 32 publications

References 78 publications

Challenges and Approaches to Genotyping Repetitive DNA

Challenges and Approaches to Genotyping Repetitive DNA

Erroneous ribosomal RNAs promote the generation of antisense ribosomal siRNA

CDE-1 suppresses the production of risiRNA by coupling polyuridylation and degradation of 26S rRNA

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