The Caenorhabditis elegans TDRD5/7-like protein, LOTR-1, interacts with the helicase ZNFX-1 to balance epigenetic signals in the germline

Marnik, Elisabeth A.; Almeida, Miguel Vasconcelos; Cipriani, Patricia Giselle; Chung, George; Caspani, Edoardo; Karaulanov, Emil; Gan, Hin Hark; Zinno, John; Isolehto, Ida J.; Kielisch, Fridolin; Butter, Falk; Sharp, Catherine S.; Flanagan, Roisin M.; Bonnet, Frédéric; Piano, Fabio; Ketting, René F.; Gunsalus, Kristin C.; Updike, Dustin L.

doi:10.1371/journal.pgen.1010245

Cited by 11 publications

(9 citation statements)

References 118 publications

(151 reference statements)

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“…LOTR-1, another LOTUS domain-containing protein, colocalized with tagRFP::ZNFX-1 and accumulated in the Z granule, as reported previously (Fig. S2A) 44 .…”

Section: Resultssupporting

confidence: 88%

“…For instance, mutator factors, including MUT-2/RDE-3, MUT-7, MUT- 8/RDE-2, MUT-14, MUT-15/RDE-5, MUT-16/RDE-6 and RDE-8, accumulate at the Mutator foci, contributing to siRNA amplification from poly(UG)-tailed RNA templates 34,41,42 . ZNFX-1, WAGO-4, PID-2/ZSP-1 and LOTR-1 accumulate in the Z granule, promoting RNAi inheritance and piRNA-induced gene silencing 14,15,43,44 . Approximately 90 C. elegans proteins have been found to be enriched in germ granules through a variety of methods, including proteomic approaches, such as TurboID/MS and IP/MS technologies 21,27,36,45,46 .…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Compartmentalized localization of perinuclear proteins within germ granules inC. elegans

Huang,

Feng,

Yan

et al. 2024

Preprint

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Biomolecular condensates are nonmembrane-enclosed organelles that play important roles in distinct biological processes. Germ granules are RNA-rich condensates that are often docked on the cytoplasmic surface of germline nuclei and exist in a variety of organisms. The C. elegans germ granule is a condensate that is subcompartmentalized into at least 6 distinct regions, including the P granule, Z granule, E granule, Mutator foci, SIMR foci and P-body. Although a number of perinuclear proteins have been found to be enriched in germ granules, their precise localization within the subcompartments of germ granules is still unclear. Here, we systematically labeled perinuclear localized proteins with fluorescent proteins via CRISPR/Cas9 technology and further explored the perinuclear localization of these proteins. Using this nematode strain library, we identified a series of proteins localized in Z or E granules. We found that proteins that participate in distinct piRNA processing steps were localized in particular subcompartments, including the P-, Z-, and E-granules. We further identified a novel subcompartment, the D granule, which was enriched between the P granule and the nuclear pore complex. Finally, we analyzed the perinuclear localization of these germ granule subcompartments in mip-1/eggd-1 mutants and found that the LOTUS domain protein MIP-1/EDDG-1 was required for the establishment of the multiphase architecture of germ granules. Overall, our work revealed germ granule architecture and redefined the localization of perinuclear proteins within germ granules. Additionally, the library of genetically modified nematode strains expressing peri-nuclear proteins labeled with fluorescent tags will facilitate research on germ granules in C. elegans.

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“…LOTR-1, another LOTUS domain-containing protein, colocalized with tagRFP::ZNFX-1 and accumulated in the Z granule, as reported previously (Fig. S2A) 44 .…”

Section: Resultssupporting

confidence: 88%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Compartmentalized localization of perinuclear proteins within germ granules inC. elegans

Huang,

Feng,

Yan

et al. 2024

Preprint

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“…TDRD5 and TDRD7 possess LOTUS and Tudor domains and are indispensable for germ granule formation in mice 93 – 95 . Recent studies conducted on C. elegans established an essential role of LOTUS domain proteins in facilitating perinuclear localization of germ granules 24 , 26 , 96 . Here, using a series of microscopy and genetic experiments, we demonstrated that the LOTUS domain protein EGGD-1 is required for the proper formation of germ granule sub-compartments including P granules, Mutator foci and Z granules (Fig.…”

Section: Discussionmentioning

confidence: 99%

C. elegans germ granules sculpt both germline and somatic RNAome

Price,

Wagner,

Pastore

et al. 2023

Nat Commun

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Germ granules are membrane-less organelles essential for small RNA biogenesis and germline development. Among the conserved properties of germ granules is their association with the nuclear membrane. Recent studies demonstrated that LOTUS domain proteins, EGGD-1 and EGGD-2 (also known as MIP-1 and MIP-2 respectively), promote the formation of perinuclear germ granules in C. elegans. This finding presents a unique opportunity to evaluate the significance of perinuclear localization of germ granules. Here we show that loss of eggd-1 causes the coalescence of germ granules and formation of abnormal cytoplasmic aggregates. Impairment of perinuclear granules affects certain germline classes of small RNAs including Piwi-interacting RNAs. Transcriptome profiling reveals overexpression of spermatogenic and cuticle-related genes in eggd-1 hermaphrodites. We further demonstrate that disruption of germ granules activates HLH-30-mediated transcriptional program in somatic tissues. Collectively, our findings underscore the essential role of EGGD-1 in germ granule organization and reveal an unexpected germ granule-to-soma communication.

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“…Public datasets for small RNA sequencing read for M. musculus (GSE213097 [60]), C. elegans (GSE192793 [61]), and A. thaliana (GSE152909 [62]) were used to demonstrate pipeline utility across species. We sequenced nine human cell line samples to demonstrate miRNA-loci calling.…”

Section: Pipeline Demonstration and Benchmarkingmentioning

confidence: 99%

sRNAfrag: A pipeline and suite of tools to analyze fragmentation in small RNA sequencing data

Nakatsu,

Jijiwa,

Khadka

et al. 2023

Preprint

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Fragments derived from RNAs such as small nucleolar RNAs hold biological relevance. However, they remain poorly understood which calls for more comprehensive methods to analyze such fragmentation. Thus, we developed sRNAfrag, a standardized workflow and set of scripts for quantifying and analyzing sRNA fragmentation. It is able to detect start and end loci of mature microRNAs fragmented from precursors and, utilizing multi-mapping events, the conserved 5' seed sequence of miRNAs. The tool detected 1411 snoRNA fragment conservation events between 2/4 eukaryotic species, providing the opportunity to explore motifs and fragmentation patterns not only within species, but between. Availability: https://github.com/kenminsoo/sRNAfrag.

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The Caenorhabditis elegans TDRD5/7-like protein, LOTR-1, interacts with the helicase ZNFX-1 to balance epigenetic signals in the germline

Cited by 11 publications

References 118 publications

Compartmentalized localization of perinuclear proteins within germ granules inC. elegans

Compartmentalized localization of perinuclear proteins within germ granules inC. elegans

C. elegans germ granules sculpt both germline and somatic RNAome

sRNAfrag: A pipeline and suite of tools to analyze fragmentation in small RNA sequencing data

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