scholarly journals Transgenerational Epigenetic Inheritance Factors Localize to Spatially and Temporally Ordered Liquid Droplet Assemblages

2017 ◽  
Author(s):  
Gang Wan ◽  
Brandon D. Fields ◽  
George Spracklin ◽  
Carolyn Phillips ◽  
Scott Kennedy
Keyword(s):  
Rna Binding ◽  
Liquid Droplet ◽  
Epigenetic Inheritance ◽  
Liquid Droplets ◽  
P Granules ◽  
Transgenerational Epigenetic Inheritance ◽  
C Elegans ◽  
Regulatory Systems ◽  
Processing Pathways ◽  
Non Coding Rnas

AbstractEpigenetic information can be inherited for multiple generations (termed transgenerational epigenetic inheritance or TEI) 1,2. Non-coding RNAs have emerged as important mediators of TEI, although the mechanism(s) by which non-coding RNAs mediate TEI remains poorly understood. dsRNA-mediated gene silencing (RNAi) in C. elegans is a robust example of RNA-directed TEI3–5. To further our understanding of RNA-directed TEI, we conducted a genetic screen in C. elegans to identify genes required for RNAi inheritance. Our screen identified the conserved RNA helicase/Zn finger protein ZNFX-1 and the Argonaute protein WAGO-4. We find that WAGO-4 and ZNFX-1 act cooperatively in inheriting generations to maintain small interfering (si)RNA expression over generational time. ZNFX-1/ WAGO-4 localize to a liquid droplet organelle termed the P granule in early germline blastomeres. Later in development, ZNFX-1/WAGO-4 appear to separate from P granules to form independent foci that are adjacent to, yet remain distinct, from P granules. ZNFX-1/WAGO-4 labeled foci exhibit properties reminiscent of liquid droplets and we name these foci Z granules. In the adult germline, Z granules assemble into ordered tri-droplet assemblages with P granules and another germline droplet-like foci termed the Mutator foci. This work identifies a conserved RNA-binding protein that drives RNA-directed TEI in C. elegans, defines a new germline foci that we term the Z granule, demonstrates that liquid droplet formation is under developmental control, and shows that liquid droplets can assemble into spatially ordered multi-droplet structures. We speculate that temporal and spatial ordering of liquid droplets helps cells organize and coordinate the complex RNA processing pathways underlying gene regulatory systems, such as RNA-directed TEI.

How do histone modifications contribute to transgenerational epigenetic inheritance in C. elegans?

2020 ◽  
Vol 48 (3) ◽  
pp. 1019-1034 ◽  
Author(s):  
Rachel M. Woodhouse ◽  
Alyson Ashe
Keyword(s):  
Histone Modifications ◽  
Molecular Mechanisms ◽  
Epigenetic Inheritance ◽  
Nematode Caenorhabditis Elegans ◽  
Histone Methyltransferases ◽  
Transgenerational Epigenetic Inheritance ◽  
C Elegans ◽  
Recent Developments ◽  
Gene Regulatory

Gene regulatory information can be inherited between generations in a phenomenon termed transgenerational epigenetic inheritance (TEI). While examples of TEI in many animals accumulate, the nematode Caenorhabditis elegans has proven particularly useful in investigating the underlying molecular mechanisms of this phenomenon. In C. elegans and other animals, the modification of histone proteins has emerged as a potential carrier and effector of transgenerational epigenetic information. In this review, we explore the contribution of histone modifications to TEI in C. elegans. We describe the role of repressive histone marks, histone methyltransferases, and associated chromatin factors in heritable gene silencing, and discuss recent developments and unanswered questions in how these factors integrate with other known TEI mechanisms. We also review the transgenerational effects of the manipulation of histone modifications on germline health and longevity.

scholarly journals C. elegans germ granules require both assembly and localized regulators for mRNA repression

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Scott Takeo Aoki ◽  
Tina R. Lynch ◽  
Sarah L. Crittenden ◽  
Craig A. Bingman ◽  
Marvin Wickens ◽  
...  
Keyword(s):  
Liquid Droplet ◽  
Scaffolding Protein ◽  
P Granules ◽  
C Elegans ◽  
Cytoplasmic Rna ◽  
And Function ◽  
Rnp Granules ◽  
Key Residues ◽  
Reporter Mrna

AbstractCytoplasmic RNA–protein (RNP) granules have diverse biophysical properties, from liquid to solid, and play enigmatic roles in RNA metabolism. Nematode P granules are paradigmatic liquid droplet granules and central to germ cell development. Here we analyze a key P granule scaffolding protein, PGL-1, to investigate the functional relationship between P granule assembly and function. Using a protein–RNA tethering assay, we find that reporter mRNA expression is repressed when recruited to PGL-1. We determine the crystal structure of the PGL-1 N-terminal region to 1.5 Å, discover its dimerization, and identify key residues at the dimer interface. Mutations of those interface residues prevent P granule assembly in vivo, de-repress PGL-1 tethered mRNA, and reduce fertility. Therefore, PGL-1 dimerization lies at the heart of both P granule assembly and function. Finally, we identify the P granule-associated Argonaute WAGO-1 as crucial for repression of PGL-1 tethered mRNA. We conclude that P granule function requires both assembly and localized regulators.

Analysis of RNA associated with P granules in germ cells of C. elegans adults

Development ◽  
2001 ◽  
Vol 128 (8) ◽  
pp. 1287-1298 ◽  
Author(s):  
J.A. Schisa ◽  
J.N. Pitt ◽  
J.R. Priess
Keyword(s):  
Germ Cells ◽  
Rna Binding ◽  
Nuclear Surface ◽  
Binding Motifs ◽  
P Granules ◽  
C Elegans ◽  
Specific Mrnas ◽  
Tubulin Mrna ◽  
Protein Components ◽  
Cytoplasmic Structures

P granules are cytoplasmic structures of unknown function that are associated with germ nuclei in the C. elegans gonad, and are localized exclusively to germ cells, or germ cell precursors, throughout the life cycle. All the known protein components of P granules contain putative RNA-binding motifs, suggesting that RNA is involved in either the structure or function of the granules. However, no specific mRNAs have been identified within P granules in the gonad. We show here that P granules normally contain a low level of RNA, and describe conditions that increase this level. We present evidence that several, diverse mRNAs, including pos-1, mex-1, par-3, skn-1, nos-2 and gld-1 mRNA, are present at least transiently within P granules. In contrast, actin and tubulin mRNA and rRNA are either not present in P granules, or are present at relatively low levels. We show that pgl-1 and the glh (Vasa-related) gene family, which encode protein components of P granules, do not appear essential for RNA to concentrate in P granules; these proteins may instead function in events that are a prerequisite for RNAs to be transported efficiently from the nuclear surface.

scholarly journals The Dynamics of P Granule Liquid Droplets Are Regulated by the Caenorhabditis elegans Germline RNA Helicase GLH-1 via Its ATP Hydrolysis Cycle

Genetics ◽  
2020 ◽  
Vol 215 (2) ◽  
pp. 421-434 ◽  
Author(s):  
Wenjun Chen ◽  
Yabing Hu ◽  
Charles F. Lang ◽  
Jordan S. Brown ◽  
Sierra Schwabach ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Cell Fate ◽  
Rna Binding ◽  
Atp Hydrolysis ◽  
Rna Binding Proteins ◽  
Rna Helicase ◽  
Liquid Droplets ◽  
P Granules ◽  
Link Type ◽  
Show Evidence

P granules are phase-separated liquid droplets that play important roles in the maintenance of germ cell fate in Caenorhabditis elegans. Both the localization and formation of P granules are highly dynamic, but mechanisms that regulate such processes remain poorly understood. Here, we show evidence that the VASA-like germline RNA helicase GLH-1 couples distinct steps of its ATPase hydrolysis cycle to control the formation and disassembly of P granules. In addition, we found that the phenylalanine-glycine-glycine repeats in GLH-1 promote its localization at the perinucleus. Proteomic analyses of the GLH-1 complex with a GLH-1 mutation that interferes with P granule disassembly revealed transient interactions of GLH-1 with several Argonautes and RNA-binding proteins. Finally, we found that defects in recruiting the P granule component PRG-1 to perinuclear foci in the adult germline correlate with the fertility defects observed in various GLH-1 mutants. Together, our results highlight the versatile roles of an RNA helicase in controlling the formation of liquid droplets in space and time.

scholarly journals piRNAs Coordinate poly(UG) Tailing to Prevent Aberrant and Permanent Gene Silencing

2021 ◽  
Author(s):  
Aditi Shukla ◽  
Roberto Perales ◽  
Scott Kennedy
Keyword(s):  
Gene Silencing ◽  
Noncoding Rna ◽  
Noncoding Rnas ◽  
Epigenetic Inheritance ◽  
The Self ◽  
Specific Class ◽  
Transgenerational Epigenetic Inheritance ◽  
Small Noncoding Rna ◽  
C Elegans ◽  
Inheritance System

AbstractNoncoding RNAs have emerged as mediators of transgenerational epigenetic inheritance (TEI) in a number of organisms. A robust example of RNA-directed TEI is the inheritance of gene silencing states following RNA interference (RNAi) in the metazoan C. elegans. During RNAi inheritance, gene silencing is transmitted by a self-perpetuating cascade of siRNA-directed poly(UG) tailing of mRNA fragments (pUGylation), followed by siRNA synthesis from poly(UG)-tailed mRNA templates (termed pUG RNA/siRNA cycling). Despite the self-perpetuating nature of pUG RNA/siRNA cycling, RNAi inheritance is finite, suggesting that systems likely exist to prevent permanent RNAi-triggered gene silencing. Here we show that, in the absence of Piwi-interacting RNAs (piRNAs), an animal-specific class of small noncoding RNA, RNAi-based gene silencing can become essentially permanent, lasting at near 100% penetrance for more than five years and hundreds of generations. This permanent gene silencing is mediated by perpetual activation of the pUG RNA/siRNA TEI pathway. Further, we find that piRNAs coordinate endogenous RNAi pathways to prevent germline-expressed genes, which are not normally subjected to TEI, from entering a state of permanent and irreversible epigenetic silencing also mediated by perpetual activation of pUG RNA/siRNA cycling. Together, our results show that one function of C. elegans piRNAs is to insulate germline-expressed genes from aberrant and runaway inactivation by the pUG RNA/siRNA epigenetic inheritance system.

scholarly journals mRNA localization is linked to translation regulation in the Caenorhabditis elegans germ lineage

2020 ◽  
Author(s):  
Dylan M. Parker ◽  
Lindsay P. Winkenbach ◽  
Samuel P. Boyson ◽  
Matthew N. Saxton ◽  
Camryn Daidone ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Regulatory Control ◽  
Translational Repression ◽  
Translation Regulation ◽  
Germline Development ◽  
P Granules ◽  
C Elegans ◽  
Early Embryos

AbstractCaenorhabditis elegans early embryos generate cell-specific transcriptomes despite lacking active transcription. This presents an opportunity to study mechanisms of post-transcriptional regulatory control. In seeking the mechanisms behind this patterning, we discovered that some cell-specific mRNAs accumulate non-homogenously within cells, localizing to membranes, P granules (associated with progenitor germ cells in the P lineage), and P-bodies (associated with RNA processing). Transcripts differed in their dependence on 3’UTRs and RNA Binding Proteins, suggesting diverse regulatory mechanisms. Notably, we found strong but imperfect correlations between low translational status and P granule localization within the progenitor germ lineage. By uncoupling these, we untangled a long-standing question: Are mRNAs directed to P granules for translational repression or do they accumulate there as a downstream step? We found translational repression preceded P granule localization and could occur independent of it. Further, disruption of translation was sufficient to send homogenously distributed mRNAs to P granules. Overall, we show transcripts important for germline development are directed to P granules by translational repression, and this, in turn, directs their accumulation in the progenitor germ lineage where their repression can ultimately be relieved.SummaryMaternally loaded mRNAs localize non-homogeneously within C. elegans early embryos correlating with their translational status and lineage-specific fates.

scholarly journals An eIF4E-binding protein regulates katanin protein levels in C. elegans embryos

2009 ◽  
Vol 187 (1) ◽  
pp. 33-42 ◽  
Author(s):  
Wei Li ◽  
Leah R. DeBella ◽  
Tugba Guven-Ozkan ◽  
Rueyling Lin ◽  
Lesilee S. Rose
Keyword(s):  
Untranslated Region ◽  
Rna Binding ◽  
Binding Protein ◽  
Degradation Pathway ◽  
Translational Repression ◽  
Spindle Orientation ◽  
P Granules ◽  
C Elegans ◽  
Microtubule Severing ◽  
Protein Levels

In Caenorhabditis elegans, the MEI-1–katanin microtubule-severing complex is required for meiosis, but must be down-regulated during the transition to embryogenesis to prevent defects in mitosis. A cullin-dependent degradation pathway for MEI-1 protein has been well documented. In this paper, we report that translational repression may also play a role in MEI-1 down-regulation. Reduction of spn-2 function results in spindle orientation defects due to ectopic MEI-1 expression during embryonic mitosis. MEL-26, which is both required for MEI-1 degradation and is itself a target of the cullin degradation pathway, is present at normal levels in spn-2 mutant embryos, suggesting that the degradation pathway is functional. Cloning of spn-2 reveals that it encodes an eIF4E-binding protein that localizes to the cytoplasm and to ribonucleoprotein particles called P granules. SPN-2 binds to the RNA-binding protein OMA-1, which in turn binds to the mei-1 3′ untranslated region. Thus, our results suggest that SPN-2 functions as an eIF4E-binding protein to negatively regulate translation of mei-1.

scholarly journals HERI-1 is a Chromodomain Protein that Negatively Regulates Transgenerational Epigenetic Inheritance

2018 ◽  
Author(s):  
Roberto Perales ◽  
Daniel Pagano ◽  
Gang Wan ◽  
Brandon Fields ◽  
Arneet L. Saltzman ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Epigenetic Inheritance ◽  
Normal Function ◽  
Negative Regulator ◽  
Rnai Pathway ◽  
Transcriptional Gene Silencing ◽  
Direct Role ◽  
Transgenerational Epigenetic Inheritance ◽  
C Elegans ◽  
Nuclear Rnai

AbstractTransgenerational epigenetic inheritance (TEI) is the inheritance of epigenetic information for two or more generations. In most cases, TEI is limited to 2-3 generations. This short-term nature of TEI could be set by innate biochemical limitations to TEI or by genetically encoded systems that actively limit TEI. dsRNA-mediated gene silencing (RNAi) can be inherited in C. elegans (termed RNAi inheritance or RNA-directed TEI). To identify systems that might actively limit RNA-directed TEI, we conducted a forward genetic screen for factors whose mutation enhanced RNAi inheritance. This screen identified the gene heritable enhancer of RNAi (heri-1), whose mutation causes RNAi inheritance to last longer (>20 generations) than normal. heri-1 encodes a protein with a chromodomain and a kinase-homology domain that is expressed in germ cells and localizes to nuclei. In C. elegans, a nuclear branch of the RNAi pathway (nuclear RNAi or NRDE pathway) is required for RNAi inheritance. We find that this NRDE pathway is hyper-responsive to RNAi in heri-1 mutant animals, suggesting that a normal function of HERI-1 is to limit nuclear RNAi and that limiting nuclear RNAi may be the mechanism by which HERI-1 limits RNAi inheritance. Interestingly, we find that HERI-1 binds to genes targeted by RNAi, suggesting that HERI-1 may have a direct role in limiting nuclear RNAi and, therefore, RNAi inheritance. Surprisingly, recruitment of the negative regulator HERI-1 to genes depends upon that same NRDE factors that drive co-transcriptional gene silencing during RNAi inheritance. We therefore speculate that the generational perdurance of RNAi inheritance is set by competing pro- and anti-silencing outputs of the NRDE nuclear RNAi machinery.

scholarly journals Multigenerational Regulation of the Caenorhabditis elegans Chromatin Landscape by Germline Small RNAs

2019 ◽  
Vol 53 (1) ◽  
pp. 289-311 ◽  
Author(s):  
Natasha E. Weiser ◽  
John K. Kim
Keyword(s):  
Gene Expression ◽  
Caenorhabditis Elegans ◽  
Small Rnas ◽  
Model Organism ◽  
Epigenetic Inheritance ◽  
Small Interfering Rnas ◽  
Transgenerational Epigenetic Inheritance ◽  
C Elegans ◽  
Small Noncoding Rnas ◽  
Rna Pathways

In animals, small noncoding RNAs that are expressed in the germline and transmitted to progeny control gene expression to promote fertility. Germline-expressed small RNAs, including endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), drive the repression of deleterious transcripts such as transposons, repetitive elements, and pseudogenes. Recent studies have highlighted an important role for small RNAs in transgenerational epigenetic inheritance via regulation of heritable chromatin marks; therefore, small RNAs are thought to convey an epigenetic memory of genomic self and nonself elements. Small RNA pathways are highly conserved in metazoans and have been best described for the model organism Caenorhabditis elegans. In this review, we describe the biogenesis, regulation, and function of C. elegans endo-siRNAs and piRNAs, along with recent insights into how these distinct pathways are integrated to collectively regulate germline gene expression, transgenerational epigenetic inheritance, and ultimately, animal fertility.

scholarly journals Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically disordered proteins in C. elegans

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Jennifer T Wang ◽  
Jarrett Smith ◽  
Bi-Chang Chen ◽  
Helen Schmidt ◽  
Dominique Rasoloson ◽  
...  
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Light Sheet ◽  
Disordered Proteins ◽  
Liquid Droplets ◽  
P Granules ◽  
C Elegans ◽  
Rna Granules ◽  
Intrinsically Disordered ◽  
Light Sheet Microscopy

RNA granules have been likened to liquid droplets whose dynamics depend on the controlled dissolution and condensation of internal components. The molecules and reactions that drive these dynamics in vivo are not well understood. In this study, we present evidence that a group of intrinsically disordered, serine-rich proteins regulate the dynamics of P granules in C. elegans embryos. The MEG (maternal-effect germline defective) proteins are germ plasm components that are required redundantly for fertility. We demonstrate that MEG-1 and MEG-3 are substrates of the kinase MBK-2/DYRK and the phosphatase PP2APPTR−½. Phosphorylation of the MEGs promotes granule disassembly and dephosphorylation promotes granule assembly. Using lattice light sheet microscopy on live embryos, we show that GFP-tagged MEG-3 localizes to a dynamic domain that surrounds and penetrates each granule. We conclude that, despite their liquid-like behavior, P granules are non-homogeneous structures whose assembly in embryos is regulated by phosphorylation.

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