Small RNA-mediated gene silencing pathways in C. elegans

ABSTRACTThe germline genome is guarded against invading foreign genetic elements by small RNA-dependent gene-silencing pathways. Components of these pathways localize to, or form distinct aggregates in the vicinity of, germ granules. These components and their dynamics in and out of granules are currently being intensively studied. Here, we report the identification of PLP-1, a Caenorhabditiselegans protein related to the human single-stranded nucleic acid-binding protein Pur-alpha, as a component of germ granules in C. elegans. We show that PLP-1 is essential for silencing different types of transgenes in the germ line and for suppressing the expression of several endogenous genes controlled by the germline gene-silencing pathways. Our results reveal that PLP-1 functions downstream of small RNA biogenesis during initiation of gene silencing. Based on these results and the earlier findings that Pur-alpha proteins interact with both RNA and protein, we propose that PLP-1 couples certain RNAs with their protein partners in the silencing complex. PLP-1 orthologs localized on RNA granules may similarly contribute to germline gene silencing in other organisms.

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GTSF-1 is required for the formation of a functional RNA-dependent RNA Polymerase complex in C. elegans

10.1101/271270 ◽

2018 ◽

Cited By ~ 1

Author(s):

Miguel Vasconcelos Almeida ◽

Sabrina Dietz ◽

Stefan Redl ◽

Emil Karaulanov ◽

Andrea Hildebrandt ◽

...

Keyword(s):

Rna Polymerase ◽

Gene Silencing ◽

Small Rna ◽

Small Rnas ◽

Zinc Fingers ◽

Specific Factor ◽

Rna Dependent Rna Polymerase ◽

C Elegans ◽

Argonaute Proteins ◽

Rna Pathways

AbstractIn every domain of life, Argonaute proteins and their associated small RNAs regulate gene expression. Despite great conservation of Argonaute proteins throughout evolution, many proteins acting in small RNA pathways are not widely conserved. Gametocyte-specific factor 1 (Gtsf1) proteins, characterized by two tandem CHHC zinc fingers and an unstructured, acidic C-terminal tail, are conserved in animals and act in small RNA pathways. In fly and mouse, they are required for fertility and have been shown to interact with Piwi clade Argonautes. We identified T06A10.3 as the Caenorhabditis elegans Gtsf1 homolog and named it gtsf-1. Given its conserved nature and roles in Piwi-mediated gene silencing, we sought out to characterize GTSF-1 in the context of the small RNA pathways of C. elegans. Like its homologs, GTSF-1 is required for normal fertility. Surprisingly, we report that GTSF-1 is not required for Piwi-mediated gene silencing. Instead, gtsf-1 mutants show strong depletion of a class of endogenous small RNAs, known as 26G-RNAs, and fully phenocopy mutants lacking RRF-3, the RNA-dependent RNA Polymerase that synthesizes 26G-RNAs. We show, both in vivo and in vitro, that GTSF-1 specifically and robustly interacts with RRF-3 via its tandem CHHC zinc fingers. Furthermore, we demonstrate that GTSF-1 is required for the assembly of a larger RRF-3 and DCR-1-containing complex, also known as ERIC, thereby allowing for 26G-RNA generation. We propose that GTSF-1 homologs may similarly act to drive the assembly of larger complexes that subsequently act in small RNA production and/or in imposing small RNA-mediated silencing activities.

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Gene silencing pathways found in the green alga Volvox carteri reveal insights into evolution and origins of small RNA systems in plants

BMC Genomics ◽

10.1186/s12864-016-3202-4 ◽

2016 ◽

Vol 17 (1) ◽

Cited By ~ 8

Author(s):

Anne Dueck ◽

Maurits Evers ◽

Stefan R. Henz ◽

Katharina Unger ◽

Norbert Eichner ◽

...

Keyword(s):

Gene Silencing ◽

Green Alga ◽

Small Rna ◽

Volvox Carteri ◽

Silencing Pathways

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Distinctive profiles of small RNA couple inverted repeat-induced post-transcriptional gene silencing with endogenous RNA silencing pathways inArabidopsis

RNA ◽

10.1261/rna.046532.114 ◽

2014 ◽

Vol 20 (12) ◽

pp. 1987-1999 ◽

Cited By ~ 11

Author(s):

Tadeusz Wroblewski ◽

Marta Matvienko ◽

Urszula Piskurewicz ◽

Huaqin Xu ◽

Belinda Martineau ◽

...

Keyword(s):

Gene Silencing ◽

Small Rna ◽

Inverted Repeat ◽

Rna Silencing ◽

Transcriptional Gene Silencing ◽

Post Transcriptional Gene Silencing ◽

Silencing Pathways

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The evolutionary study of small RNA-directed gene silencing pathways by investigating RNase III enzymes

Gene ◽

10.1016/j.gene.2008.12.022 ◽

2009 ◽

Vol 435 (1-2) ◽

pp. 1-8 ◽

Cited By ~ 3

Author(s):

Lihua Jin ◽

Kirill Kryukov ◽

Yoshiyuki Suzuki ◽

Tadashi Imanishi ◽

Kazuho Ikeo ◽

...

Keyword(s):

Gene Silencing ◽

Small Rna ◽

Rnase Iii ◽

Evolutionary Study ◽

Silencing Pathways

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Faculty Opinions recommendation of E-cadherin is transcriptionally activated via suppression of ZEB1 transcriptional repressor by small RNA-mediated gene silencing.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.13436964.14811067 ◽

2012 ◽

Author(s):

Marjori Matzke

Keyword(s):

Gene Silencing ◽

Small Rna ◽

Transcriptional Repressor ◽

E Cadherin

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Faculty Opinions recommendation of A Tunable Mechanism Determines the Duration of the Transgenerational Small RNA Inheritance in C. elegans.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.726236698.793546887 ◽

2018 ◽

Author(s):

Mariusz Nowacki

Keyword(s):

Small Rna ◽

C Elegans

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Faculty Opinions recommendation of A Tunable Mechanism Determines the Duration of the Transgenerational Small RNA Inheritance in C. elegans.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.726236698.793524091 ◽

2016 ◽

Author(s):

Peter Boag

Keyword(s):

Small Rna ◽

C Elegans

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Simultaneous silencing of two different Arabidopsis genes with a novel virus-induced gene silencing vector

Plant Methods ◽

10.1186/s13007-020-00701-6 ◽

2021 ◽

Vol 17 (1) ◽

Author(s):

Kunxin Wu ◽

Yadan Wu ◽

Chunwei Zhang ◽

Yan Fu ◽

Zhixin Liu ◽

...

Keyword(s):

Gene Silencing ◽

Double Mutant ◽

Target Genes ◽

Rna Binding ◽

Protein Product ◽

Antiviral Defense ◽

Virus Induced Gene Silencing ◽

Argonaute 2 ◽

Plant Genes ◽

Silencing Pathways

Abstract Background Virus-induced gene silencing (VIGS) is a useful tool for functional characterizations of plant genes. However, the penetrance of VIGS varies depending on the genes to be silenced, and has to be evaluated by examining the transcript levels of target genes. Results In this report, we report the development of a novel VIGS vector that permits a preliminary assessment of the silencing penetrance. This new vector is based on an attenuated variant of Turnip crinkle virus (TCV) known as CPB that can be readily used in Arabidopsis thaliana to interrogate genes of this model plant. A CPB derivative, designated CPB1B, was produced by inserting a 46 nucleotide section of the Arabidopsis PHYTOENE DESATURASE (PDS) gene into CPB, in antisense orientation. CPB1B induced robust PDS silencing, causing easily visible photobleaching in systemically infected Arabidopsis leaves. More importantly, CPB1B can accommodate additional inserts, derived from other Arabidopsis genes, causing the silencing of two or more genes simultaneously. With photobleaching as a visual marker, we adopted the CPB1B vector to validate the involvement of DICER-LIKE 4 (DCL4) in antiviral defense against TCV. We further revealed the involvement of ARGONAUTE 2 (AGO2) in PDS silencing and antiviral defense against TCV in dcl2drb4 double mutant plants. These results demonstrated that DOUBLE-STRANDED RNA-BINDING PROTEIN 4 (DRB4), whose protein product (DRB4) commonly partners with DCL4 in the antiviral silencing pathway, was dispensable for PDS silencing induced by CPB1B derivative in dcl2drb4 double mutant plants. Conclusions The CPB1B-based vector developed in this work is a valuable tool with visualizable indicator of the silencing penetrance for interrogating Arabidopsis genes, especially those involved in the RNA silencing pathways.

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The IDR-containing protein PID-2 affects Z granules and is required for piRNA-induced silencing in the embryo

10.1101/2020.04.14.040584 ◽

2020 ◽

Author(s):

Maria Placentino ◽

António Miguel de Jesus Domingues ◽

Jan Schreier ◽

Sabrina Dietz ◽

Svenja Hellmann ◽

...

Keyword(s):

Gene Regulation ◽

Caenorhabditis Elegans ◽

Rna Polymerase ◽

Small Rna ◽

Rna Silencing ◽

Rna Dependent Rna Polymerase ◽

Prolyl Aminopeptidase ◽

C Elegans

AbstractIn Caenorhabditis elegans, the piRNA (21U RNA) pathway is required to establish proper gene regulation and an immortal germline. To achieve this, PRG-1-bound 21U RNAs trigger silencing mechanisms mediated by RNA-dependent RNA polymerase (RdRP)-synthetized 22G RNAs. This silencing can become PRG-1-independent, and heritable over many generations. This state is named RNAe. It is unknown how and when RNAe is established, and how it is maintained. We show that maternally provided 21U RNAs can be sufficient to trigger RNAe in embryos. Additionally, we identify the IDR-containing protein PID-2, as a factor required to establish and maintain RNAe. PID-2 interacts with two novel, partially redundant, eTudor domain proteins, PID-4 and PID-5. Additionally, PID-5 has a domain related to the X-prolyl aminopeptidase protein APP-1, and binds APP-1, implicating N-terminal proteolysis in RNAe. All three proteins are required for germline immortality, localize to perinuclear foci, affect Z granules, and are required for balancing of 22G RNA populations. Overall, our study identifies three new proteins with crucial functions in the C. elegans small RNA silencing network.

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