The 5′ Spreading of Small RNAs in Dictyostelium discoideum Depends on the RNA-Dependent RNA Polymerase RrpC and on the Dicer-Related Nuclease DrnB

Abstract The Dictyostelium Intermediate Repeat Sequence 1 (DIRS-1) is the name-giving member of the DIRS order of tyrosine recombinase retrotransposons. In Dictyostelium discoideum, DIRS-1 is highly amplified and enriched in heterochromatic centromers of the D. discoideum genome. We show here that DIRS-1 it tightly controlled by the D. discoideum RNA interference machinery and is only mobilized in mutants lacking either the RNA dependent RNA polymerase RrpC or the Argonaute protein AgnA. DIRS retrotransposons contain an internal complementary region (ICR) that is thought to be required to reconstitute a full-length element from incomplete RNA transcripts. Using different versions of D. discoideum DIRS-1 equipped with retrotransposition marker genes, we show experimentally that the ICR is in fact essential to complete retrotransposition. We further show that DIRS-1 produces a mixture of single-stranded, mostly linear extrachromosomal cDNA intermediates. If this cDNA is isolated and transformed into D. discoideum cells, it can be used by DIRS-1 proteins to complete productive retrotransposition. This work provides the first experimental evidence to propose a general retrotransposition mechanism of the class of DIRS like tyrosine recombinase retrotransposons.

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Intronic regions of plant genes potentially encode RDR (RNA-dependent RNA polymerase)-dependent small RNAs

Journal of Experimental Botany ◽

10.1093/jxb/eru542 ◽

2015 ◽

Vol 66 (7) ◽

pp. 1763-1768 ◽

Cited By ~ 2

Author(s):

Jingping Qin ◽

Xiaoxia Ma ◽

Zili Yi ◽

Yijun Meng ◽

Zhonghai Tang

Keyword(s):

Rna Polymerase ◽

Small Rnas ◽

Rna Dependent Rna Polymerase ◽

Double Stranded Rna ◽

Plant Genes ◽

Dependent Pathway

The opinion is put forward here that certain intronic regions of plant genes could be converted to double-stranded RNA precursors for sRNA production through an RDR-dependent pathway.

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Translation and codon usage regulate Argonaute slicer activity to trigger small RNA biogenesis

10.1101/2020.09.04.282863 ◽

2020 ◽

Author(s):

Meetali Singh ◽

Eric Cornes ◽

Blaise Li ◽

Piergiuseppe Quarato ◽

Loan Bourdon ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Embryonic Development ◽

Rna Polymerase ◽

Codon Usage ◽

Small Rna ◽

Small Rnas ◽

Rna Dependent Rna Polymerase ◽

Coding Sequences ◽

Germ Granules ◽

Rna Biogenesis

In the Caenorhabditis elegans germline, thousands of mRNAs are concomitantly expressed with antisense 22G-RNAs, which are loaded into the Argonaute CSR-1. Despite their essential functions for animal fertility and embryonic development, how CSR-1 22G-RNAs are produced remains unknown. Here, we show that CSR-1 slicer activity is primarily involved in triggering the synthesis of small RNAs on the coding sequences of germline mRNAs and post-transcriptionally regulates a fraction of targets. CSR-1-cleaved mRNAs prime the RNA-dependent RNA polymerase, EGO-1, to synthesize 22G-RNAs in phase with ribosome translation in the cytoplasm, in contrast to other 22G-RNAs mostly synthesized in germ granules. Moreover, codon optimality and efficient translation antagonize CSR-1 slicing and 22G-RNAs biogenesis. We propose that codon usage differences encoded into mRNA sequences might be a conserved strategy in eukaryotes to regulate small RNA biogenesis and Argonaute targeting.

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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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The Dictyostelium discoideum RNA-dependent RNA polymerase RrpC silences the centromeric retrotransposon DIRS-1 post-transcriptionally and is required for the spreading of RNA silencing signals

Nucleic Acids Research ◽

10.1093/nar/gkt1337 ◽

2013 ◽

Vol 42 (5) ◽

pp. 3330-3345 ◽

Cited By ~ 9

Author(s):

Stephan Wiegand ◽

Doreen Meier ◽

Carsten Seehafer ◽

Marek Malicki ◽

Patrick Hofmann ◽

...

Keyword(s):

Rna Polymerase ◽

Dictyostelium Discoideum ◽

Rna Silencing ◽

Repeat Sequence ◽

Transcriptional Level ◽

Asymmetric Distribution ◽

Messenger Rnas ◽

Long Terminal Repeats ◽

Rna Dependent Rna Polymerase ◽

Antisense Orientation

Abstract Dictyostelium intermediate repeat sequence 1 (DIRS-1) is the founding member of a poorly characterized class of retrotransposable elements that contain inverse long terminal repeats and tyrosine recombinase instead of DDE-type integrase enzymes. In Dictyostelium discoideum, DIRS-1 forms clusters that adopt the function of centromeres, rendering tight retrotransposition control critical to maintaining chromosome integrity. We report that in deletion strains of the RNA-dependent RNA polymerase RrpC, full-length and shorter DIRS-1 messenger RNAs are strongly enriched. Shorter versions of a hitherto unknown long non-coding RNA in DIRS-1 antisense orientation are also enriched in rrpC– strains. Concurrent with the accumulation of long transcripts, the vast majority of small (21 mer) DIRS-1 RNAs vanish in rrpC– strains. RNASeq reveals an asymmetric distribution of the DIRS-1 small RNAs, both along DIRS-1 and with respect to sense and antisense orientation. We show that RrpC is required for post-transcriptional DIRS-1 silencing and also for spreading of RNA silencing signals. Finally, DIRS-1 mis-regulation in the absence of RrpC leads to retrotransposon mobilization. In summary, our data reveal RrpC as a key player in the silencing of centromeric retrotransposon DIRS-1. RrpC acts at the post-transcriptional level and is involved in spreading of RNA silencing signals, both in the 5′ and 3′ directions.

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Translation and codon usage regulate Argonaute slicer activity to trigger small RNA biogenesis

10.21203/rs.3.rs-87655/v1 ◽

2020 ◽

Author(s):

Germano Cecere ◽

Meetali Singh ◽

Eric Cornes ◽

Blaise Li ◽

Piergiuseppe Quarato ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Embryonic Development ◽

Rna Polymerase ◽

Codon Usage ◽

Small Rna ◽

Small Rnas ◽

Rna Dependent Rna Polymerase ◽

Coding Sequences ◽

Germ Granules ◽

Rna Biogenesis

Abstract In the Caenorhabditis elegans germline, thousands of mRNAs are concomitantly expressed with antisense 22G-RNAs, which are loaded into the Argonaute CSR-1. Despite their essential functions for animal fertility and embryonic development, how CSR-1 22G-RNAs are produced remains unknown. Here, we show that CSR-1 slicer activity is primarily involved in triggering the synthesis of small RNAs on the coding sequences of germline mRNAs and post-transcriptionally regulates a fraction of targets. CSR-1-cleaved mRNAs prime the RNA-dependent RNA polymerase, EGO-1, to synthesize 22G-RNAs in phase with ribosome translation in the cytoplasm, in contrast to other 22G-RNAs mostly synthesized in germ granules. Moreover, codon optimality and efficient translation antagonize CSR-1 slicing and 22G-RNAs biogenesis. We propose that codon usage differences encoded into mRNA sequences might be a conserved strategy in eukaryotes to regulate small RNA biogenesis and Argonaute targeting.

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Loss of RNA–Dependent RNA Polymerase 2 (RDR2) Function Causes Widespread and Unexpected Changes in the Expression of Transposons, Genes, and 24-nt Small RNAs

PLoS Genetics ◽

10.1371/journal.pgen.1000737 ◽

2009 ◽

Vol 5 (11) ◽

pp. e1000737 ◽

Cited By ~ 70

Author(s):

Yi Jia ◽

Damon R. Lisch ◽

Kazuhiro Ohtsu ◽

Michael J. Scanlon ◽

Dan Nettleton ◽

...

Keyword(s):

Rna Polymerase ◽

Small Rnas ◽

Rna Dependent Rna Polymerase

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MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant

Genome Research ◽

10.1101/gr.5530106 ◽

2006 ◽

Vol 16 (10) ◽

pp. 1276-1288 ◽

Cited By ~ 212

Author(s):

C. Lu ◽

K. Kulkarni ◽

F. F. Souret ◽

R. MuthuValliappan ◽

S. S. Tej ◽

...

Keyword(s):

Rna Polymerase ◽

Small Rnas ◽

Rna Dependent Rna Polymerase

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Global Analysis of RNA-Dependent RNA Polymerase-Dependent Small RNAs Reveals New Substrates and Functions for These Proteins and SGS3 in Arabidopsis

Non-Coding RNA ◽

10.3390/ncrna7020028 ◽

2021 ◽

Vol 7 (2) ◽

pp. 28

Author(s):

Xia Hua ◽

Nathan D. Berkowitz ◽

Matthew R. Willmann ◽

Xiang Yu ◽

Eric Lyons ◽

...

Keyword(s):

Rna Polymerase ◽

Stress Responses ◽

Small Rnas ◽

Rna Silencing ◽

Rna Binding ◽

Global Analysis ◽

Genomic Analysis ◽

Rna Dependent Rna Polymerase ◽

Eukaryotic Gene ◽

Full Complement

RNA silencing pathways control eukaryotic gene expression transcriptionally or posttranscriptionally in a sequence-specific manner. In RNA silencing, the production of double-stranded RNA (dsRNA) gives rise to various classes of 20–24 nucleotide (nt) small RNAs (smRNAs). In Arabidopsis thaliana, smRNAs are often derived from long dsRNA molecules synthesized by one of the six genomically encoded RNA-dependent RNA Polymerase (RDR) proteins. However, the full complement of the RDR-dependent smRNAs and functions that these proteins and their RNA-binding cofactors play in plant RNA silencing has not been fully uncovered. To address this gap, we performed a global genomic analysis of all six RDRs and two of their cofactors to find new substrates for RDRs and targets of the resulting RDR-derived siRNAs to uncover new functions for these proteins in plants. Based on these analyses, we identified substrates for the three RDRγ clade proteins (RDR3–5), which had not been well-characterized previously. We also identified new substrates for the other three RDRs (RDR1, RDR2, and RDR6) as well as the RDR2 cofactor RNA-directed DNA methylation 12 (RDM12) and the RDR6 cofactor suppressor of gene silencing 3 (SGS3). These findings revealed that the target substrates of SGS3 are not limited to those solely utilized by RDR6, but that this protein seems to be a more general cofactor for the RDR family of proteins. Additionally, we found that RDR6 and SGS3 are involved in the production of smRNAs that target transcripts related to abiotic stresses, including water deprivation, salt stress, and ABA response, and as expected the levels of these mRNAs are increased in rdr6 and sgs3 mutant plants. Correspondingly, plants that lack these proteins (rdr6 and sgs3 mutants) are hypersensitive to ABA treatment, tolerant to high levels of PEG8000, and have a higher survival rate under salt treatment in comparison to wild-type plants. In total, our analyses have provided an extremely data-rich resource for uncovering new functions of RDR-dependent RNA silencing in plants, while also revealing a previously unexplored link between the RDR6/SGS3-dependent pathway and plant abiotic stress responses.

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Translation and codon usage regulate Argonaute slicer activity to trigger small RNA biogenesis

Nature Communications ◽

10.1038/s41467-021-23615-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Meetali Singh ◽

Eric Cornes ◽

Blaise Li ◽

Piergiuseppe Quarato ◽

Loan Bourdon ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Embryonic Development ◽

Rna Polymerase ◽

Codon Usage ◽

Small Rna ◽

Small Rnas ◽

Rna Dependent Rna Polymerase ◽

Coding Sequences ◽

Germ Granules ◽

Rna Biogenesis

AbstractIn the Caenorhabditis elegans germline, thousands of mRNAs are concomitantly expressed with antisense 22G-RNAs, which are loaded into the Argonaute CSR-1. Despite their essential functions for animal fertility and embryonic development, how CSR-1 22G-RNAs are produced remains unknown. Here, we show that CSR-1 slicer activity is primarily involved in triggering the synthesis of small RNAs on the coding sequences of germline mRNAs and post-transcriptionally regulates a fraction of targets. CSR-1-cleaved mRNAs prime the RNA-dependent RNA polymerase, EGO-1, to synthesize 22G-RNAs in phase with translating ribosomes, in contrast to other 22G-RNAs mostly synthesized in germ granules. Moreover, codon optimality and efficient translation antagonize CSR-1 slicing and 22G-RNAs biogenesis. We propose that codon usage differences encoded into mRNA sequences might be a conserved strategy in eukaryotes to regulate small RNA biogenesis and Argonaute targeting.

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