The Conserved Intron Binding Protein EMB-4 Plays Differential Roles in Germline Small RNA Pathways of C. elegans

Tyc, Katarzyna M.; Nabih, Amena; Wu, Monica Z.; Wedeles, Christopher J.; Sobotka, Julia A.; Claycomb, Julie M.

doi:10.1016/j.devcel.2017.07.003

Cited by 28 publications

(22 citation statements)

References 56 publications

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“…The human ortholog Aquarius is an RNA helicase with ATPase activity, and it binds to introns to assist intron splicing in vitro (Hirose et al, 2006;De et al, 2015). The C. elegans ortholog EMB-4 was reported to act in the nuclear RNAi pathway, where it interacts with nuclear AGOs and functions in germline-specific chromatin remodeling (Checchi and Kelly, 2006;Akay et al, 2017;Tyc et al, 2017). In Arabidopsis, MAC7 is involved in plant defense and was predicted to be an essential gene (Tzafrir et al, 2004;Monaghan et al, 2009).…”

Section: Discussionmentioning

confidence: 99%

“…Recent publications show that EMB-4, the Caenorhabditis elegans homolog of MAC7, physically interacts with germline AGOs. It participates in the nuclear RNAi pathway and maintains the homeostasis of germline transcriptome in worms (Akay et al, 2017;Tyc et al, 2017). MAC7 was predicted to be an essential gene for embryo development (EMB gene) in Arabidopsis based on sequence similarity with EMB genes found in other eukaryotes (Tzafrir et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

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The Arabidopsis MOS4-Associated Complex Promotes MicroRNA Biogenesis and Precursor Messenger RNA Splicing

et al. 2017

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In , the MOS4-ASSOCIATED COMPLEX (MAC) is required for defense and development. The evolutionarily conserved, putative RNA helicase MAC7 is a component of the Arabidopsis MAC, and the human MAC7 homolog, Aquarius, is implicated in pre-mRNA splicing. Here, we show that, a partial loss-of-function mutant in , and two other MAC subunit mutants, and (), exhibit reduced microRNA (miRNA) levels, indicating that MAC promotes miRNA biogenesis. The mutant shows reduced primary miRNA (pri-miRNA) levels without affecting miRNA gene () promoter activity or the half-life of pri-miRNA transcripts. As a nuclear protein, MAC7 is not concentrated in dicing bodies, but it affects the localization of HYPONASTIC LEAVES1 (HYL1), a key protein in pri-miRNA processing, to dicing bodies. Immunoprecipitation of HYL1 retrieved 11 known MAC subunits, including MAC7, indicating association between HYL1 and MAC. We propose that MAC7 links transcription to pri-miRNA processing. RNA-seq analysis showed that downregulated genes in MAC subunit mutants are mostly involved in plant defense and stimulus responses, confirming a role of MAC in biotic and abiotic stress responses. We also discovered global intron retention defects in mutants in three subunits of MAC, thus linking MAC function to splicing in Arabidopsis.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The Arabidopsis MOS4-Associated Complex Promotes MicroRNA Biogenesis and Precursor Messenger RNA Splicing

et al. 2017

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“…We speculate that nuclear RNA accumulation of the endogenous HRDE-1 targets may reflect aberrant structures or deficiencies in RNA-processing of these transcripts. Such connections have been found in S. pombe [41,42] and recently in C. elegans [43,44]. Investigating the cause of the nuclear enrichment will provide insights into the triggering mechanism of nuclear RNAi in C. elegans.…”

Section: Is Nuclear Accumulation a Sign Of "Foreign"?mentioning

confidence: 68%

The spatial and temporal dynamics of the nuclear RNAi-targeted RNA transcripts inCaenorhabditis elegans

Kalinava

Mendoza

et al. 2018

Preprint

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Small RNA-guided chromatin silencing, also referred to as nuclear RNAi, plays an essential role in genome surveillance in eukaryotes and provides a unique paradigm to explore the complexity in RNA-mediated chromatin regulation and transgenerational epigenetics. A well-recognized paradox in this research area is that transcription of the target loci is necessary for the initiation and maintenance of the silencing at the same loci. How the two opposing activities (transcriptional activation and repression) are coordinated during animal development is poorly understood. To resolve this gap, we took single-molecule RNA imaging, deep-sequencing, and genetic approaches towards delineating the developmental regulation and subcellular localization of RNA transcripts of two exemplary endogenous germline nuclear RNAi targets in C. elegans, Cer3 and Cer8 LTR retrotransposons.By examining the wild type and a collection of mutant strains, we found that transcription and silencing cycle of Cer3 and Cer8 is tightly coupled with the early embryogenesis and germline mitotic and meiotic cell cycles. Strikingly, Cer3 and Cer8 transcripts are exclusively localized in the nuclei of germ cells in both wild type and germline nuclear RNAi-defective mutant animals. RNA-sequencing analysis found that this nuclear enrichment feature is a general feature for the endogenous targets of the germline nuclear RNAi pathway. In addition, the germline and somatic repressions of Cer3 have different genetic requirement for the three H3K9 histone methyltransferases, MET-2, SET-25, and SET-32, in conjunction with the nuclear Argonaute protein WAGO-9/HRDE-1. These results provide a first comprehensive cellular and developmental characterization of the nuclear RNAi-targeted endogenous targets throughout animal reproductive cycle. Altogether, these results support a model in which (1) both the transcriptional activation and repression steps of the germline nuclear RNAi pathway are tightly coupled with animal development, (2) the endogenous targets exhibit a hallmark of nuclear enrichment of their transcripts, and (3) different heterochromatin enzymes play distinct roles in somatic and germline silencing of the endogenous targets.

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“…On the contrary, a significant depletion was found for genes known to be targeted by CSR-1-carried small RNAs, a pathway that was suggested to support the expression of targeted genes (Claycomb et al, 2009;Shen et al, 2018). The helicase EMB-4 (Akay et al, 2017;Tyc et al, 2017) was shown to preferably bind introns of genes targeted by CSR-1; We could not detect a significant enrichment or depletion for genes whose introns are bound by EMB-4. All together, these results suggest that SET-25 is required for the maintenance of a specific sub-class of HRDE-1 and WAGO-1 small RNAs, associated with the Mutator and piRNA pathways, which target protein-coding ( Figure S2).…”

Section: Set-25 Is Required For the Maintenance Of A Specific Class Omentioning

confidence: 99%

H3K9me3 is Required for Inheritance of Small RNAs that Target a Unique Subset of Newly Evolved Genes

Lev

Gingold

Rechavi

2018

Preprint

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In Caenorhabditis elegans, RNA interference (RNAi) responses can transmit across generations via heritable small RNAs. Heritable RNAi memory is associated with Histone-3-Lysine-9 tri-methylation (H3K9me3) of the targeted genes. In other organisms, maintenance of silencing responses requires a feedforward loop between H3K9me3 and small RNAs. In C. elegans, however, we find that the effect of H3K9 methyltransferase mutants on heritable RNAi is more complex. In this paper, we show that not only that H3K9me3 is unnecessary for inheritance, the effect of this modification depends on the identity of the RNAi-targeted gene. We found an asymmetry in the requirement for H3K9me3 and the two main worm H3K9me3 methyltransferases, SET-25 and SET-32. Both methyltransferases promote heritable silencing of the foreign gene gfp, but are dispensable for silencing of the endogenous gene oma-1.Genome-wide examination of heritable endogenous small interfering RNAs (endo-siRNAs) revealed that the heritable endo-siRNAs which are lost in set-25 mutants target newly acquired and highly H3K9me3 marked C. elegans genes. Thus, "repressive" chromatin marks could be important specifically for heritable RNAi silencing of genes which are flagged as "foreign", such as gfp.

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The Conserved Intron Binding Protein EMB-4 Plays Differential Roles in Germline Small RNA Pathways of C. elegans

Cited by 28 publications

References 56 publications

The Arabidopsis MOS4-Associated Complex Promotes MicroRNA Biogenesis and Precursor Messenger RNA Splicing

The Arabidopsis MOS4-Associated Complex Promotes MicroRNA Biogenesis and Precursor Messenger RNA Splicing

The spatial and temporal dynamics of the nuclear RNAi-targeted RNA transcripts inCaenorhabditis elegans

H3K9me3 is Required for Inheritance of Small RNAs that Target a Unique Subset of Newly Evolved Genes

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