The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis

Scheer, Hélène; Almeida, Caroline de; Ferrier, Emilie; Simonnot, Quentin; Poirier, Laure; Pflieger, David; Sement, François M.; Koechler, Sandrine; Piermaria, Christina; Krawczyk, Paweł S.; Mroczek, Seweryn; Chicher, Johana; Kuhn, Lauriane; Dziembowski, Andrzej; Hammann, Philippe; Zuber, Hélène; Gagliardi, Dominique

doi:10.1038/s41467-021-21382-2

Cited by 41 publications

(44 citation statements)

References 76 publications

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“…The pPABP2-PABP2-RFP reporter lines in wild-type and hsp101 background were described in Merret et al (2017). The pUBQ-DCP5-GFP like was a kind gift from the laboratory of Scheer, Hélène (Scheer et al, 2021) while the hsp101 mutant and complementation line used for the germination phenotypes of Supporting Information Fig. S5 (see later) were a kind gift from Elizabeth Vierling (McLoughlin et al, 2019).…”

Section: Plant Materialsmentioning

confidence: 99%

The mRNA‐binding proteome of a critical phase transition during Arabidopsis seed germination

Sajeev

Baral

America³

et al. 2021

New Phytologist

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Arabidopsis thaliana seed germination is marked by extensive translational control at two critical phase transitions. The first transition refers to the start of hydration, the hydration translational shift. The second shift, the germination translational shift (GTS) is the phase between testa rupture and radicle protrusion at which the seed makes the all or nothing decision to germinate.The mechanism behind the translational regulation at these phase transitions is unknown. RNA binding proteins (RBPs) are versatile players in the post-transcriptional control of messenger RNAs (mRNAs) and as such candidates for regulating translation during seed germination.Here, we report the mRNA binding protein repertoire of seeds during the GTS. Thirty seed specific RBPs and 22 dynamic RBPs were identified during the GTS, like the putative RBP Vacuolar ATPase subunit A and RBP HSP101. Several stress granule markers were identified in this study, which suggests that seeds are prepared to quickly adapt the translation of specific mRNAs in response to changes in environmental conditions during the GTS.Taken together this study provides a detailed insight into the world of RBPs during seed germination and their possible regulatory role during this developmentally regulated process.

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Section: Plant Materialsmentioning

confidence: 99%

The mRNA‐binding proteome of a critical phase transition during Arabidopsis seed germination

Sajeev

Baral

America³

et al. 2021

New Phytologist

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“…Important roles for this new regulation layer were identified in specific processes like antiviral response [8], transposon control [9], germline development [10,11], or RNA degradation triggered by apoptosis [12]. Still, the significance of pervasive mRNA uridylation in the context of bulk mRNA turnover is unclear, and elimination of uridylation generates no detectable consequences for the physiology of somatic cells and only limited molecular manifestations [7,11,13].…”

Section: Introductionmentioning

confidence: 99%

Pervasive mRNA uridylation in fission yeast catalysed by both Cid1 and Cid16 terminal uridyltransferases

Lipińska-Zubrycka

Grochowski

Bähler

et al. 2022

Preprint

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Messenger RNA uridylation is pervasive and conserved among eukaryotes, but the consequences of this modification for mRNA fate are still under debate. Utilising a simple model organism to study uridylation may facilitate efforts to understand the cellular function of this process. Here we demonstrate that uridylation can be detected using simple bioinformatics approach. We utilise it to unravel widespread transcript uridylation in fission yeast and demonstrate the contribution of both Cid1 and Cid16, the only two annotated terminal uridyltransferases (TUT-ases) in this yeast. To detect uridylation in transcriptome data, we used a RNA-sequencing (RNA-seq) library preparation protocol involving initial linker ligation to fragmented RNA. We next explored the data to detect uridylation marks. Our analysis shows that uridylation in yeast is pervasive, similarly to the ones in multicellular organisms. Importantly, our results confirm the role of the cytoplasmic uridyltransferase Cid1 as the primary uridylation catalyst. However, we also observed an auxiliary role of the second uridyltransferase, Cid16. Thus both fission yeast uridyltransferases are involved in mRNA uridylation. Intriguingly, we found no physiological phenotype of the single and double deletion mutants of cid1 and cid16 and only limited impact of uridylation on steady-state mRNA levels. Our work establishes fission yeast as a potent model to study uridylation in a simple eukaryote, and we demonstrate that it is possible to detect uridylation marks in RNA-seq data without the need for specific methodologies.

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“…We validated the siRNA counting function using publicly available datasets from Scheer et al (2021). This study sequenced sRNAs from wildtype and three mutant strains of Arabidopsis and identified siRNAs within those four datasets.…”

Section: Resultsmentioning

confidence: 99%

“…2012, Wei et al . 2019, Rogers and Phillips 2020, Scheer et al . 2021), or (ii) identifying subsets of siRNAs by immunoprecipitating a specific Argonaute protein and recovering associated sRNAs (e.g., Claycomb et al .…”

Section: Introductionmentioning

confidence: 99%

“…There have been two main approaches to identifying siRNAs: (i) computationally predicting siRNAs from sRNA sequencing data (e.g., Montgomery et al 2012, Wei et al 2019, Rogers and Phillips 2020, Scheer et al 2021, or (ii) identifying subsets of siRNAs by immunoprecipitating a specific Argonaute protein and recovering associated sRNAs (e.g., Claycomb et al 2009, Chaves et al 2021, de Albuquerque et al 2015, Svendsen et al 2019, Xu et al, 2018. Unfortunately, computational approaches used by most published studies to identify siRNAs remain cryptic and difficult to apply broadly.…”

Section: Introductionmentioning

confidence: 99%

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smalldisco, a pipeline for siRNA discovery and 3’ tail identification

Caldas

Kelley

Ahmed-Braimah

et al. 2022

Preprint

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Capturing and sequencing small RNAs is standard practice, however identification of a group of these small RNAssmall interfering RNAs (siRNAs)has historically been an inconsistent and vague practice. We present smalldisco, a command-line tool for small interfering RNA discovery and annotation from small RNA-seq datasets. smalldisco can distinguish short reads that map antisense to exons, termed siRNAs, annotate these siRNAs by genomic feature (e.g., gene or exon) defined by the user, and quantify their abundance. smalldisco also uses the program Tailor to quantify 3 non-templated nucleotides of siRNAs or any small RNA species. smalldisco is available for download from GitHub (https://github.com/ianvcaldas/smalldisco).

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The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis

Cited by 41 publications

References 76 publications

The mRNA‐binding proteome of a critical phase transition during Arabidopsis seed germination

The mRNA‐binding proteome of a critical phase transition during Arabidopsis seed germination

Pervasive mRNA uridylation in fission yeast catalysed by both Cid1 and Cid16 terminal uridyltransferases

smalldisco, a pipeline for siRNA discovery and 3’ tail identification

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