Biology subjects

Pouclet, A.

Publications and source records attributed to Pouclet, A..

2 recordsLinked to original sources

bioRxiv2024

A multi-transcriptomics approach reveals the coordinated action of the endoribonuclease DNE1 and the decapping machinery in orchestrating mRNA decay

Decapping is a crucial step of mRNA degradation in eucaryotes and requires the formation of the holoenzyme complex between the decapping enzyme DCP2 and the decapping enhancer DCP1. In Arabidopsis, we recently identified DNE1, a NYN domain endoribonuclease, as a direct protein partner of DCP1. The function of both DNE1 and decapping are necessary to maintain phyllotaxis, the regularity of organ emergence in the apex. In this study we combined in vivo mRNA editing, RNA degradome, transcriptomics and small RNA-omics to identify targets of DNE1 and study how DNE1 and DCP2 cooperate in controlling mRNA fate. Our data reveal that DNE1 mainly contacts and cleaves mRNAs in the CDS and has sequence cleavage preferences. We found that DNE1 targets are also degraded through decapping, and that both RNA degradation pathways influence the production of mRNA-derived siRNAs. Finally, we detected mRNA features enriched in DNE1 targets including RNA G-quadruplexes and translated upstream-ORFs. Combining these four complementary high-throughput sequencing strategies greatly expands the range of DNE1 targets and allowed us to build a conceptual framework describing the influence of DNE1 and decapping on mRNA fate. These data will be crucial to unveil the specificity of DNE1 action and understand its importance for developmental patterning.

plant biology↗

bioRxiv2021

A NYN domain protein directly interacts with DCP1 and is required for phyllotactic pattern in Arabidopsis.

In eukaryotes, general mRNA decay requires the decapping complex. The activity of this complex depends on its catalytic subunit, DCP2 and its interaction with decapping enhancers, including its main partner DCP1. Here, we report that in Arabidopsis, DCP1 also interacts with a NYN domain endoribonuclease, hence named DCP1-ASSOCIATED NYN ENDORIBONUCLEASE 1 (DNE1). Interestingly, we find DNE1 predominantly associated with DCP1 but not with DCP2 and reciprocally, suggesting the existence of two distinct protein complexes. We also show that the catalytic residues of DNE1 are required to repress the expression of mRNAs in planta upon transient expression. The overexpression of DNE1 in transgenic lines leads to growth defects and transcriptomic changes related to the one observed upon inactivation of the decapping complex. Finally, the combination of dne1 and dcp2 mutations, revealed a functional redundancy between DNE1 and DCP2 in controlling phyllotactic pattern formation in Arabidopsis. Our work identifies DNE1, a hitherto unknown DCP1 protein partner highly conserved in the plant kingdom and identifies its importance for developmental robustness. One-sentence summaryDNE1, a NYN domain protein interacts with the decapping activator DCP1 and, together with DCP2, specify phyllotactic patterns in Arabidopsis.

plant biology↗