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N6-Methyladenosine modification of mRNA regulates the transition from 2D to 3D growth in the moss Physcomitrium patens [MeRIP-seq]

ABSTRACT: In this study, we identified the main genes of the m6A methyltransferase complex (MTC) in P. patens and we demonstrate that their inactivation by genome editing leads to loss of m6A presence in mRNA and results in defects in the moss life cycle. We detected a delay in the formation of gametophore buds, affecting the transition from 2D to 3D growth and subsequent gametophore formation in all MTC mutant plants. We also observed a defect in spore development, with mutant lines producing reduced-size spores that completely failed to germinate. We performed a genome-wide analysis that revealed several transcripts being affected in the Ppmta background. In addition, we demonstrate that the PpAPB1-4 transcripts, known to be central factors regulating the 2D to 3D transition, are m6A-modified, while in the Ppmta mutant the lack of the m6A mark is associated with a corresponding decrease in their transcript accumulation.

ORGANISM(S): Physcomitrium patens

PROVIDER: GSE213347 | GEO | 2023/04/11

REPOSITORIES: GEO

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N6-Methyladenosine modification of mRNA regulates the transition from 2D to 3D growth in the moss Physcomitrium patens [RNA-seq]

Project description:In this study, we identified the main genes of the m6A methyltransferase complex (MTC) in P. patens and we demonstrate that their inactivation by genome editing leads to loss of m6A presence in mRNA and results in defects in the moss life cycle. We detected a delay in the formation of gametophore buds, affecting the transition from 2D to 3D growth and subsequent gametophore formation in all MTC mutant plants. We also observed a defect in spore development, with mutant lines producing reduced-size spores that completely failed to germinate. We performed a genome-wide analysis that revealed several transcripts being affected in the Ppmta background. In addition, we demonstrate that the PpAPB1-4 transcripts, known to be central factors regulating the 2D to 3D transition, are m6A-modified, while in the Ppmta mutant the lack of the m6A mark is associated with a corresponding decrease in their transcript accumulation.

2023-05-10 | GSE213344 | GEO

Small RNAs from the moss Physcomitrella patens

Project description:High-throughput sequencing of endogenous small RNAs from the moss Physcomitrella patens. This dataset encompasses microRNAs and other small RNAs of ~20-24 nucleotides expressed in the moss P. patens. SAMPLES UPDATED JULY 9, 2007 TO INCLUDE DATA ON SEQUENCED SMALL RNAS THAT DO NOT MATCH THE P. PATENS GENOME Keywords: High throughput small RNA sequencing

2006-08-15 | GSE5103 | GEO

Quantitative proteomic dataset of the moss Physcomitrium patens SMG1 KO mutant line

Project description:Here, we provide an isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomic dataset of the moss Physcomitrium patens smg1 knockout line. The kinase SMG1 is one of the key components of the NMD system in many organisms, including plants. Several lines with a deleted SMG1 in a land Physcomitrium patens subsp. patens (“Gransden 2004”, Frieburg) were produced by James P. B. Lloyd [doi.org/10.1111/tpj.12329]. One of these lines, SMG1 KO mutant line 2, was used for this study. Protonemata of WT and mutant lines were grown in200 ml liquid BCD medium supplemented with 5 mM ammonium tartrate (BCDAT) during a 16-h photoperiod at 250C for 8 days [https://doi.org/10.1101/pdb.prot5136]. All experiments were performed in three biological replicates.

2021-11-02 | PXD029205 | Pride

Bulk segregant analysis of 3D growth defective mutant in Physcomitrella patens (nog2)

Project description:This project aimed to discover genes that regulate the transition from 2D to 3D growth in the moss Physcomitrella patens. Mutants were generated that do not pattern 3D growth. Bulk segregant analysis was conducted to identify the causative genes. This experiment contains two samples - WT-pool, Mt-pool.

2020-12-11 | E-MTAB-7502 | biostudies-arrayexpress

Bulk segregant analysis of 3D growth defective mutant in Physcomitrella patens (Vx501).

Project description:This project aimed to discover genes that regulate the transition from 2D to 3D growth in the moss Physcomitrella patens. Mutants were generated that failed to initiate 3D growth. Bulk segregant analysis was conducted to identify the causative genes. This experiment contains four samples - GdGFP, VxmCherry, WT-pool, Mt-pool.

2018-09-19 | E-MTAB-5096 | biostudies-arrayexpress

Dynamics of the transcriptome response to heat in the moss, Physcomitrella Patens

Project description:The moss Physcomitrella patens was employed to study abiotic stress responses in order to understand the effects of mild (30°C) and strong (37°C) continuous heat stresses from 1h to 24h at a transcriptomic level.

2020-04-17 | GSE138467 | GEO

The DNA damage response transcriptome of the moss Physcomitrella patens

Project description:The moss Physcomitrella patens is remarkable for the ease with which mutant alleles of any gene can be generated by highly efficient homologous recombination-mediated gene targeting. Targeted transgene integration is believed to be mediated through the capture of transforming DNA by the homologous recombination DNA repair pathway. To identify components of this pathway in P. patens we have undertaken a transcriptomic analysis of the response to the sublethal induction of bleomycin-induced DNA double-strand breaks using massively parallel (Illumina) cDNA sequencing. Transcripts significantly increased in bleomycin-treated tissue include a number encoding conserved DNA-DSB components in both the homology-dependent pathway (including Rad51, CTiP, DNA ligase 1, Replication protein A, ATR) and the non-homologous end-joining pathway (including Xrcc4, DNA ligase 4, Ku70, Ku80, PARP). Differentially regulated cell-cycle components include up-regulated Rad9 and Hus1 DNA-damage-related checkpoint proteins and down-regulated D-type cyclins and B-type CDKs, commensurate with the imposition of a checkpoint in the G2 stage of the cell cycle characteristic of homology-dependent DNA-DSB repair. Comparison of the DNA damage transcriptome of P. patens with that of A. thaliana reveals significant up-regulation of a number of P. patens genes encoding ATP-dependent chromatin remodelling helicases of the SNF-2 class. These represent candidates for investigation of their role in mediating efficient gene targeting in P. patens.

2010-11-10 | GSE25237 | GEO

Quantitative proteomic dataset of the moss Physcomitrium patens PpRALF knockout lines

Project description:RAPID ALKALINIZATION FACTOR (RALF) peptides are shown to regulate multiple physiological processes in plants, including modulation of immune response in angiosperms. This family of cysteine-rich peptide hormones has considerably expanded during land plant evolution, but the ancestral roles of RALF peptides in stress response remains poorly understood. Here, we used the moss Physcomitrium patens as a model to gain insight into the function of PpRALF peptides in response to abiotic and biotic stress factors in non-vascular plants. The quantitative proteomic analysis revealed cooperative down-regulation of M6 metalloproteases and membrane proteins, including those involved in stress response, in PpRALF1, 2 and 3 knockout (KO) lines.

2023-01-20 | PXD037111 | Pride

Genome-wide transcriptomic analysis of the sporophyte of the moss Physcomitrella patens

Project description:Bryophytes are the most basal of the extant land plants. A major feature of these plants is the biphasic alteration of generations between a dominant haploid gametophyte and a minor diploid sporophyte phase. To analyse the differences in the transcriptome of the early gametophyte (protonema) and early and mid-sporophyte phases of the moss Physcomitrella patens, microarray gene expression profiles were performed using dissected sporophyte tissue. Through further analysis the early and mid-sporophyte phases were compared.

2013-07-29 | GSE32928 | GEO

The DNA damage response transcriptome of the moss Physcomitrella patens

2010-11-10 | E-GEOD-25237 | biostudies-arrayexpress

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