Conservation of chromatin states and their association with transcription in land plants
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ABSTRACT:
PROVIDER: PRJNA1289709 | ENA |
REPOSITORIES: ENA
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Project description:The complexity of varied modifications of chromatin composition is reduced to archetypal combinations called chromatin states that broadly define the local potential for transcription. The degree of conservation of chromatin states has not been established amongst plants, and how they interact with transcription factors is unknown. We have identified and characterized chromatin states in the flowering plant Arabidopsis thaliana and the bryophyte Marchantia polymorpha, showing a large degree of functional conservation over more than 450 million years of land plant evolution. We analyzed the interplay between transcription factors and chromatin states to understand their influence on gene regulation. Combining binding sites with activity of transcription factors, we have shown their preferential association with specific chromatin states in both species. These associations define three main groups of transcription factors that bind in the promoter 5’ of the transcription start site, at the +1 nucleosome or inside the gene body downstream of the transcription start site. These groups broadly associate with distinct functions, such as house-keeping genes, putative pioneer factors, development, and response to the environment, suggesting co-evolution of the chromatin regulatory mechanisms with transcription factors.
2025-08-19 | GSE302232 | GEO
Project description:The rapid production of reactive oxygen species (ROS) is a key signaling output in plant immunity. In the angiosperm model species, Arabidopsis thaliana (hereafter Arabidopsis), recognition of non- or altered-self elicitor patterns by cell-surface immune receptors activates the receptor-like cytoplasmic kinases (RLCKs) of the AVRPPHB SUSCEPTIBLE 1 (PBS1)-like (PBL) family, particularly BOTRYTIS-INDUCED KINASE1 (BIK1)1–3. BIK1/PBLs in turn phosphorylate the nicotinamide adenine dinucleotide phosphate (NADPH) oxidase RESPIRATORY BURST OXIDASE HOMOLOG D (RBOHD) to induce apoplastic ROS production4,5. PBL and RBOH functions in plant immunity have been extensively characterized in flowering plants. Much less is known about the conservation of pattern-triggered ROS signaling pathways in non-flowering plants. In this study, we show that, in the liverwort Marchantia polymorpha (hereafter Marchantia), single members of RBOH and PBL families, namely MpRBOH1 and MpPBLa, are required for chitin-induced ROS production. MpPBLa directly interacts with and phosphorylates MpRBOH1 at specific, conserved sites within its cytosolic N-terminus and this phosphorylation is essential for chitin-induced MpRBOH1-mediated ROS production. Collectively, our work reveals the functional conservation of the PBL-RBOH module that controls pattern-triggered ROS production in land plants.
2023-02-06 | PXD038639 | Pride
Project description:Telomerase RNA and telomere evolution in land plants
| PRJNA941781 | ENA
Project description:The development of cells specialized for water conduction or support is a striking innovation of plants that has enabled them to colonize land. The NAC transcription factors regulate differentiation of these cells in vascular plants. However, the path by which plants with these cells have evolved from those of their non-vascular ancestors is unclear. We investigated genes of the moss Physcomitrella patens that encode NAC proteins. Loss-of-function mutants formed abnormal water-conducting and supporting cells, and overexpression induced ectopic differentiation of water-conducting-like cells. Our results show conservation of transcriptional regulation and cellular function between moss and Arabidopsis water-conduction cells. The conserved genetic basis suggests roles for NAC proteins in the adaptation of plants to land. Note: All samples in SRA were assigned the same sample accession (DRS013839). This is incorrect as there are different samples, hence “Source Name” was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
2014-05-23 | E-MTAB-4115 | biostudies-arrayexpress
Project description:The lipid-derived phytohormone jasmonoyl-isoleucine (JA-Ile) regulates plant immunity, growth and development in vascular plants by activating genome-wide transcriptional reprogramming. In Arabidopsis, this is largely orchestrated by the master regulator MYC2 and related transcription factors (TFs). However, the TFs activating this pathway in basal plant lineages are currently unknown. We report the functional conservation of MYC-related TFs between the eudicot Arabidopsis thaliana and the liverwort Marchantia polymorpha, a plant belonging to one of the most basal land-plants lineages. Phylogenetic analysis suggests that MYC function first appeared in charophycean algae, and therefore predates the evolutionary appearance of any other jasmonate pathway component. Marchantia possesses two functionally interchangeable MYC genes, one in females and one in males. Similar to AtMYC2, MpMYCs showed nuclear localization, interaction with JAZ-repressors, and regulation by light. Phenotypic and molecular characterization of loss- or gain-of-function mutants demonstrated that MpMYCs are necessary and sufficient for the activation of the pathway in Marchantia, but unlike their Arabidopsis orthologs, do not regulate fertility. Our results show that despite 450 million years of independent evolution, MYCs are functionally conserved between bryophytes and eudicots. Genetic conservation in one of the most basal lineages suggests that MYC function existed in the common ancestor of land plants and evolved from a pre-existing MYC function in charophycean algae.
2019-03-19 | GSE124159 | GEO
Project description:In plants, miR390 directs the production of tasiRNAs from TRANS-ACTING SIRNA 3 (TAS3) transcripts to regulate AUXIN RESPONSIVE FACTOR (ARF) genes, transcription factors critical for auxin signaling; these tasiRNAs are known as tasiARFs. This pathway is highly conserved, with the TAS3 as the only one noncoding gene present almost ubiquitously in land plants. To understand the evolution of this miR390-TAS3-ARF pathway, we characterized homologs of these three genes from thousands of plant species, from bryophytes to angiosperms. Both miR390 and TAS3 are present and functional in liverworts, confirming their ancestral role to regulate ARFs in land plants. We found the lower-stem region of MIR390 genes, critical for accurate DCL1 (DICER-LIKE 1) processing, is conserved in sequence in seed plants. We propose a model for the transition of functional tasiRNA sequences in TAS3 genes occurred at the emergence of vascular plants, in which the two miR390 target sites of TAS3 genes showed distinct pairing patterns in different plant lineages. Based on the cleavability of miR390 target sites and the distance between target site and tasiARF we inferred a potential bidirectional processing mechanism exists for some TAS3 genes. We also demonstrated a tight mutual selection between tasiARF and its target genes, and characterized unusual aspects and diversity of regulatory components of this pathway. Taken together, these data illuminate the evolutionary path of the miR390-TAS3-ARF pathway in land plants, and demonstrate the significant variation that occurs in the production of phasiRNAs in plants, even in the functionally important and archetypal miR390-TAS3-ARF regulatory circuit.
2017-08-31 | GSE90706 | GEO
Project description:Pathways underlying miRNA biogenesis, degradation, and activity were established early in land plant evolution, but the 24-nt siRNA pathway that guides DNA methylation was incomplete in early land plants, especially lycophytes. We show that the functional diversification of key gene families such as DICER-LIKE and ARGONAUTE (AGO) as observed in angiosperms occurred early in land plants followed by parallel expansion of the AGO family in ferns and angiosperms. We uncovered an unexpected AGO family specific to lycophytes and ferns. Our phylogenetic analyses of miRNAs in lycophytes, bryophytes, ferns, and angiosperms refined the temporal origination of conserved miRNA families in land plants.
2017-07-20 | GSE98408 | GEO
Project description:Six transcriptomes were generated for vegetative and reproductive plants of the lycophyte Selaginella nipponica, aiming at the molecular basis of the transition between the two growth phases, which is important to clarify the conservation of the SPL regulation in growth phase transition within land plants.
2021-01-01 | GSE164112 | GEO
Project description:Proteomics data used in the evaluation of Micromonas pusilla as part of a larger comparison associated with marine diversity and ancestral characteristics of land plants
2016-01-26 | MSV000079483 | MassIVE
Project description:Jasmonoyl-isoleucine regulates defence, growth and developmental responses in eudicots. Bryophyte genomes have conserved sequences for all JA-Ile signalling pathway components, but in contrast to higher plants, the bioactive hormone has not been identified. We show that the JA-Ile receptor COI1 is functionally conserved in the bryophyte Marchantia polymorpha, but responds to a different ligand. Although Marchantia plants neither synthesize nor respond to JA-Ile, loss-of-function Mpcoi1 mutants have phenotypic defects reminiscent of COI1-dependent functions in Arabidopsis. AtCOI1 functionally complements Mpcoi1 mutation and confers JA-Ile responsiveness on M. polymorpha, as does a single amino acid substitution in MpCOI1 that switches ligand specificity. Mass spectrometry quantification of cyclopentenone derivatives, bioactivity analysis and COI1-ligand interaction assays pinpointed two isomers of the JA-Ile precursor dinor-OPDA (dinor-cis-OPDA and dinor-iso-OPDA) as the natural MpCOI1 ligands. Our results identify the ancestral jasmonate, confirm the functional conservation of its signalling pathway, and show that JA-Ile and COI1 emergence in higher plants from their ancestral counterparts required co-evolution of hormone biosynthetic complexity and receptor specificity.
2018-04-10 | GSE99727 | GEO