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Integrated analysis of transcriptome and small RNAome reveals the regulatory network for rapid growth in Mikania micrantha [RNA-seq]

ABSTRACT: M. micrantha has caused huge ecological damage and economic losses worldwide due to its rapid growth and serious invasion. However, the underlying molecular mechanisms of its rapid growth and environmental adaption remain unclear. Here, we performed transcriptome and small RNA sequencing with five tissues of M. micrantha to dissect miRNA-mediated regulation in M. micrantha. WGCNA and GO enrichment analysis of transcriptome identified the gene association patterns and potential key regulatory genes for plant growth in each tissue. The genes highly correlated with leaf and stem tissues were mainly involved in the chlorophyll synthesis, response to auxin, the CAM pathway and other photosynthesis-related processes, which promoted the fast growth of M. micrantha. Importantly, we identified 350 conserved and 192 novel miRNAs, many of which displayed differential expression patterns among tissues. PsRNA target prediction analysis uncovered target genes of both conserved and novel miRNAs, including GRFs and TCPs, which were essential for plant growth and development. Further analysis revealed that miRNAs contributed to the regulation of tissue-specific gene expression in M. micrantha, such as mmi-miR396 and mmi-miR319. Taken together, our study uncovered the miRNA-mRNA regulatory networks and the potential vital roles of miRNAs in modulating the rapid growth of M. micrantha.

ORGANISM(S): Mikania micrantha

PROVIDER: GSE210298 | GEO | 2023/08/01

REPOSITORIES: GEO

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Integrated analysis of transcriptome and small RNAome reveals the regulatory network for rapid growth in Mikania micrantha [sRNA-seq]

Project description:M. micrantha has caused huge ecological damage and economic losses worldwide due to its rapid growth and serious invasion. However, the underlying molecular mechanisms of its rapid growth and environmental adaption remain unclear. Here, we performed transcriptome and small RNA sequencing with five tissues of M. micrantha to dissect miRNA-mediated regulation in M. micrantha. WGCNA and GO enrichment analysis of transcriptome identified the gene association patterns and potential key regulatory genes for plant growth in each tissue. The genes highly correlated with leaf and stem tissues were mainly involved in the chlorophyll synthesis, response to auxin, the CAM pathway and other photosynthesis-related processes, which promoted the fast growth of M. micrantha. Importantly, we identified 350 conserved and 192 novel miRNAs, many of which displayed differential expression patterns among tissues. PsRNA target prediction analysis uncovered target genes of both conserved and novel miRNAs, including GRFs and TCPs, which were essential for plant growth and development. Further analysis revealed that miRNAs contributed to the regulation of tissue-specific gene expression in M. micrantha, such as mmi-miR396 and mmi-miR319. Taken together, our study uncovered the miRNA-mRNA regulatory networks and the potential vital roles of miRNAs in modulating the rapid growth of M. micrantha.

2023-08-01 | GSE210299 | GEO

Expression data from rGRF3, 35S:GIF1 and rGRF3x35S:GIF1 plants

Project description:The Growth Regulating Factors (GRFs) are plant specific transcription factors. They form complexes with GRF Interacting Factors (GIFs), a small family of transcriptional co-activators. In Arabidopsis thaliana, seven out of the nine GRFs are regulated by microRNA miR396. A detailed analysis of GRF3 revealed that a modified transgene, insensitive to the regulation of miR396, causes a strong increase in the number of cells in leaves, while an additional increase of GIF1 expression further enhances the number of cells synergistically. Genome-wide transcript profiling revealed that simultaneous increase of GRF3 and GIF1 levels causes additional effects in gene expression compared to either of the transgenes alone. We observed that GIF1 interacts in vivo with GRF3, as well as chromatin remodeling complexes, providing a mechanistic explanation for the additional activities of a GRF3-GIF1 complex. Interestingly, we found that the GRF system also regulates leaf longevity. Genetic and molecular analysis revealed that the functions of GRFs in leaf size and senescence can be uncoupled, demonstrating that the GRFs control different stages of leaf development. The results provide new insights into the functions of a complex regulatory network composed of microRNAs, transcription factors, and co-transcription factors. We used microarrays to obtain the transcription profile of plants overexpressing GRF3, GIF1 or both genes toghether. We compared the transcriptome of 35S:GIF1, rGRF3 and rGRF3x35S:GIF1 plants vs wild-type plants (Col-0 accession), using ATH1 Affymetrics microarrays. For these experiments we collected vegetative apices together with the leaf primordia from plants of 20 days growth in short-day. For each genotype (Col-0, rGRF3, 35S:GIF1 and rGRF3x35S:GIF1) we collected two samples.

2014-06-17 | E-GEOD-53438 | biostudies-arrayexpress

Expression data from rGRF3, 35S:GIF1 and rGRF3x35S:GIF1 plants

2014-06-17 | GSE53438 | GEO

miR396e-OsGRF7 module controls rice plant architecture (RNA-Seq)

Project description:Plant-specific growth-regulating factors (GRFs) participate in multiple central developmental processes including root and leaf development, flower and seed formation, plant senescence, and tolerance to stress. While the role of the miRNA-GRFs regulatory module in determining gross morphology, which is one of the most important agronomic traits for crops, have not been comprehensively unraveled yet. Here, we reported that OsGRF7, a target of miR396e and co-activated with OsGIFs, is essential for determining plant architecture in rice. Overexpression of OsGRF7 leads to decreased tiller number, leaf length and leaf angle, reduced plant height and increased grain size, which are mediated by shortened cell length and disordered cell arrangement. Further analyses indicate that OsGRF7 binds the ACRGDA motif in promoters of OsNSP2, OsGASR1 and OsCYP714B1, OsCga1 and OsARF12, which are involved in the synthesis of strigolactones, gibberellins and cytokinins or related to auxin signaling pathway. Our findings establish OsGRF7 as a crucial component in the miR396-OsGRFs/OsGIFs-plant hormone regulatory network that controls rice growth and plant architecture.This dataset records the differential expressed genes between GRF7OE and WT plants.

2020-04-19 | GSE109801 | GEO

miR396e-OsGRF7 module controls rice plant architecture (ChIP-Seq)

Project description:Plant-specific growth-regulating factors (GRFs) participate in multiple central developmental processes including root and leaf development, flower and seed formation, plant senescence, and tolerance to stress. While the role of the miRNA-GRFs regulatory module in determining gross morphology, which is one of the most important agronomic traits for crops, have not been comprehensively unraveled yet. Here, we reported that OsGRF7, a target of miR396e and co-activated with OsGIFs, is essential for determining plant architecture in rice. Overexpression of OsGRF7 leads to decreased tiller number, leaf length and leaf angle, reduced plant height and increased grain size, which are mediated by shortened cell length and disordered cell arrangement. Further analyses indicate that OsGRF7 binds the ACRGDA motif in promoters of OsNSP2, OsGASR1 and OsCYP714B1, OsCga1 and OsARF12, which are involved in the synthesis of strigolactones, gibberellins and cytokinins or related to auxin signaling pathway. Our findings establish OsGRF7 as a crucial component in the miR396-OsGRFs/OsGIFs-plant hormone regulatory network that controls rice growth and plant architecture.This dataset records the profile of the binding peaks of OsGRF7 with GFP antibody in 35S:GRF7-GFP overexpression lines.

2020-04-19 | GSE109800 | GEO

The Arabidopsis miR396 mediates pathogen-associated molecular pattern-triggered immune responses against fungal pathogens

Project description:A first line of defense against pathogen infections is the recognition of pathogen-associated molecular patterns (PAMPs), leading to PAMP-triggered immunity (PTI). MicroRNAs (miRNAs) are primarily known as central regulators of plant development, but a few have also been connected to immunity. We have found that several fungal pathogens lead to a reduction in miR396 levels, suggesting that miR396 are negative regulators of downstream defense responses. In agreement with such as scenario, constitutive attenuation of miR396 activity enhances resistance to infection by fungal pathogens, while increased miR396 activity reduces pathogen resistance. We conclude that constitutive reduction of miR396 levels confer a primed state for enhanced defense reactions

2017-02-28 | GSE76819 | GEO

miRNA Expression data from maize young leaf and developing seed

Project description:miRNAs of at least 2 times expression level higher in seeds were all from the miR319, miR171 and miR166 family. In leaves, most up-regulated miRNAs included miR399a/c/d/e, miR408, miR159c/d, miR156k/j, miR160a/b/c/d/e and miR164a/b/c/d We intend to identify the up-regulated miRNAs in maize seed and screen for key miRNAs involved in maize seed development

2012-08-06 | E-GEOD-37322 | biostudies-arrayexpress

Small RNA transcriptome of Hibiscus syriacus provides insights into the potential influence of microRNAs in flower development and terpene synthesis

Project description:MicroRNAs (miRNAs) are essential small RNA molecules that regulate the expression of target mRNAs in plants and animals. Here, we aimed to identify miRNAs and their putative targets in Hibiscus syriacus, the national flower of South Korea. Therefore, we employed high-throughput sequencing of small RNAs obtained from four different tissues (i.e., leaf, root, flower, and ovary) and identified 33 conserved and 30 novel miRNA families, many of which showed differential tissue-specific expressions. In addition, we computationally predicted novel targets of miRNAs and validated some of them using 5′ rapid amplification of cDNA ends analysis. One of the validated novel targets of miR477 was a terpene synthase, the primary gene involved in the formation of disease-resistant terpene metabolites such as sterols and phytoalexins. In addition, a predicted target of conserved miRNAs, miR396, is SHORT VEGETATIVE PHASE, which is involved in flower initiation and is duplicated in Hibiscus syriacus. Collectively, this study provides the first reliable draft of the Hibiscus syriacus miRNA transcriptome that should constitute a basis for understanding the biological roles of miRNAs in Hibiscus syriacus.

2017-09-08 | GSE99329 | GEO

Specific combinatorial mutations in MIR396 genes enlarge the grain size and modulate the plant architecture in rice

Project description:miR396 is a key growth regulator in plants, however, the molecular mechanisms underlying its functions remained to be revealed. Here, through systematically gene-editing, we found that among the MIR396 family genes, MIR396e and -f were the main regulators of rice growth. mir396ef mutations could increase the grain yield through significantly enlarging the grain size. In addition, mir396ef mutations promoted the seedling growth and modulated the plant architecture by promoting the elongations of leaves (including leaf blades and sheaths) and panicles but suppressing the elongation of internodes, especially the uppermost internode. Our research reveals that mir396ef mutations promote the growth and organ elongation by significantly increasing the level of the gibberellin (GA) precursor, mevalonic acid (MVA), which subsequently activates the GA pathway. Our results also indicate that miR396 regulates the internode elongation through a different mechanism (probably through controlling SD37 expression) from the GA pathway. These results reveal two pathways by which miR396 regulates rice growth and provide valuable gene-editing targets to increase rice productivity.

2019-07-24 | GSE113319 | GEO

miRNA Expression data from maize young leaf and developing seed

2012-08-07 | GSE37322 | GEO

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