Abstract:MicroRNAs are short (19–24-nucleotide-long), non-coding RNA molecules. They downregulate gene expression by triggering the cleavage or translational inhibition of complementary mRNAs. Senescence is a stage of development following growth completion and is dependent on the expression of specific genes. MicroRNAs control the gene expression responsible for plant competence to answer senescence signals. Therefore, they coordinate the juvenile-to-adult phase transition of the whole plant, the growth and senescence… Show more
“…The same predicted miR319 target has been previously found in RNA-Seq of Pi-starved tobacco plants [93]. Its targets, the plant GAMyb TFs, have been shown to activate gibberellin-responsive gene expression of α-amylase in barley [94,95]. Our degradome data indicate the possible cleavage of various mRNA isoforms encoding nuclear transcription factor Y subunit A-4 (NFYA4, HORVU4Hr1G005670, TargetSeek: score = 3, MFE = -27.6, PAREsnip2: score = 2, MFE = -28.1) mediated by miR169d (20 nt, id = 84) (Table 1), what is consistent with previous studies on Cunninghamia lanceolata L. showing that NFYA4 mRNA is targeted by miR169d (authors used PAREsnip approach) [96].…”
Section: Pi-responsive Motifs Found In the Promoters Of Degssupporting
Background: Small RNAs (sRNAs) are 20–30 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration triggers plant responses to balance the internal Pi level. Results: In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) RNA-Seq data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs. We find that differentially and significantly expressed miRNAs (DEMs, p-value < 0.05) are represented by 162 (44.88 % of total differentially expressed small RNAs) molecules in shoot and 138 (7.14 %) in root; mainly various miR399 and miR827 isomiRs. The remaining small RNAs (i.e., those without perfect match to reference sequences deposited in miRBase) are considered as differentially expressed other sRNAs (DESs, p-value Bonferroni correction < 0.05). In roots, a more abundant and diverse set of other sRNAs (DESs, 1796 unique sequences, 0.13 % from total unique reads obtained under low-Pi) contributes more to the compensation of low-Pi stress than that in shoots (DESs, 199 unique sequences, 0.01 %). More than 80 % of differentially expressed other sRNAs are up-regulated in both organs. Additionally, in barley shoots, up-regulation of small RNAs is accompanied by strong induction of two nucleases (S1/P1 endonuclease and 3’-5’ exonuclease). This suggests that most small RNAs may be generated upon endonucleolytic cleavage to increase the internal Pi pool. Transcriptomic profiling of Pi-starved barley shoots identifies 98 differentially expressed genes (DEGs). A majority of the DEGs possess characteristic Pi-responsive cis-regulatory elements (P1BS and/or PHO element), located mostly in the proximal promoter regions. GO analysis shows that the discovered DEGs primarily alter plant defense, plant stress response, nutrient mobilization, or pathways involved in the gathering and recycling of phosphorus from organic pools.Conclusions: Our results provide comprehensive data to demonstrate complex responses at the RNA level in barley to maintain Pi homeostasis and indicate that barley adapts to Pi-starvation through elicitation of RNA degradation. Novel P-responsive genes were selected as putative candidates to overcome low-Pi stress in barley plants.
“…The same predicted miR319 target has been previously found in RNA-Seq of Pi-starved tobacco plants [93]. Its targets, the plant GAMyb TFs, have been shown to activate gibberellin-responsive gene expression of α-amylase in barley [94,95]. Our degradome data indicate the possible cleavage of various mRNA isoforms encoding nuclear transcription factor Y subunit A-4 (NFYA4, HORVU4Hr1G005670, TargetSeek: score = 3, MFE = -27.6, PAREsnip2: score = 2, MFE = -28.1) mediated by miR169d (20 nt, id = 84) (Table 1), what is consistent with previous studies on Cunninghamia lanceolata L. showing that NFYA4 mRNA is targeted by miR169d (authors used PAREsnip approach) [96].…”
Section: Pi-responsive Motifs Found In the Promoters Of Degssupporting
Background: Small RNAs (sRNAs) are 20–30 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration triggers plant responses to balance the internal Pi level. Results: In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) RNA-Seq data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs. We find that differentially and significantly expressed miRNAs (DEMs, p-value < 0.05) are represented by 162 (44.88 % of total differentially expressed small RNAs) molecules in shoot and 138 (7.14 %) in root; mainly various miR399 and miR827 isomiRs. The remaining small RNAs (i.e., those without perfect match to reference sequences deposited in miRBase) are considered as differentially expressed other sRNAs (DESs, p-value Bonferroni correction < 0.05). In roots, a more abundant and diverse set of other sRNAs (DESs, 1796 unique sequences, 0.13 % from total unique reads obtained under low-Pi) contributes more to the compensation of low-Pi stress than that in shoots (DESs, 199 unique sequences, 0.01 %). More than 80 % of differentially expressed other sRNAs are up-regulated in both organs. Additionally, in barley shoots, up-regulation of small RNAs is accompanied by strong induction of two nucleases (S1/P1 endonuclease and 3’-5’ exonuclease). This suggests that most small RNAs may be generated upon endonucleolytic cleavage to increase the internal Pi pool. Transcriptomic profiling of Pi-starved barley shoots identifies 98 differentially expressed genes (DEGs). A majority of the DEGs possess characteristic Pi-responsive cis-regulatory elements (P1BS and/or PHO element), located mostly in the proximal promoter regions. GO analysis shows that the discovered DEGs primarily alter plant defense, plant stress response, nutrient mobilization, or pathways involved in the gathering and recycling of phosphorus from organic pools.Conclusions: Our results provide comprehensive data to demonstrate complex responses at the RNA level in barley to maintain Pi homeostasis and indicate that barley adapts to Pi-starvation through elicitation of RNA degradation. Novel P-responsive genes were selected as putative candidates to overcome low-Pi stress in barley plants.
“…The miR319b guides for cleavage PCF6 TF and two GaMyb-like TFs (Table 1 ). The plant GAMyb TFs, have been shown to activate gibberellin-responsive gene expression of α-amylase in barley [ 90 , 91 ]. Fig.…”
Background
Small RNAs (sRNAs) are 20–30 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration triggers plant responses to balance the internal Pi level.
Results
In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) RNA-Seq data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs. We find that differentially and significantly expressed miRNAs (DEMs, Bonferroni adjusted p-value < 0.05) are represented by 15 molecules in shoot and 13 in root; mainly various miR399 and miR827 isomiRs. The remaining small RNAs (i.e., those without perfect match to reference sequences deposited in miRBase) are considered as differentially expressed other sRNAs (DESs, p-value Bonferroni correction < 0.05). In roots, a more abundant and diverse set of other sRNAs (DESs, 1796 unique sequences, 0.13% from the average of the unique small RNA expressed under low-Pi) contributes more to the compensation of low-Pi stress than that in shoots (DESs, 199 unique sequences, 0.01%). More than 80% of differentially expressed other sRNAs are up-regulated in both organs. Additionally, in barley shoots, up-regulation of small RNAs is accompanied by strong induction of two nucleases (S1/P1 endonuclease and 3′-5′ exonuclease). This suggests that most small RNAs may be generated upon nucleolytic cleavage to increase the internal Pi pool. Transcriptomic profiling of Pi-starved barley shoots identifies 98 differentially expressed genes (DEGs). A majority of the DEGs possess characteristic Pi-responsive cis-regulatory elements (P1BS and/or PHO element), located mostly in the proximal promoter regions. GO analysis shows that the discovered DEGs primarily alter plant defense, plant stress response, nutrient mobilization, or pathways involved in the gathering and recycling of phosphorus from organic pools.
Conclusions
Our results provide comprehensive data to demonstrate complex responses at the RNA level in barley to maintain Pi homeostasis and indicate that barley adapts to Pi-starvation through elicitation of RNA degradation. Novel P-responsive genes were selected as putative candidates to overcome low-Pi stress in barley plants.
“…We got approval of animal experimental procedures from the Institutional Animal Care and Use Committee of A liated Hospital of Youjiang Medical University for Nationalities. Of each BALB/c nude mouse (5-6 weeks of age, 20-22 g) we injected a suspension of HuH-7 cells (1×10 7 ) into the right ank subcutaneously. From the Laboratory Animal Center (Shanghai, China), we purchased all mice and maintained them under speci c pathogen-free conditions in laminar ow cabinets.…”
“…MicroRNAs (miRNAs), about 19-24 nt in length, are endogenous non-coding small RNA exerting important in uences in animals and plants, which is through targeting the target gene mRNA at its 3terminal non-coding region thus causing transcriptional repression or regulating mRNA degradation [7,8].…”
Background: MicroRNAs (miRNAs), functioning as tumor suppressors or oncogenes, exert a considerable regulative influence in biological processes. Previous studies showed that miR-455-3p was significantly down-regulated in hepatocellular carcinoma (HCC), while the specific role of miR-455-3p in HCC is unclear. Methods: QRT-PCR was used to detect miR-455-3p expression levels in HCC cells and tissues. We adopted colony formation, EdU, CCK-8, transwell assays and wound-healing to identify the influences of miR-455-3p on proliferation, invasion and migration in HHCC and HuH-7 cells. Western blot analysis, angiogenesis assays, dual-luciferase reporter gene assay and bioinformatics analysis were also adopted to investigate the underlying molecular mechanisms. Results: MiR-455-3p was down-regulated in HCC tissues and cells. In vitro experiments identified miR-455-3p overexpression inhibited HCC cell proliferation, migration and invasion. Interestingly, it was identified that vascular endothelial growth factor C (VEGFC) was the downstream target gene of miR-455-3p. Additionally, overexpression of miR-455-3p in HCC cells and human umbilical vein endothelial cells (HUVECs) cells led to decreased expression of VEGFC, vascular endothelial growth factor receptor (VEGFR)-2, and subsequently decreased phosphatidylinositol 3-kinase (AKT) signaling pathway. Furthermore, in vivo restoration of miR-455-3p significantly suppressed tumorigenicity of HuH-7 cells in nude mice and inhibited both angiogenesis and lymphangiogenesis of tumor xenografts. Conclusions: Our findings suggest that miR-455-3p could play a role in HCC tumorigenesis at least in part by modulation of angiogenesis and lymphangiogenesis through targeting VEGFC, and could simultaneously block AKT signaling pathways.
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