MiRNA Expression data from maize young leaf and developing seed
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ABSTRACT:
ORGANISM(S): Zea mays synthetic construct
PROVIDER: GSE37322 | GEO | 2012/08/07
SECONDARY ACCESSION(S): PRJNA159463
REPOSITORIES: GEO
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2012-08-06 | E-GEOD-37322 | biostudies-arrayexpress
Project description:Seed expansion in peanut is a complex biological process involving many gene regulatory pathways. MicroRNAs (miRNAs) play important regulatory roles in plant growth and development, but little is known about their functions during seed expansion, or how they contribute to seed expansion in different peanut lines. We examined seed miRNA expression patterns at 15 and 35 days after flowering ( DAF ) in two peanut 8th generation recombinant inbred lines (RIL8); 8106, a medium-pod variety, and 8107, a super-pod variety. Using high-throughput sequencing, we identified 1082 miRNAs in developing peanut seeds including 434 novel miRNAs. We identified 316 differentially expressed miRNAs by comparing expression levels between the two peanut lines. Interestingly, 24 miRNAs showed contrasting patterns of expression in the two RILs, and 149 miRNAs were expressed predominantly in only one RIL at 35 DAF. Also, potential target genes for some conserved and novel miRNAs were identified by degradome sequencing; target genes were predicted to be involved in auxin mediated signaling pathways and cell division. We validated the expression patterns of some representative miRNAs and 12 target genes by qPCR, and found negative correlations between the expression level of miRNAs and their targets. miR156e, miR159b, miR160a, miR164a, miR166b, miR168a, miR171n, miR172c-5p, and miR319d and their corresponding target genes may play key roles in seed expansion in peanut. The results of our study also provide novel insights into the dynamic changes in miRNAs that occur during peanut seed development, and increase our understanding of miRNA function in seed expansion.
2021-01-31 | GSE110195 | GEO
Project description:Maize is a globally important food and feed crop, and a low-phosphate (Pi) supply in the soil frequently limits maize yield in many areas. MicroRNAs (miRNAs) play important roles in the development and adaptation of plants to the environment. In this study, the spatio-temporal miRNA transcript profiling of the maize inbred line Q319 root and leaf in response to low Pi was analyzed with high-throughput sequencing technologies, and the expression patterns of certain target genes were detected by real-time RT-PCR. Complex small RNA populations were detected after low-Pi culture and displayed different patterns in the root and leaf. miRNAs identified as responding to Pi deficiency can be grouped into ‘early’ miRNAs that respond rapidly, and often non-specifically, to Pi deficiency, and ‘late’ miRNAs that alter the morphology, physiology or metabolism of plants upon prolonged Pi deficiency. The miR827-Nitrogen limitation adaptation (NLA)-mediated post-transcriptional pathway was conserved in response to Pi availability of maize, but the miR399-mediated post-transcriptional pathway was different from Arabidopsis. Abiotic stress-related miRNAs engaged in interactions of different signaling and/or metabolic pathways. Auxin-related miRNAs (zma-miR393, zma-miR160a/b/c, zma-miR160d/e/g, zma-miR167a/b/c/d and zma-miR164a/b/c/d/g) and their targets play important roles in promoting primary root growth, inhibiting lateral root development and retarding upland growth of maize when subjected to low Pi. The changes in expression of miRNAs and their target genes suggest that the miRNA regulation/alterations compose an important mechanism in the adaptation of maize to a low-Pi environment; certain miRNAs participate in root architecture modification via the regulation of auxin signaling. A complex regulatory mechanism of miRNAs in response to a low-Pi environment exists in maize, revealing obvious differences from that in Arabidopsis.
2015-07-08 | GSE70612 | GEO
Project description:In this study, two small RNA libraries were sequenced, and a total reads of 9,705,761 and 9,005,563 were generated from developing seeds and growing leaves, respectively. Further analysis identified 125 known miRNAs in seeds and 127 known miRNAs in leaves. 54 novel miRNAs were identified and they were not reported in other plants.
2012-08-07 | GSE37551 | GEO
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Project description:Rose (Rosa hybrida L.) is a major cut flowers in the world. Studying the molecular mechanism of auxin regulation in growth is of great significance for enhancing the understanding of the growth and development processes of rose and informing accurate exogenous auxin application in rose production. However, the response mechanism of rose to miRNA-mediated auxin signal transduction is unclear. In this study, rose plants were treated with IAA, and 75 known miRNAs and 168 novel miRNAs were identified by small RNA sequencing. Among them, 19 known miRNAs and 42 miRNAs were differentially expressed. Many differential miRNAs demonstrated staged responses to auxin treatment. The targeted relationship between miRNA and key transcription factors regulated by auxin in rose was analyzed, and the target genes in the ARF family and AUX/IAA family were screened. By using quantitative real-time PCR(qRT-PCR) to verify the expression patterns of the miRNA regulating the auxin signal transduction pathway and its target gene, we found that miR156a, miR160a, miR164a, miR167d, miR396b-3p, novel_miR_189, novel_miR_74, novel_miR_8, and novel_miR_207 interacted negatively with the ARF family, and miR390a-3p and novel_miR_101 interacted negatively with the AUX/IAA family. These results provide a theoretical basis for further studies on the auxin regulatory mechanisms in rose.
2023-02-28 | GSE225844 | GEO
Project description:Arabidopsis ABA HYPERSENSITIVE1 (ABH1) / CAP-BINDING-PROTEIN80 functions in cap-binding, splicing, ABA and stress response signaling and in the biogenesis of microRNAs (miRNAs). SUPPRESSOR OF GENE SILENCING3 (SGS3) plays a crucial role in post transcriptional gene silencing (PTGS). We show that abh1 sgs3 double mutant manifests pleiotropic phenotypes including altered ABA sensitivity in seed germination, fused cotyledons, delayed growth in root initiation and leaf production, accelerated juvenile-to-adult phase transition and flowering time, short and bent siliques with ectopic carpelloid tissues, reduced seed set due to altered carpel structure and pollen tube growth, and increased resistance to powdery mildew infection. A systems approach using meta-analysis of whole genome tiling microarray datasets for mutants of PTGS, RNA processing, and responses to environmental stress was taken to design a 135k feature custom microarray to probe the molecular bases of these phenotypes. Results confirmed documented effects of ABA or abh1 on precursor MIRNA expression (pre-MIR159, pre-MIR168) and identified novel miRNAs and their targets regulated by ABA (pre-MIR408, LACCASE12 and -13; pre-MIR824) or elevated in abh1 sgs3 double mutant (pre-MIR156A,C; pre-MIR164B, pre-MIR167A, pre-MIR408, At5g15845/CONSTANS-LIKE1-cis-NAT-RNA). miR156 targets SQUAMOSA-PROMOTER-BINDING-PROTEIN-LIKE genes that spawn siRNAs and control phase change; miR164 targets CUP-SHAPED-COTYLEDON1 and -2 genes; miR166 methylates target PHABULOSA genomic DNA in trans; miR167 targets AUXIN RESPONSE FACTOR 6 (ARF6) and ARF8 which regulate both female and male reproduction; miR408 targets a plantacyanin which is expressed predominantly in the transmitting tract of the pistil and affects pollen tube guidance on the stigma. We also identified sgs3 by ABA interactions on gene expression which reveal potential nodes in regulatory networks linking ABA, mRNA processing and PTGS with development.
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Project description:In this study, two small RNA libraries were sequenced, and a total reads of 9,705,761 and 9,005,563 were generated from developing seeds and growing leaves, respectively. Further analysis identified 125 known miRNAs in seeds and 127 known miRNAs in leaves. 54 novel miRNAs were identified and they were not reported in other plants. Identification of known and novel miRNAs essential to maize seed development
2012-08-07 | E-GEOD-37551 | biostudies-arrayexpress
Project description:miRNA levels depend on both biogenesis and turnover. The methyltransferase HEN1 stabilizes plant miRNAs, animal piRNAs, and siRNAs in both kingdoms via 3' terminal methylation. Loss of HEN1 in plants results in non-templated oligo-uridylation and accelerated degradation of miRNAs. In hen1 mutants from Arabidopsis and rice, we found that the patterns of miRNA truncation and uridylation differ substantially among miRNA families, but such patterns for the same miRNA are conserved between species. miR166 and miR163 are truncated predominantly to ~17 and ~16 nt, and subsequently recover via uridylation to approximately their original sizes, 21 and 24 nt, suggesting that in these cases miRNA truncation triggers uridylation. miR171 is untruncated but uridylated to 22 nt in hen1 mutants, gaining the ability to trigger production of phased, secondary siRNAs. Truncated and tailed variants were bound by ARGONAUTE1 (AGO1) in hen1, implying that these events occur while miRNAs are still bound by AGO1. Unexpectedly, a portion of miR158 in wildtype remains unmethylated and thus subject to uridylation and destabilization, suggesting that plants naturally utilize miRNA methylation to modulate miRNA accumulation. Our results suggest that the AGO1-containing RISC complex may undergo programming to reflect each bound miRNA, determining a defined, distinct decay destiny.
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Project description:Here, a combined small RNA and transcriptome sequencing analysis was performed on the BPH6-transgenic and Nipponbare plants sheath samples at the different feeding stage by BPH, and differentially expressed microRNAs (DEMs) and genes (DEGs) were identified and further analyzed for a possible involvement in BPH6 mediated resistance mechanism. A total of 217 DEMs and 7,874 DEGs were identified in the BPH6-transgenic and Nipponbare plants after BPH feeding. At the miRNA level, 29 miRNAs, including the members of miR160, miR166, miR169, miR1861, miR319 and miR390 family and other miRNAs, appeared opposite expression at early or late feeding stages between the two varieties, and 9 miRNAs specially expressed in the BPH6-transgenic plans, suggesting these miRNAs might play an important role in BPH6-mediated resistance to BPH. For the transcriptome, 949 DEGs appeared opposite expression at early or late feeding stages of two rice genotypes were identified and enriched in metabolic process, cellular development, cell wall organization, cellular component movement and hormone transport, and in involved in certain kinds of primary and secondary metabolite synthesis by GO and KEGG enrichment analysis. 24 genes were further selected to be considered as BPH resistance related gene candidates. Finally, integrated analysis of DEMs and DEGs showed that 34 miRNAs corresponding to 42 target genes were selected as BPH resistance related miRNA-mRNA interaction candidates.
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