scholarly journals Integrated microRNA and transcriptome profiling reveal key miRNA-mRNA interaction pairs associated with seed development in Tartary buckwheat (Fagopyrum tataricum)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Hongyou Li ◽  
Hengling Meng ◽  
Xiaoqian Sun ◽  
Jiao Deng ◽  
Taoxiong Shi ◽  
...  
Keyword(s):  
Seed Development ◽  
Target Genes ◽  
Developmental Stages ◽  
Transcriptome Profiling ◽  
Mineral Elements ◽  
Endosperm Development ◽  
Tartary Buckwheat ◽  
Integrated Analysis ◽  
Fagopyrum Tataricum ◽  
Regulatory Pathways

Abstract Background Tartary buckwheat seed development is an extremely complex process involving many gene regulatory pathways. MicroRNAs (miRNAs) have been identified as the important negative regulators of gene expression and performed crucial regulatory roles in various plant biological processes. However, whether miRNAs participate in Tartary buckwheat seed development remains unexplored. Results In this study, we first identified 26 miRNA biosynthesis genes in the Tartary buckwheat genome and described their phylogeny and expression profiling. Then we performed small RNA (sRNA) sequencing for Tartary buckwheat seeds at three developmental stages to identify the miRNAs associated with seed development. In total, 230 miRNAs, including 101 conserved and 129 novel miRNAs, were first identified in Tartary buckwheat, and 3268 target genes were successfully predicted. Among these miRNAs, 76 exhibited differential expression during seed development, and 1534 target genes which correspond to 74 differentially expressed miRNAs (DEMs) were identified. Based on integrated analysis of DEMs and their targets expression, 65 miRNA-mRNA interaction pairs (25 DEMs corresponding to 65 target genes) were identified that exhibited significantly opposite expression during Tartary buckwheat seed development, and 6 of the miRNA-mRNA pairs were further verified by quantitative real-time polymerase chain reaction (qRT-PCR) and ligase-mediated rapid amplification of 5′ cDNA ends (5′-RLM-RACE). Functional annotation of the 65 target mRNAs showed that 56 miRNA-mRNA interaction pairs major involved in cell differentiation and proliferation, cell elongation, hormones response, organogenesis, embryo and endosperm development, seed size, mineral elements transport, and flavonoid biosynthesis, which indicated that they are the key miRNA-mRNA pairs for Tartary buckwheat seed development. Conclusions Our findings provided insights for the first time into miRNA-mediated regulatory pathways in Tartary buckwheat seed development and suggested that miRNAs play important role in Tartary buckwheat seed development. These findings will be help to study the roles and regulatory mechanism of miRNAs in Tartary buckwheat seed development.

Spatially resolved distributions of the mineral elements in the grain of tartary buckwheat (Fagopyrum tataricum)

2013 ◽  
Vol 54 (1) ◽  
pp. 125-131 ◽  
Author(s):  
Paula Pongrac ◽  
Katarina Vogel-Mikuš ◽  
Luka Jeromel ◽  
Primož Vavpetič ◽  
Primož Pelicon ◽  
...  
Keyword(s):  
Mineral Elements ◽  
Tartary Buckwheat ◽  
Fagopyrum Tataricum ◽  
Spatially Resolved

scholarly journals Characterization of cDNA Encoding Resveratrol Synthase and Accumulation of Resveratrol in Tartary Buckwheat

2013 ◽  
Vol 8 (11) ◽  
pp. 1934578X1300801 ◽  
Author(s):  
Yeon Bok Kim ◽  
Aye Aye Thwe ◽  
YeJi Kim ◽  
Sun Kyung Yeo ◽  
Chanhui Lee ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Light Condition ◽  
Tartary Buckwheat ◽  
Dark Condition ◽  
Fagopyrum Tataricum ◽  
Reading Frame ◽  
Expression Levels ◽  
Resveratrol Synthase ◽  
Key Enzyme

Resveratrol synthase (RS) is the key enzyme for biosynthesis of resveratrol which come from coumaroyl-coenzyme A (CoA) and malonyl-CoA. Here, we report the cloning and characterization of a RS gene and accumulation of resveratrol in tartary buckwheat ( Fagopyrum tataricum). FtRS was composed of 1173 bp open reading frame and 390 amino acid residues and had a theoretical molecular weight and isoelectric point value of 43.70 kDa and 6.24, respectively. The FtRS expression levels were examined in sprouts and different organs of two tartary buckwheat cultivars, Hokkai T8 (T8) and Hokkai T10 (T10). FtRS transcript levels and resveratrol contents were higher under the dark condition compared with light condition. The expression levels of different organs of T10 was not observed significant variations compared to different organs of T8. Interestingly, resveratrol was detected in the sprouts developmental stages, but no resveratrol could not detect in any other organs of both T8 and T10. Therefore, we suggest that the resveratrol content in tartary buckwheat sprouts may be attributed mainly to the dark condition. The characterization of FtRS will be helpful for better understanding of the resveratrol biosynthesis in tartary buckwheat.

scholarly journals Insights into the correlation between Physiological changes in and seed development of tartary buckwheat (Fagopyrum tataricum Gaertn.)

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Moyang Liu ◽  
Zhaotang Ma ◽  
Tianrun Zheng ◽  
Wenjun Sun ◽  
Yanjun Zhang ◽  
...  
Keyword(s):  
Seed Development ◽  
Tartary Buckwheat ◽  
Physiological Changes ◽  
Fagopyrum Tataricum

scholarly journals Identification and verification of seed development related miRNAs in kernel almond by small RNA sequencing and qPCR

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260492
Author(s):  
Marjan Jafari ◽  
Behrouz Shiran ◽  
Gholamreza Rabiei ◽  
Roudabeh Ravash ◽  
Badraldin Ebrahim Sayed Tabatabaei ◽  
...  
Keyword(s):  
Seed Development ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Developmental Stages ◽  
Small Rna Sequencing ◽  
Kernel Size ◽  
Short Rnas ◽  
Genes Encoding ◽  
Negative Effect

Many studies have investigated the role of miRNAs on the yield of various plants, but so far, no report is available on the identification and role of miRNAs in fruit and seed development of almonds. In this study, preliminary analysis by high-throughput sequencing of short RNAs of kernels from the crosses between almond cultivars ‘Sefid’ × ‘Mamaee’ (with small and large kernels, respectively) and ‘Sefid’ × ‘P. orientalis’ (with small kernels) showed that the expressions of several miRNAs such as Pdu-miR395a-3p, Pdu-miR8123-5p, Pdu-miR482f, Pdu-miR6285, and Pdu-miR396a were significantly different. These miRNAs targeted genes encoding different proteins such as NYFB-3, SPX1, PGSIP3 (GUX2), GH3.9, and BEN1. The result of RT-qPCR revealed that the expression of these genes showed significant differences between the crosses and developmental stages of the seeds, suggesting that these genes might be involved in controlling kernel size because the presence of these miRNAs had a negative effect on their target genes. Pollen source can influence kernel size by affecting hormonal signaling and metabolic pathways through related miRNAs, a phenomenon known as xenia.

scholarly journals Variations in Accumulation of Lignin and Cellulose and Metabolic Changes in Seed Hull Provide Insight into Dehulling Characteristic of Tartary Buckwheat Seeds

2019 ◽  
Vol 20 (3) ◽  
pp. 524 ◽  
Author(s):  
Chao Song ◽  
Chengrui Ma ◽  
Dabing Xiang
Keyword(s):  
Seed Development ◽  
Principal Component ◽  
Total Content ◽  
Metabolic Changes ◽  
Tartary Buckwheat ◽  
Gas Chromatography Mass Spectrometry ◽  
Fagopyrum Tataricum ◽  
Developing Seed ◽  
Seed Hull ◽  
Dehulling Efficiency

Tartary buckwheat (Fagopyrum tataricum) is considered a profitable crop that possesses medicinal properties, because of its flavonoid compounds. However, the dehulling issue is becoming the bottleneck for consumption of Tartary buckwheat seed. In this study, we investigated the relation between dehulling efficiency and content of lignin and cellulose in the seed hull. Moreover, the untargeted metabolomics analysis, including partial least squares discriminant analysis (PLS-DA) and principal component analysis (PCA), were performed to examine the pattern of metabolic changes in the hull of Tartary buckwheat seeds, XQ 1 and MQ 1, during seed development using gas chromatography mass spectrometry (GC-MS). In mature seed hull the accumulation of highest lignin and lowest cellulose were observed in the hull of MQ 1 seed, a dehulling-friendly variety with highest dehulling efficiency (93%), than that in other dehulling recalcitrant varieties, such as XQ 1 with a range of dehulling efficiency from 2% to 6%. During seed development, the total content of lignin and cellulose increased. MQ 1 and XQ 1 displayed a similar trend in the change of lignin and cellulose that the content was decreased in lignin and increased in cellulose. PCA result showed the metabolic differentiations between MQ 1 and XQ 1 during seed development. The results of our study suggest the compensatory regulation of lignin and cellulose deposition in the hull of mature and developing seed, and deviation of MQ 1 from the ratio of lignin to cellulose of other dehulling recalcitrant varieties may have been a contributing factor that resulted in the dehulling differentia.

scholarly journals Transcriptome-wide identification and characterization of microRNAs in diverse phases of wood formation in Populus trichocarpa

2020 ◽  
Author(s):  
Ruiqi Wang ◽  
Mengxuan Ren ◽  
Shuanghui Tian ◽  
Cong Liu ◽  
He Cheng ◽  
...  
Keyword(s):  
Cell Wall ◽  
Target Genes ◽  
Developmental Stages ◽  
Populus Trichocarpa ◽  
Wood Formation ◽  
Pcr Analysis ◽  
Integrated Analysis ◽  
Cell Wall Modification ◽  
Dynamic Regulation ◽  
Genome Wide

Abstract Background: MicroRNAs (miRNAs) are small, non-coding RNAs that have important regulatory functions in plant growth and development. However, the miRNAs that are involved in different developmental stages of tree stems have not been systemically characterized. In this study, we applied miRNA expression profiling method to the Populus trichocarpa trunks of the three distinct developmental stages defined as the primary stem (PS), transitional stem (TS), and secondary stem (SS) to investigate the miRNA species, their dynamic regulation and functions during the transitions of wood formation in different developmental stages at the genome-wide scale by Solexa sequencing.Results: We obtained 892, 872, and 882 known miRNAs and 1,727, 1,723, and 1,597 novel miRNAs, from PS, TS, and SS, respectively. And identified 114, 306, and 152 differentially expressed miRNAs (DE-miRNAs) with 921, 2,639, and 2,042 candidate target genes (CTGs), which formed 158, 855, and 297 DE-miRNA-CTG pairs in PS vs TS, PS vs SS, and TS vs SS , respectively. Among these, 47, 439, and 71 DE-miRNA-CTG pairs showed a significant negative correlation, respectively. Finally, we identified 39, 9, and 92 miRNA-CTG pairs involved in PS, TS, and SS, respectively. These DE-miRNA-CTG pairs in poplar or whose counterparts in other plant species are known to be transcriptional factors or structural genes involved in cell division and differentiation, cell wall modification, secondary cell wall (SCW) biosynthesis, lignification, and programmed cell death processes of wood formation. Moreover, qRT–PCR analysis confirmed that the results of small RNA-seq were robust and reliable and most miRNA-CTG pairs exhibited an inverse correlation.Conclusions: This is the first report on an integrated analysis of genome-wide mRNA and miRNA profiling of diverse phases of wood formation in poplar trunks. We showed that even though miRNAs involved in diverse developmental phases were not in a considerable number, their roles in the regulatory network that govern wood formation during different developmental stages cannot be negligible or underestimated. The information and data obtained in this paper significantly advanced our understanding of these miRNAs and their essential, dynamic and diversified roles as well as functions in diverse phases of wood formation in tree species.

scholarly journals Systems-level identification of transcription factors critical for mouse embryonic development

2017 ◽  
Author(s):  
Kai Zhang ◽  
Mengchi Wang ◽  
Ying Zhao ◽  
Wei Wang
Keyword(s):  
Transcription Factors ◽  
Embryonic Development ◽  
Target Genes ◽  
Developmental Stages ◽  
Cell Types ◽  
Integrated Analysis ◽  
Chromatin Interactions ◽  
Regulatory Circuit ◽  
Transcriptional Regulatory ◽  
Comprehensive Survey

AbstractDynamic changes in the transcriptional regulatory circuit can influence the specification of distinct cell types. Numerous transcription factors (TFs) have been shown to function through dynamic rewiring during embryonic development but a comprehensive survey on the global regulatory network is still lacking. Here, we performed an integrated analysis of epigenomic and transcriptomic data to reveal key regulators from 2 cells to postnatal day 0 in mouse embryogenesis. We predicted 3D chromatin interactions including enhancer-promoter interactions in 12 tissues across 8 developmental stages, which facilitates linking TFs to their target genes for constructing genetic networks. To identify driver TFs particularly those not necessarily differentially expressed ones, we developed a new algorithm, dubbed as Taiji, to assess the global importance of TFs in development. Through comparative analysis across tissues and developmental stages, we systematically uncovered TFs that are critical for lineage-specific and stage-dependent tissue specification. Most interestingly, we have identified TF combinations that function in spatiotemporal order to form transcriptional waves regulating developmental progress and differentiation. Not only does our analysis provide the first comprehensive map of transcriptional regulatory circuits during mouse embryonic development, the identified novel regulators and the predicted 3D chromatin interactions also provide a valuable resource to guide further mechanistic studies.

scholarly journals Transcriptome-wide identification and characterization of microRNAs in diverse phases of wood formation in Populus trichocarpa

2021 ◽  
Author(s):  
Ruiqi Wang ◽  
Mengxuan Reng ◽  
Shuanghui Tian ◽  
Cong Liu ◽  
He Cheng ◽  
...  
Keyword(s):  
Cell Wall ◽  
Target Genes ◽  
Developmental Stages ◽  
Process Analysis ◽  
Populus Trichocarpa ◽  
Secondary Growth ◽  
Integrated Analysis ◽  
Cell Wall Modification ◽  
Individual Mirnas ◽  
Mirna Species

Abstract We applied miRNA expression profiling method to Populus trichocarpa stems of the three developmental stages, primary stem (PS), transitional stem (TS), and secondary stem (SS), to investigate miRNA species and their regulation on lignocellulosic synthesis and related processes. We obtained 892, 872, and 882 known miRNAs and 1,727, 1,723, and 1,597 novel miRNAs, from PS, TS, and SS, respectively. Comparisons of these miRNA species among different developmental stages led to the identification of 114, 306, and 152 differentially expressed miRNAs (DE-miRNAs), which had 921, 2,639, and 2,042 candidate target genes (CTGs) in the three respective stages of the same order. Corelation analysis revealed 47, 439, and 71 DE-miRNA-CTG pairs of high negative correlation in PS, TS and SS, respectively. Through biological process analysis, we finally identified 34, 6, and 76 miRNA-CTG pairs from PS, TS, and SS, respectively, and the miRNA target genes in these pairs regulate or participate lignocellulosic biosynthesis related biological processes: cell division and differentiation, cell wall modification, secondary cell wall biosynthesis, lignification, and programmed cell death processes. This is the first report on an integrated analysis of genome-wide mRNA and miRNA profilings during multiple phases of poplar stem development. Our analysis results imply that individual miRNAs modulate secondary growth and lignocellulosic biosynthesis through regulating transcription factors and lignocellulosic biosynthetic pathway genes, resulting in more dynamic promotion, suppression, or regulatory circuits. This study advanced our understanding of many individual miRNAs and their essential, diversified roles in dynamic regulation of secondary growth in woody tree species.

scholarly journals Identification of Biomarkers Controlling Cell Fate In Blood Cell Development

2021 ◽  
Vol 1 ◽  
Author(s):  
Maryam Nazarieh ◽  
Marc Hoeppner ◽  
Volkhard Helms
Keyword(s):  
Blood Cell ◽  
Cell Fate ◽  
Gene Networks ◽  
Target Genes ◽  
Developmental Stages ◽  
Cell Formation ◽  
Cell Lineage ◽  
Marker Genes ◽  
Specific Marker ◽  
Regulatory Pathways

A blood cell lineage consists of several consecutive developmental stages starting from the pluri- or multipotent stem cell to a state of terminal differentiation. Despite their importance for human biology, the regulatory pathways and gene networks that govern these differentiation processes are not yet fully understood. This is in part due to challenges associated with delineating the interactions between transcription factors (TFs) and their corresponding target genes. A possible step forward in this case is provided by the increasing amount of expression data, as a basis for linking differentiation stages and gene activities. Here, we present a novel hierarchical approach to identify characteristic expression peak patterns that global regulators excert along the differentiation path of cell lineages. Based on such simple patterns, we identified cell state-specific marker genes and extracted TFs that likely drive their differentiation. Integration of the mean expression values of stage-specific “key player” genes yielded a distinct peaking pattern for each lineage that was used to identify further genes in the dataset which behave similarly. Incorporating the set of TFs that regulate these genes led to a set of stage-specific regulators that control the biological process of cell fate. As proof of concept, we considered two expression datasets covering key differentiation events in blood cell formation of mice.

scholarly journals Identification of transcription factors and construction of a novel miRNA regulatory network in primary osteoarthritis by integrated analysis

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ying Jiang ◽  
Yi Shen ◽  
Liyan Ding ◽  
Shengli Xia ◽  
Liying Jiang
Keyword(s):  
Regulatory Networks ◽  
Target Genes ◽  
Therapeutic Targets ◽  
Microarray Dataset ◽  
Integrated Analysis ◽  
Rna Seq ◽  
Hub Genes ◽  
Serum Samples ◽  
Regulatory Pathways ◽  
Novel Mirna

Abstract Backgrounds As osteoarthritis (OA) disease-modifying therapies are not available, novel therapeutic targets need to be discovered and prioritized. Here, we aim to identify miRNA signatures in patients to fully elucidate regulatory mechanism of OA pathogenesis and advance in basic understanding of the genetic etiology of OA. Methods Six participants (3 OA and 3 controls) were recruited and serum samples were assayed through RNA sequencing (RNA-seq). And, RNA-seq dataset was analysed to identify genes, pathways and regulatory networks dysregulated in OA. The overlapped differentially expressed microRNAs (DEMs) were further screened in combination with the microarray dataset GSE143514. The expression levels of candidate miRNAs were further validated by quantitative real-time PCR (qRT-PCR) based on the GEO dataset (GSE114007). Results Serum samples were sequenced interrogating 382 miRNAs. After screening of independent samples and GEO database, the two comparison datasets shared 19 overlapped candidate micRNAs. Of these, 9 up-regulated DEMs and 10 down-regulated DEMs were detected, respectively. There were 236 target genes for up-regulated DEMs and 400 target genes for those down-regulated DEMs. For up-regulated DEMs, the top 10 hub genes were KRAS, NRAS, CDC42, GDNF, SOS1, PIK3R3, GSK3B, IRS2, GNG12, and PRKCA; for down-regulated DEMs, the top 10 hub genes were NR3C1, PPARGC1A, SUMO1, MEF2C, FOXO3, PPP1CB, MAP2K1, RARA, RHOC, CDC23, and CREB3L2. Mir-584-5p-KRAS, mir-183-5p-NRAS, mir-4435-PIK3R3, and mir-4435-SOS1 were identified as four potential regulatory pathways by integrated analysis. Conclusions We have integrated differential expression data to reveal putative genes and detected four potential miRNA-target gene pathways through bioinformatics analysis that represent new mediators of abnormal gene expression and promising therapeutic targets in OA.

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