scholarly journals Genome-wide identification and expression analysis of rice NLR genes responsive to the infections of Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae

2019 ◽  
Author(s):  
Li Ding ◽  
Xiameng Xu ◽  
Weiwen Kong ◽  
Xue Xia ◽  
Shengwei Zhang ◽  
...  
Keyword(s):  
Magnaporthe Oryzae ◽  
Critical Role ◽  
Regulatory Elements ◽  
Xanthomonas Oryzae ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Promoter Regions ◽  
Medium Level ◽  
Rice Disease ◽  
The Veil

Abstract Background Nucleotide-binding site, leucine-rich repeat (NLR) genes play a critical role in rice disease resistance. However, the transcriptional activities of rice NLR genes during pathogen invasions are still unclear.Results To uncover the veil, we identified a total of 430 regular rice NLR genes with both NBS and LRR domains, consisting of 192 CNL and 238 XNL (without a CC motif) members. We performed individual and integrative analyses based on 69 samples from rice microarray after the infections of Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae (Mor). 397 NLR genes were found to be expressed at low/medium level, while 10 NLR genes were observed to show high levels of expression. 400 NLR genes were discovered to be differentially expressed in at least one sample. Further, 46 NLR genes were identified to be differentially expressed in rice response to the two pathogens and 38 of them could be validated by RNA-seq data. Six cis-regulatory elements (MYC, STRE, MYB, ABRE, G-box, and AS-1) were observed to occur frequently in the promoter regions of rice NLR genes. Ten NLR genes were selected for in lab analysis, and qRT-PCR results of seven NLR genes verified the validity of the microarray and RNA-Seq data.Conclusions Our results would shed new light on revealing the roles of NLR genes in rice resistance to Xoo and Mor.

scholarly journals Assessment of Embryo-Induced Transcriptomic Changes in Hamster Uterus Using RNA-Seq

2018 ◽  
Vol 46 (5) ◽  
pp. 1868-1878 ◽  
Author(s):  
Ming-Yu Huang ◽  
Wen-Qian Zhang ◽  
Miao Zhao ◽  
Can Zhu ◽  
Jia-Peng He ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Embryo Implantation ◽  
Bioinformatic Analysis ◽  
Differentially Expressed ◽  
Implantation Site ◽  
Rna Seq ◽  
Promoter Regions ◽  
Functional Clustering ◽  
Gene Network Analysis ◽  
Transcriptomic Changes

Background/Aims: The mouse is widely used as an animal model for studying human embryo implantation. However, the mouse is unique in that both ovarian progesterone and estrogen are critical to implantation, whereas in the majority of species (e.g. human and hamster) implantation can occur in the presence of progesterone alone. Methods: In this study, we analyzed embryo-induced transcriptomic changes in the hamster uterus during embryo implantation by using RNA-seq. Differentially expressed genes were characterized by bioinformatic analysis. Results: We identified a total of 781 differentially expressed genes, of which 367 genes were up-regulated and 414 genes were down-regulated at the implantation site compared to the inter-implantation site. Functional clustering and gene network analysis highlighted the cell cycle process in uterus upon embryo implantation. By examining of the promoter regions of differentially expressed genes, we identified 7 causal transcription factors. Additionally, through connectivity map (CMap) analysis, multiple compounds were identified to have potential anti-implantation effects due to their ability to reverse embryo-induced transcriptomic changes. Conclusion: Our study provides a valuable resource for in-depth understanding of the mechanism underlying embryo implantation.

scholarly journals Identification and characterization of genes frequently responsive to Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae infections in rice

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Weiwen Kong ◽  
Li Ding ◽  
Xue Xia
Keyword(s):  
Disease Resistance ◽  
Magnaporthe Oryzae ◽  
Enrichment Analysis ◽  
Defense Responses ◽  
Resistance Mechanisms ◽  
Xanthomonas Oryzae ◽  
Transcriptional Reprogramming ◽  
Go Enrichment ◽  
Phenylpropanoid Biosynthesis ◽  
Rice Disease

Abstract Background Disease resistance is an important factor that impacts rice production. However, the mechanisms underlying rice disease resistance remain to be elucidated. Results Here, we show that a robust set of genes has been defined in rice response to the infections of Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae (Mor). We conducted a comprehensive analysis of the available microarray data from a variety of rice samples with inoculation of Xoo and Mor. A set of 12,932 genes was identified to be regulated by Xoo and another set of 2709 Mor-regulated genes was determined. GO enrichment analysis of the regulated genes by Xoo or Mor suggested mitochondrion may be an arena for the up-regulated genes and chloroplast be another for the down-regulated genes by Xoo or Mor. Cytokinin-related processes were most frequently repressed by Xoo, while processes relevant to jasmonic acid and abscisic acid were most frequently activated by Xoo and Mor. Among genes responsive to Xoo and Mor, defense responses and diverse signaling pathways were the most frequently enriched resistance mechanisms. InterPro annotation showed the zinc finger domain family, WRKY proteins, and Myb domain proteins were the most significant transcription factors regulated by Xoo and Mor. KEGG analysis demonstrated pathways including ‘phenylpropanoid biosynthesis’, ‘biosynthesis of antibiotics’, ‘phenylalanine metabolism’, and ‘biosynthesis of secondary metabolites’ were most frequently triggered by Xoo and Mor, whereas ‘circadian rhythm-plant’ was the most frequent pathway repressed by Xoo and Mor. Conclusions The genes identified here represent a robust set of genes responsive to the infections of Xoo and Mor, which provides an overview of transcriptional reprogramming during rice defense against Xoo and Mor infections. Our study would be helpful in understanding the mechanisms of rice disease resistance.

scholarly journals Transcriptome analysis reveals the roles of stem nodes in cadmium transport to rice grain

2019 ◽  
Author(s):  
Ailing Liu ◽  
Zhibo Zhou ◽  
Yake Yi ◽  
Guanghui Chen
Keyword(s):  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Critical Role ◽  
Differentially Expressed ◽  
Rice Grain ◽  
Rna Seq ◽  
Cd Stress ◽  
Cd Accumulation ◽  
Cadmium Transport ◽  
Central Organ

Abstract Background: Node is the central organ of xylem to phloem transfer of nutrients and ions in plants. Cadmium (Cd)-induced crop pollution threatens food safety. Breeding cultivar with low Cd accumulation is a chance to resolve this universal problem. This study was performed to identify tissue specific genes involved in Cd accumulation in different rice stem nodes. Panicle node and the first node under panicle (node I) were sampled in two rice cultivars: Xiangwanxian No. 12 with low Cd accumulation and Yuzhenxiang with high Cd accumulation in the grains. RNA-seq analysis was performed to identify differentially expressed genes (DEGs) and microRNAs. Results: Xiangwanxian No. 12 had lower Cd concentration in panicle node, node I and grain compared with Yuzhenxiang , and node Ⅰ had the highest Cd concentration in the two cultivars. RNA seq analysis identified 4,535 differentially expressed genes and 70 miRNAs between the two cultivars. Most genes ( OsIRT1 , OsNramp5, OsVIT2 , OsNRT1.5A, and OsABCC1 ) related to the “transporter activity” blocked the transport of Cd up to panicle and accumulation in grains of low Cd-accumulative cultivar. Among the genes related to “response to stimulus”, we identified OsHSP70 and OsHSFA2d/B2c in “X”, but not in “y”, were all down-regulated by Cd stimulus. The up-regulation of miRNAs ( osa-miR528 and osa-miR408 ) played a potent role in lowering Cd accumulation via down regulation of genes, such as bZIP , ERF , MYB , SnRK1 and HSPs in Xiangwanxian No. 12 cultivar. Conclusions: Both panicle node and node I of Xiangwanxian No. 12 played a key role in blocking the upward transportation of Cd, while node I played a critical role in Yuzhenxiang . Distinct expression patterns of various transporter genes such as OsNRT1.5A, OsNramp5, OsIRT1, OsVIT2 and OsABCC1 resulted in differential Cd accumulation in different nodes. Likewise, distinct expression patterns of these transporter genes are likely responsible for the low Cd accumulation in Xiangwanxian No. 12 cultivar . MiRNAs drove multiple transcription factors, such as OsbZIPs, OsERFs, OsMYBs , to play a role in stress response, which contribute to the response to Cd stress in rice.

scholarly journals BcSas2-Mediated Histone H4K16 Acetylation Is Critical for Virulence and Oxidative Stress Response of Botrytis cinerea

2020 ◽  
Vol 33 (10) ◽  
pp. 1242-1251
Author(s):  
Guangyuan Wang ◽  
Limin Song ◽  
Tingting Bai ◽  
Wenxing Liang
Keyword(s):  
Oxidative Stress ◽  
Botrytis Cinerea ◽  
Target Genes ◽  
Histone Acetyltransferase ◽  
Critical Role ◽  
Rna Seq ◽  
Histone H4 ◽  
Promoter Regions ◽  
Worldwide Distribution ◽  
H4k16 Acetylation

Histone acetyltransferase plays a critical role in transcriptional regulation by increasing accessibility of target genes to transcriptional activators. Botrytis cinerea is an important necrotrophic fungal pathogen with worldwide distribution and a very wide host range, but little is known of how the fungus regulates the transition from saprophytic growth to infectious growth. Here, the function of BcSas2, a histone acetyltransferase of B. cinerea, was investigated. Deletion of the BcSAS2 gene resulted in significantly reduced acetylation levels of histone H4, particularly of H4K16ac. The deletion mutant ΔBcSas2.1 was not only less pathogenic but also more sensitive to oxidative stress than the wild-type strain. RNA-Seq analysis revealed that a total of 13 B. cinerea genes associated with pathogenicity were down-regulated in the ΔBcSas2.1 mutant. Independent knockouts of two of these genes, BcXYGA (xyloglucanase) and BcCAT (catalase), led to dramatically decreased virulence and hypersensitivity to oxidative stress, respectively. Chromatin immunoprecipitation followed by quantitative PCR confirmed that BcSas2 bound directly to the promoter regions of both these pathogenicity-related genes. These observations indicated that BcSas2 regulated the transcription of pathogenicity-related genes by controlling the acetylation level of H4K16, thereby affecting the virulence and oxidative sensitivity of B. cinerea.

Characterization of the Short RNA Transcriptome of the Anucleate Platelet

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 4990-4990
Author(s):  
Eric R. Londin ◽  
Phillipe Loher ◽  
Leonard C. Edelstein ◽  
Kathy Delgrosso ◽  
Paolo M. Fortina ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Conflicts Of Interest ◽  
Critical Role ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Ensembl Database ◽  
Protein Coding ◽  
Repeat Elements ◽  
Short Rnas ◽  
Genomic Locations

Abstract The anucleate platelets play a critical role in the formation of thrombi and prevention of bleeding. In recent years, next-generation RNA sequencing (RNA-seq) has proven very useful in shedding light on the specifics of the platelet transcriptome. For example, RNA-seq of the long RNAs in platelets has revealed many non-coding RNAs (ncRNAs) as well as a diverse set of protein-coding genes whose mRNAs are highly correlated amongst individuals but only weakly linked to the currently available platelet proteome. By comparison, the short RNA transcriptome has not been as thoroughly characterized. As a matter of fact, these studies have so far focused on the 100’s of microRNAs (miRNAs) that are present in platelets leaving large swaths of the short RNA-ome uncharacterized. To gauge the complexity of the platelet short RNA-ome we performed short RNA-seq of leukocyte-depleted platelets from 10 healthy males (5 white and 5 black). The sequencing was done on the SOLiD 5500 XL platform and generated over 1.5 billion sequenced reads. To comprehensively characterize the complete short RNA-ome we only considered sequence reads that mapped on the genome without any mismatches but allowed a read to map to as many as 10,000 locations within the genome. This approach gave us the ability to simultaneously examine both the uniquely-present and the repeat-derived expressed elements of the genome. Using this approach, we were able to map ~50% of the sequenced reads. We found that for ~55% of the mapped reads their sequences are present at multiple genomic locations whereas the remaining ~45% originated from unique locations. Of the RNAs with unique genomic origins: ~50% correspond to miRNAs (with miR-223-3p being the most abundant miRNA across all 10 individuals), ~20% originate from various classes of repeat elements, and, the remaining 30% correspond to non-annotated regions of the genome that were non-annotated a of Release 75 of the ENSEMBL database. By comparison, of the RNAs with ambiguous genomic origins: ~20% belong to miRNAs (with miR-103a-3p, a miRNA present in two locations in the genome, being the most abundant miRNA across all 10 individuals) and ~60% correspond to various classes of repeat elements (with members of the HY4 scRNA ncRNAs accounting for nearly a third of all sequence reads). These findings make it evident that the platelet transcriptome has a considerable richness in short RNAs that arise from repetitive elements. To further characterize those RNAs that map to regions of the genome that are not currently annotated, we considered the possibility that they may be novel miRNAs. Using the miRDeep2 algorithm, we sought novel miRNAs among the uncharacterized transcripts and identified 47 of them; the sequences for 18 of these 47 appear at multiple genomic locations in analogy to miR-103/107, miR-19a/19b, etc. Lastly, as our ten samples represented two races, we hypothesized that a subset of the identified sequences would be differentially expressed between the two groups. Using DESeq2, we identified over 157 sequences to be differentially expressed. The most highly differentially expressed sequences corresponded to a miRNA and a repeat element. In summary, our RNA-seq analyses have revealed a very diverse spectrum of platelet short RNAs that transcends the miRNA category. Indeed, we find that short transcripts that have their source in genomic loci that have not been previously discussed or analyzed in the platelet context represent a very significant portion of all short RNAs in platelets. This in turn highlights an unanticipated richness, and presumably commensurate complexity, for the platelet transcriptome. While the role of these novel non-protein coding short RNAs is currently unknown it is expected that at least some of them may be of functional significance. Consequently, they could contribute to processes beyond thrombosis and hemostasis and may permit a better understanding of the molecular mechanisms that regulate platelet physiology. Disclosures No relevant conflicts of interest to declare.

scholarly journals Comparative Analysis of Transcriptome and sRNAs Expression Patterns in the Brachypodium distachyon— Magnaporthe oryzae Pathosystems

2021 ◽  
Vol 22 (2) ◽  
pp. 650
Author(s):  
Silvia Zanini ◽  
Ena Šečić ◽  
Tobias Busche ◽  
Matteo Galli ◽  
Ying Zheng ◽  
...  
Keyword(s):  
Magnaporthe Oryzae ◽  
Brachypodium Distachyon ◽  
Expression Patterns ◽  
Critical Role ◽  
Differentially Expressed ◽  
Post Inoculation ◽  
Plant Host ◽  
Fungal Cell ◽  
Fungal Virulence ◽  
Leaves And Roots

The hemibiotrophic fungus Magnaporthe oryzae (Mo) is the causative agent of rice blast and can infect aerial and root tissues of a variety of Poaceae, including the model Brachypodium distachyon (Bd). To gain insight in gene regulation processes occurring at early disease stages, we comparatively analyzed fungal and plant mRNA and sRNA expression in leaves and roots. A total of 310 Mo genes were detected consistently and differentially expressed in both leaves and roots. Contrary to Mo, only minor overlaps were observed in plant differentially expressed genes (DEGs), with 233 Bd-DEGs in infected leaves at 2 days post inoculation (DPI), compared to 4978 at 4 DPI, and 138 in infected roots. sRNA sequencing revealed a broad spectrum of Mo-sRNAs that accumulated in infected tissues, including candidates predicted to target Bd mRNAs. Conversely, we identified a subset of potential Bd-sRNAs directed against fungal cell wall components, virulence genes and transcription factors. We also show a requirement of operable RNAi genes from the DICER-like (DCL) and ARGONAUTE (AGO) families for fungal virulence. Overall, our work elucidates the extensive reprogramming of transcriptomes and sRNAs in both plant host (Bd) and fungal pathogen (Mo), further corroborating the critical role played by sRNA species in the establishment of the interaction and its outcome.

scholarly journals Proteomic analysis of rice leaves following treatment of Xanthomonas oryzae pv. oryzae secreted cell wall degrading enzyme

2021 ◽  
Author(s):  
Anirudh Kumar ◽  
Kamal Kumar Malukani ◽  
Ramya Pamidimukkala ◽  
Hitendra K. Patel ◽  
Ramesh V Sonti
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Redox Regulation ◽  
Plant Cell Wall ◽  
Regulatory Elements ◽  
Xanthomonas Oryzae ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Proteomics Data ◽  
Cell Wall Degrading Enzymes

Bacterial Blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases in various rice cultivating countries. Xoo secretes a mixture of plant cell wall degrading enzymes (CWDEs) such as cellulases, lipases, xylanases, and proteases to degrade different components of the plant cell wall. LipA; a lipase/esterase, is one such Xoo secreted CWDE and is an important virulence factor of Xoo. Treatment of rice tissue with purified LipA induces immune responses. In this study, a LC-MS based proteomics study was performed to identify the differentially expressed proteins (DEPs) in rice following LipA treatment. A total of 212 proteins were identified in control and 201 proteins in LipA treated samples. There were 151 proteins common between control and treatment. Fold change analysis of these common proteins through SIEVE identified 26 upregulated and 49 downregulated proteins by at least ≥1.5 fold in the LipA treated sample. Pathway analysis indicated that many proteins related to redox regulation, photosynthesis, and translation are differentially expressed after LipA treatment. We also observed that some of the differentially expressed proteins contain translation regulatory elements that may regulate translation after LipA treatment. The comparison of proteomics data with previously performed transcriptome analysis indicated that different sets of genes and pathways are altered in both the analyses.

scholarly journals Folding and Persistence Time of Intramolecular G-Quadruplexes Transiently Embedded in a DNA duplex

2021 ◽  
Author(s):  
Phong Lan Thao Tran ◽  
Martin Rieu ◽  
Samar Hodeib ◽  
Alexandra Joubert ◽  
Jimmy Ouellet ◽  
...  
Keyword(s):  
Single Molecule ◽  
Critical Role ◽  
Genetic Regulation ◽  
Regulatory Elements ◽  
Promoter Regions ◽  
Folding Rate ◽  
Persistence Time ◽  
G4 Dna

ABSTRACTG-quadruplex (G4) DNA structures have emerged as important regulatory elements during DNA replication, transcription or repair. While many in-vitro studies have focused on the kinetics of G4 formation within DNA single-strands, G4 are found in-vivo in double-stranded DNA regions, where their formation is challenged by pairing between the two complementary strands. Since the energy of hybridization of Watson-Crick structures dominates the energy of G4 folding, this competition should play a critical role on the persistence of G4 in vivo. To address this issue, we designed a single molecule assay allowing measuring G4 folding and persistence while the structure is periodically challenged by the complementary strand. We quantified both the folding rate and the persistence time of biologically relevant G4 structures and showed that the dynamics of G4 formation depends strongly on the genomic location. G4 are found much more stable in promoter regions and replication origins than in telomeric regions. In addition, we characterized how G4 dynamics was affected by G4 ligands and showed that both folding rate and persistence increased. Our assay opens new perspectives for the measurement of G4 dynamics, which is critical to understand their role in genetic regulation.

scholarly journals Transcriptome analysis reveals the roles of stem nodes in cadmium transport to rice grain

2019 ◽  
Author(s):  
Ailing Liu ◽  
Zhibo Zhou ◽  
Yake Yi ◽  
Guanghui Chen
Keyword(s):  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Critical Role ◽  
Differentially Expressed ◽  
Rice Grain ◽  
Rna Seq ◽  
Cd Accumulation ◽  
Cadmium Transport ◽  
Upward Transport ◽  
Central Organ

Abstract Background: Node is the central organ of xylem to phloem transfer of nutrients and ions in plants. Cadmium (Cd)-induced crop pollution threatens food safety. Breeding cultivar with low Cd accumulation is a chance to resolve this universal problem. This study was performed to identify tissue specific genes involved in Cd accumulation in different rice stem nodes. Panicle node and the first node under panicle (node I) were sampled in two rice cultivars: Xiangwanxian No. 12 with low Cd accumulation and Yuzhenxiang with high Cd accumulation in the grains. RNA-seq analysis was performed to identify differentially expressed genes (DEGs) and microRNAs. Results: Xiangwanxian No. 12 had lower Cd concentration in panicle node, node I and grain compared with Yuzhenxiang, and node Ⅰ had the highest Cd concentration in the two cultivars. RNA seq analysis identified 4,535 differentially expressed genes and 70 miRNAs between the two cultivars. Most genes (OsIRT1, OsNramp5, OsVIT2, OsNRT1.5A, and OsABCC1) related to the “transporter activity” play roles in blocking the upward transport of Cd in the low Cd-accumulative cultivar. Among the genes related to “response to stimulus”, we identified OsHSP70 and OsHSFA2d/B2c in Xiangwanxian No. 12, but not in Yuzhenxiang, were all down-regulated by Cd stimulus. The up-regulation of miRNAs (osa-miR528 and osa-miR408) played a potent role in lowering Cd accumulation via down regulation of genes, such as bZIP, ERF, MYB, SnRK1 and HSPs in Xiangwanxian No. 12 cultivar. Conclusions: Both panicle node and node I of Xiangwanxian No. 12 played a key role in blocking the upward transportation of Cd, while node I played a critical role in Yuzhenxiang. Distinct expression patterns of various transporter genes such as OsNRT1.5A, OsNramp5, OsIRT1, OsVIT2 and OsABCC1 resulted in differential Cd accumulation in different nodes. Likewise, distinct expression patterns of these transporter genes are likely responsible for the low Cd accumulation in Xiangwanxian No. 12 cultivar. MiRNAs drove multiple transcription factors, such as OsbZIPs, OsERFs, OsMYBs, to play a role in stress response, which contribute to the response to Cd stress in rice.

cDNA cloning and promoter analysis of rat caspase-9

2001 ◽  
Vol 360 (1) ◽  
pp. 49-56 ◽  
Author(s):  
Junichiro NISHIYAMA ◽  
Xiaolan YI ◽  
Manjeri A. VENKATACHALAM ◽  
Zheng DONG
Keyword(s):  
Critical Role ◽  
Hypoxia Inducible Factor ◽  
Gene Promoter ◽  
Regulatory Elements ◽  
Mitochondrial Pathway ◽  
Genomic Segment ◽  
Caspase 9 ◽  
Promoter Regions ◽  
Genomic Walking ◽  
Flanking Regions

Caspase-9 is the apex caspase of the mitochondrial pathway of apoptosis, which plays a critical role in apoptotic initiation and progression. However, gene regulation of caspase-9 is largely unknown. This is in part due to the lack of information on the gene promoter. Here we have cloned the full-length cDNA of rat caspase-9 and have isolated promoter regions of this gene. The rat caspase-9 cDNA of 2058bp predicts a protein of 454 amino acids, which contains a caspase-recruitment domain (‘CARD’) at the N-terminus and enzymic domains at the C-terminus. The enzyme's active site, with a characteristic motif of QACGG, was also identified. Overall, rat and human caspase-9 have 71% identity. With the cDNA sequence, we subsequently isolated the proximal 5′-flanking regions of rat caspase-9 by the procedure of genomic walking. The 2270bp genomic segment is ‘TATA-less’, but contains several GC boxes. Elements binding known transcription factors such as Sp-1, Pit-1, CCAAT-enhancer-binding protein (C/EBP), glucocorticoid receptor and hypoxia-inducible factor 1 (HIF-1) were also identified. When cloned into reporter gene vectors, the genomic segment showed significant promoter activity, indicating that the 5′-flanking regions isolated by genomic walking contain the gene promoter of rat caspase-9. Of significance is that the cloned promoter segments were activated by severe hypoxia, conditions inducing caspase-9 transcription. Thus, the genomic sequences reported here contain not only the basal promoter of rat caspase-9 but also regulatory elements responsive to pathophysiological stimuli including hypoxia.

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