Transcriptome profiling of soybean root tips

2011 ◽  
Vol 38 (6) ◽  
pp. 451 ◽  
Author(s):  
Farzad Haerizadeh ◽  
Mohan B. Singh ◽  
Prem L. Bhalla
Keyword(s):  
Gene Expression ◽  
Expression Profile ◽  
Target Genes ◽  
Animal Feed ◽  
Positive Impact ◽  
Root Apical Meristem ◽  
Root Tip ◽  
Symbiotic Association ◽  
Root Tips ◽  
Soybean Root

Soybean (Glycine max L.), a major legume crop, is important to human nutrition and is a source of animal feed. Similar to many legumes, a key feature of the soybean is its symbiotic association with soil bacteria that fix atmospheric nitrogen. However, knowledge of the gene expression of its root system, particularly the root meristematic region, is limited. Here, we have addressed this by investigating the gene expression profile of the soybean root tip, using soybean Affymetrix chips containing 37 500 probe sets (Affymetrix Inc.) and have compared this expression profile with that of the nonmeristematic tissue. We identified a total of 5012 upregulated and 4136 downregulated genes in the soybean root tip. Among the upregulated genes, 559 showed strong preferential expression in the root tip, indicating that they are likely to be associated with root apical meristem specificity and root tip function. Genes involved in membrane transport, defence signalling and metabolism were upregulated in the soybean root tip. Further, our data provide a resource of novel target genes for further studies involving root development and biology, and will possibly have a positive impact on future crop breeding.

scholarly journals Effect of destrin mutations on the gene expression profile in vivo

2008 ◽  
Vol 34 (1) ◽  
pp. 9-21 ◽  
Author(s):  
Angela M. Verdoni ◽  
Natsuyo Aoyama ◽  
Akihiro Ikeda ◽  
Sakae Ikeda
Keyword(s):  
Gene Expression ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Target Genes ◽  
Actin Dynamics ◽  
In Vivo Model ◽  
Strong Impact ◽  
Filamentous Actin ◽  
Control Of Gene Expression

Remodeling of the actin cytoskeleton through actin dynamics (assembly and disassembly of filamentous actin) is known to be essential for numerous basic biological processes. In addition, recent studies have provided evidence that actin dynamics participate in the control of gene expression. A spontaneous mouse mutant, corneal disease 1 ( corn1), is deficient for a regulator of actin dynamics, destrin (DSTN, also known as ADF), which causes epithelial hyperproliferation and neovascularization in the cornea. Dstn corn1 mice exhibit an actin dynamics defect in the corneal epithelial cells, offering an in vivo model to investigate cellular mechanisms affected by the Dstn mutation and resultant actin dynamics abnormalities. To examine the effect of the Dstn corn1 mutation on the gene expression profile, we performed a microarray analysis using the cornea from Dstn corn1 and wild-type mice. A dramatic alteration of the gene expression profile was observed in the Dstn corn1 cornea, with 1,226 annotated genes differentially expressed. Functional annotation of these genes revealed that the most significantly enriched functional categories are associated with actin and/or cytoskeleton. Among genes that belong to these categories, a considerable number of serum response factor target genes were found, indicating the possible existence of an actin-SRF pathway of transcriptional regulation in vivo. A comparative study using an allelic mutant strain with milder corneal phenotypes suggested that the level of filamentous actin may correlate with the level of gene expression changes. Our study shows that Dstn mutations and resultant actin dynamics abnormalities have a strong impact on the gene expression profile in vivo.

scholarly journals Supra-physiological levels of Gibberellins/DELLAs alter the patterning, morphology and abundance of root hairs in root tips of A. thaliana seedlings

2021 ◽  
Author(s):  
Iva McCarthy-Suarez
Keyword(s):  
Gene Expression ◽  
Cell Fate ◽  
Epidermal Cell ◽  
Root Hair ◽  
Root Hairs ◽  
Root Tip ◽  
Spatial Patterning ◽  
Root Tips ◽  
Root Epidermis

In spite of the known role of gibberellins (GAs), and of their antagonistic proteins, the DELLAs, in leaf hair production, no investigations, however, have assessed their hypothetical function in the production of root hairs. To this aim, the effects of supra-physiological levels of GAs/DELLAs on the spatial patterning of gene expression of the root hair (CPC) and root non-hair (GL2, EGL3 and WER) epidermal cell fate markers, as well as on the distribution, morphology and abundance of root hairs, were studied in root tips of 5-day-old A. thaliana seedlings. Results showed that excessive levels of GAs/DELLAs impaired the spatial patterning of gene expression of the root hair/non-hair epidermal cell fate markers, as well as the arrangement, shape and frequency of root hairs, giving rise to ectopic hairs and ectopic non-hairs, two-haired cells, two-tipped hairs, branched hairs, longer and denser hairs near the root tip under excessive DELLAs, and shorter and scarcer hairs near the root tip under excessive GAs. However, when the gai-1 (GA-insensitive-1) DELLA mutant protein was specifically over-expressed at the root epidermis, no changes in the patterning or abundance of root hairs occurred. Thus, these results suggest that, in seedlings of A. thaliana, the GAs/DELLAs might have a role in regulating the patterning, morphology and abundance of root hairs by acting from the sub-epidermal tissues of the root.

scholarly journals Impact of the Phytoestrogen Content of Laboratory Animal Feed on the Gene Expression Profile of the Reproductive System in the Immature Female Rat

2004 ◽  
Vol 112 (15) ◽  
pp. 1519-1526 ◽  
Author(s):  
Jorge M. Naciff ◽  
Gary J. Overmann ◽  
Suzanne M. Torontali ◽  
Gregory J. Carr ◽  
Jay P. Tiesman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Reproductive System ◽  
Laboratory Animal ◽  
Animal Feed ◽  
Female Rat ◽  
Immature Female

scholarly journals High Levels of Prebiotic Resistant Starch in Diet Modulate a Specific Pattern of miRNAs Expression Profile Associated to a Better Overall Survival in Pancreatic Cancer

Biomolecules ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 26
Author(s):  
Nadia Trivieri ◽  
Concetta Panebianco ◽  
Annacandida Villani ◽  
Riccardo Pracella ◽  
Tiziana Pia Latiano ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pancreatic Cancer ◽  
Overall Survival ◽  
Tumor Growth ◽  
Expression Profile ◽  
Resistant Starch ◽  
Target Genes ◽  
Human Pancreatic Cancer ◽  
Integrative Approach ◽  
The Impact

Dietary patterns are well known risk factors involved in cancer initiation, progression, and in cancer protection. Previous in vitro and in vivo studies underline the link between a diet rich in resistant starch (RS) and slowing of tumor growth and gene expression in pancreatic cancer xenograft mice. The aim of this study was to investigate the impact of a diet rich in resistant starch on miRNAs and miRNAs-target genes expression profile and on biological processes and pathways, that play a critical role in pancreatic tumors of xenografted mice. miRNA expression profiles on tumor tissues displayed 19 miRNAs as dysregulated in mice fed with RS diet as compared to those fed with control diet and differentially expressed miRNA-target genes were predicted by integrating (our data) with a public human pancreatic cancer gene expression dataset (GSE16515). Functional and pathway enrichment analyses unveiled that miRNAs involved in RS diet are critical regulators of genes that control tumor growth and cell migration and metastasis, inflammatory response, and, as expected, synthesis of carbohydrate and glucose metabolism disorder. Mostly, overall survival analysis with clinical data from TCGA (n = 175) displayed that almost four miRNAs (miRNA-375, miRNA-148a-3p, miRNA-125a-5p, and miRNA-200a-3p) upregulated in tumors from mice fed with RS were a predictor of good prognosis for pancreatic cancer patients. These findings contribute to the understanding of the potential mechanisms through which resistant starch may affect cancer progression, suggesting also a possible integrative approach for enhancing the efficacy of existing cancer treatments.

scholarly journals Integrated MicroRNA Expression Profile Reveals Dysregulated miR-20a-5p and miR-200a-3p in Liver Fibrosis

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Mu Ye ◽  
Sheng Wang ◽  
Peilong Sun ◽  
Jingbo Qie
Keyword(s):  
Gene Expression ◽  
Liver Fibrosis ◽  
Expression Profile ◽  
Target Genes ◽  
Mirna Gene ◽  
Ppi Network ◽  
Hub Genes ◽  
Fibrotic Liver ◽  
Kegg Analysis ◽  
Liver Fibrogenesis

MicroRNAs (miRNAs) have been demonstrated to involve in liver fibrogenesis. However, the miRNA-gene regulation in liver fibrosis is still unclear. Herein, the miRNA expression profile GSE40744 was obtained to analyze the dysregulated miRNAs between liver fibrosis and normal samples. Then, we predicted the target genes of screened miRNAs by miRTarBase, followed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Then, the protein-protein interaction (PPI) network was constructed to identify the functional miRNA-gene regulatory modules. Furthermore, we verified the hub gene expression using the gene expression profile GSE14323. Finally, 89 DEMs were identified in fibrotic liver samples compared to normal liver samples. The top 3 upregulated DEMs (miR-200b-3p, miR-200a-3p, and miR-182-5p) and downregulated DEMs (miR-20a-5p, miR-194-3p, and miR-148a-3p) were further studied. 516 and 1416 target genes were predicted, respectively. KEGG analysis demonstrated that the predicted genes were enriched in the p53 signaling pathway and hepatitis B, etc. Through constructing a PPI network, the genes with the highest connectivity were identified as hub genes. Of note, most of the hub genes were potentially targeted by miR-20a-5p and miR-200a-3p. Based on the data from GSE14323, the expression of EGFR, STAT3, CTNNB1, and TP53 targeted by miR-200a-3p was significantly downregulated in fibrotic liver samples. Oppositely, the expression of PTEN, MYC, MAPK1, UBC, and CCND1 potentially targeted by miR-20a-5p was significantly upregulated. In conclusion, it is demonstrated that miR-20a-5p and miR-200a-3p were identified as the novel liver fibrosis-associated miRNAs, which may play critical roles in liver fibrogenesis.

Identification of target genes using gene expression profile of granulocytes from patients with chronic myeloid leukemia treated with tyrosine kinase inhibitors

2014 ◽  
Vol 55 (8) ◽  
pp. 1861-1869 ◽  
Author(s):  
Cintia do Couto Mascarenhas ◽  
Anderson Ferreira da Cunha ◽  
Ana Flávia Brugnerotto ◽  
Sheley Gambero ◽  
Maria Helena de Almeida ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chronic Myeloid Leukemia ◽  
Tyrosine Kinase ◽  
Tyrosine Kinase Inhibitors ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Myeloid Leukemia ◽  
Target Genes ◽  
Kinase Inhibitors

scholarly journals Early Gene Expression Response of Barley Root Tip to Toxic Concentrations of Cadmium

2021 ◽  
Author(s):  
Ľubica Liptáková ◽  
Loriana Demecsová ◽  
Katarína Valentovičová ◽  
Veronika Zelinová ◽  
Ladislav Tamás
Keyword(s):  
Gene Expression ◽  
Barley Root ◽  
Early Gene ◽  
Root Tip ◽  
Auxin Signaling ◽  
Allene Oxide ◽  
Cd Stress ◽  
Root Tips ◽  
Gene Expression Response ◽  
Early Activation

Abstract Even a short, 30 min, Cd treatment of roots induced a considerable alteration in gene expression in the barley root tips within an hour after the treatments. The very early activation of MYB1 transcription factor expression is partially regulated by auxin signaling in mildly stressed seedlings. An increase in allene oxide cyclase and NADPH oxidase expression was a distinguishing feature of root tips response to mild Cd stress and their expression is activated via IAA signaling. Meanwhile, early changes in the level of dehydrin transcripts were detected in moderately and severely stressed root tips, and their induction is related to altered ROS homeostasis in cells. The early activation of glutathione peroxidase expression by mild Cd stress indicates the involvement of IAA in the signaling process. In contrast, early APX expression was induced only with Cd treatment causing severe stress and ROS play central roles in its induction. The expression of cysteine protease was activated similarly in both mildly and severely Cd-stressed roots; consequently, both increased IAA and ROS levels take part in the regulation of C-Prot expression. The Cd-evoked accumulation of BAX Inhibitor-1 mRNA was characteristic for moderately and severely stressed roots. Whereas decreased IAA level did not affect its expression, rotenone-mediated ROS depletion markedly reduced the Cd-induced expression of BAX Inhibitor-1. An early increase of alternative oxidase levels in the root tip cells indicated that the reduction of mitochondrial superoxide generation is an important component of barley root response to severe Cd stress.

scholarly journals KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors

2019 ◽  
Vol 48 (D1) ◽  
pp. D93-D100 ◽  
Author(s):  
Chenchen Feng ◽  
Chao Song ◽  
Yuejuan Liu ◽  
Fengcui Qian ◽  
Yu Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Target Genes ◽  
Human Gene ◽  
Biological Effects ◽  
Tissue Cell ◽  
Human Gene Expression ◽  
Network Analyses

Abstract Transcription factors (TFs) and their target genes have important functions in human diseases and biological processes. Gene expression profile analysis before and after knockdown or knockout is one of the most important strategies for obtaining target genes of TFs and exploring TF functions. Human gene expression profile datasets with TF knockdown and knockout are accumulating rapidly. Based on the urgent need to comprehensively and effectively collect and process these data, we developed KnockTF (http://www.licpathway.net/KnockTF/index.html), a comprehensive human gene expression profile database of TF knockdown and knockout. KnockTF provides a number of resources for human gene expression profile datasets associated with TF knockdown and knockout and annotates TFs and their target genes in a tissue/cell type-specific manner. The current version of KnockTF has 570 manually curated RNA-seq and microarray datasets associated with 308 TFs disrupted by different knockdown and knockout techniques and across multiple tissue/cell types. KnockTF collects upstream pathway information of TFs and functional annotation results of downstream target genes. It provides details about TFs binding to promoters, super-enhancers and typical enhancers of target genes. KnockTF constructs a TF-differentially expressed gene network and performs network analyses for genes of interest. KnockTF will help elucidate TF-related functions and potential biological effects.

Development of an approach to knockdown of DUX4 gene by siRNA in myoblasts derived from patients with FSHD

2021 ◽  
pp. 47-56
Author(s):  
И. А. Кривошеева ◽  
Ю. В. Вяхирева ◽  
В. Ю. Табаков ◽  
М. Ю. Скоблов
Keyword(s):  
Gene Expression ◽  
Gene Therapy ◽  
Expression Profile ◽  
Target Genes ◽  
Ectopic Expression ◽  
Muscle Cells ◽  
Hereditary Disease ◽  
Facioscapulohumeral Dystrophy ◽  
Safe Method ◽  
The Future

Миодистрофия Ландузи-Дежерина (МЛД) - распространённое наследственное заболевание, вызываемое эктопической экспрессией гена DUX4 в мышечных клетках. Метод подавления экспрессии генов при помощи siРНК зарекомендовал себя как эффективный и безопасный способ генной терапии без вмешательства непосредственно в геном. В данной работе мы продемонстрировали возможность трансфекции миобластов человека целевыми siРНК без ущерба жизнеспособности и дальнейшей дифференцировке этих клеток в миотубы. Также мы показали различия в профиле экспрессии генов-мишеней DUX4 между миобластами, полученными от здоровых людей и от пациентов с МЛД. В дальнейшем эти данные могут помочь при разработке эффективных и специфичных siРНК для терапии МЛД. Facioscapulohumeral dystrophy (FSHD) is a common hereditary disease caused by ectopic expression of the DUX4 gene in muscle cells. The method of suppressing gene expression using siRNA has been shown to be an effective and safe method of gene therapy without interfering directly with the genome. In this work, we demonstrated the possibility of transfecting human myoblasts with targeted siRNAs without compromising the viability and further differentiation of these cells into myotubes. We also showed differences in the expression profile of DUX4 target genes between healthy and patient-derived myoblasts. In the future, these data can be used to develop effective and specific siRNAs for the treatment of FSHD.

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