scholarly journals Transcriptome profiling of developing leaf and shoot apices to reveal the molecular mechanism and co-expression genes responsible for the wheat heading date

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yuxin Yang ◽  
Xueying Zhang ◽  
Lifen Wu ◽  
Lichao Zhang ◽  
Guoxiang Liu ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Flowering Time ◽  
Heading Date ◽  
Yield Component ◽  
Potential Candidate ◽  
Rna Seq ◽  
Nucleotide Synthesis ◽  
Light Reaction ◽  
Grain Number Per Spike ◽  
Double Ridge

Abstract Background Wheat is one of the most widely planted crops worldwide. The heading date is important for wheat environmental adaptability, as it not only controls flowering time but also determines the yield component in terms of grain number per spike. Results In this research, homozygous genotypes with early and late heading dates derived from backcrossed progeny were selected to conduct RNA-Seq analysis at the double ridge stage (W2.0) and androgynous primordium differentiation stage (W3.5) of the leaf and apical meristem, respectively. In total, 18,352 differentially expressed genes (DEGs) were identified, many of which are strongly associated with wheat heading date genes. Gene Ontology (GO) enrichment analysis revealed that carbohydrate metabolism, trehalose metabolic process, photosynthesis, and light reaction are closely related to the flowering time regulation pathway. Based on MapMan metabolic analysis, the DEGs are mainly involved in the light reaction, hormone signaling, lipid metabolism, secondary metabolism, and nucleotide synthesis. In addition, 1,225 DEGs were annotated to 45 transcription factor gene families, including LFY, SBP, and MADS-box transcription factors closely related to flowering time. Weighted gene co-expression network analysis (WGCNA) showed that 16, 336, 446, and 124 DEGs have biological connections with Vrn1-5 A, Vrn3-7B, Ppd-1D, and WSOC1, respectively. Furthermore, TraesCS2D02G181400 encodes a MADS-MIKC transcription factor and is co-expressed with Vrn1-5 A, which indicates that this gene may be related to flowering time. Conclusions RNA-Seq analysis provided transcriptome data for the wheat heading date at key flower development stages of double ridge (W2.0) and androgynous primordium differentiation (W3.5). Based on the DEGs identified, co-expression networks of key flowering time genes in Vrn1-5 A, Vrn3-7B, WSOC1, and Ppd-1D were established. Moreover, we discovered a potential candidate flowering time gene, TraesCS2D02G181400. Taken together, these results serve as a foundation for further study on the regulatory mechanism of the wheat heading date.

scholarly journals Transcriptome profiling of developing leaf and shoot apices to reveal the molecular mechanism and co-expression genes responsible for the wheat heading date

2020 ◽  
Author(s):  
Yuxin Yang ◽  
Xueying Zhang ◽  
Lifen Wu ◽  
Lichao Zhang ◽  
Guoxiang Liu ◽  
...  
Keyword(s):  
Flowering Time ◽  
Heading Date ◽  
Gene Families ◽  
Yield Component ◽  
Potential Candidate ◽  
Rna Seq ◽  
Nucleotide Synthesis ◽  
Light Reaction ◽  
Grain Number Per Spike ◽  
Double Ridge

Abstract Background: Wheat is one of the most widely planted crops worldwide. The heading date is important for wheat environmental adaptability; it not only controls flowering time but also determines the yield component in terms of the grain number per spike. Results: In this research, homozygous genotypes with early and late heading dates derived from backcrossed progeny were selected to conduct RNA-seq analysis at the double ridge stage (W2.0) and androgynous primordium differentiation stage (W3.5) of the leaf and apical meristem, respectively. In total, 18,352 differentially expressed genes (DEGs) were identified, many of which are strongly associated with the wheat heading date genes. Gene Ontology (GO) enrichment analysis revealed that carbohydrate metabolism, trehalose metabolic process, photosynthesis, and light reaction are closely related to the flowering time regulation pathway. MapMan metabolic analysis showed that the DEGs mainly functioned in light reaction, hormone signaling, lipid metabolism, secondary metabolism, and nucleotide synthesis. In addition, 1,225 DEGs were annotated to 45 transcription factor gene families, including LFY, SBP, and MADS-box transcription factors that closely related to the flowering time. Weighted gene co-expression network analysis (WGCNA) showed that 16, 336, 446, and 124 DEGs had biological connections with Vrn1-5A, Vrn3-7B, Ppd-1D, and WSOC1, respectively. Furthermore, TraesCS2D02G181400 is a MADS-MIKC transcriptional factor that is co-expressed with Vrn1-5A, which indicates this gene is a potential gene related to the flowering timeConclusions: The RNA-seq analysis enriched the transcriptome data of wheat heading date at the key flower development stages of double ridge (W2.0) and androgynous primordium differentiation (W3.5). Based on the DEGs, the co-expression networks of key flowering time genes in Vrn1-5A, Vrn3-7B, WSOC1, and Ppd-1D were established. Moreover, we discovered a potential candidate flowering time gene TraesCS2D02G181400. Taken together, these results serve as a foundation for further study on the regulatory mechanism of wheat heading date.

scholarly journals Transcriptome Profiling of Developing Leaf and Shoot Apices to Reveal the Molecular Mechanism and Coexpression Genes Responsible for the Wheat Heading Date

2020 ◽  
Author(s):  
Yuxin Yang ◽  
Xueying Zhang ◽  
Lichao Zhang ◽  
Guoxiang Liu ◽  
Chuan Xia ◽  
...  
Keyword(s):  
Flowering Time ◽  
Molecular Mechanism ◽  
Expression Patterns ◽  
Heading Date ◽  
Transcriptome Profiling ◽  
Gene Families ◽  
Yield Component ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Grain Number Per Spike

Abstract Background: Wheat is one of the most widely planted crops worldwide. The heading date is important for wheat environmental adaptability; it not only controls flowering time but also determines the yield component in terms of the grain number per spike. Results: In this research, homozygous genotypes with early and late heading dates derived from backcrossed progeny were selected to conduct RNA-seq analysis at the double ridge stage and androgynous primordium differentiation stage of the leaf and apical meristem, respectively. In total, 18,352 differentially expressed genes (DEGs) were identified. Five common GO terms and 214 common metabolic pathways were obtained by MapMan software. In addition, 1,225 DEGs were annotated to 52 transcription factor gene families, and we discovered that most of the LFY, SBP, and MADS-box genes were highly expressed during the apical development of wheat with the early heading date. Additionally, weighted gene coexpression network analysis (WGCNA) found that the DEGs clustered into 17 coexpression modules, and 16, 336, 446, and 124 DEGs had biological connections with Vrn1-5A, Vrn3-7B, Ppd-1D, and WSOC1, respectively. The 16 genes connected with Vrn1-5A were divided into three types of expression patterns. We further identified one important flowering time gene, TraesCS2D02G181400, which is a MADS-MIKC transcriptional factor and has a biological connection with Vrn1-5A. Gene function showed that this gene was differentially expressed at the A2.0 and L3.5 stages between the genotypes with early and late heading.Conclusions: The RNA-seq analysis results in our present research are a valuable bioinformatics resource for further study of the molecular mechanism of the wheat heading date. Overall, our results shed light on the genetic architecture of wheat flowering time.

scholarly journals O-linked N-acetylglucosamine transferase is involved in fine regulation of flowering time in winter wheat

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Min Fan ◽  
Fang Miao ◽  
Haiyan Jia ◽  
Genqiao Li ◽  
Carol Powers ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Flowering Time ◽  
Heading Date ◽  
Wheat Cultivars ◽  
Gene Encoding ◽  
Constitutive Overexpression ◽  
Winter Wheat Cultivars ◽  
Fine Regulation ◽  
Trait Locus ◽  
Glcnac Transferase

AbstractVernalization genes underlying dramatic differences in flowering time between spring wheat and winter wheat have been studied extensively, but little is known about genes that regulate subtler differences in flowering time among winter wheat cultivars, which account for approximately 75% of wheat grown worldwide. Here, we identify a gene encoding anO-linkedN-acetylglucosamine (O-GlcNAc) transferase (OGT) that differentiates heading date between winter wheat cultivars Duster and Billings. We clone thisTaOGT1gene from a quantitative trait locus (QTL) for heading date in a mapping population derived from these two bread wheat cultivars and analyzed in various environments. Transgenic complementation analysis shows that constitutive overexpression ofTaOGT1bfrom Billings accelerates the heading of transgenic Duster plants.TaOGT1 is able to transfer anO-GlcNAc group to wheat proteinTaGRP2. Our findings establish important roles forTaOGT1in winter wheat in adaptation to global warming in the future climate scenarios.

scholarly journals EPEN-30. C11ORF95-RELA FUSION PROTEIN ENGAGES NOVEL GENOMIC LOCI TO DRIVE MURINE EPENDYMOMA GROWTH

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii314-iii314
Author(s):  
Amir Arabzade ◽  
Yanhua Zhao ◽  
Srinidhi Varadharajan ◽  
Hsiao-Chi Chen ◽  
Austin Stuckert ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Molecular Targets ◽  
Lead Target ◽  
Open Chromatin ◽  
Rna Seq ◽  
In Utero Electroporation ◽  
Pathway Activation ◽  
Mouse Cells ◽  
Shed Light

Abstract RATIONALE Over 70% of supratentorial (ST) ependymoma are characterized by an oncogenic fusion between C11ORF95 and RELA. C11ORF95-RELA fusion is frequently the sole genetic driver detected in ST ependymoma, thus ranking this genomic event as a lead target for therapeutic investigation. RELA is a transcription factor (TF) central to mediating NF-kB pathway activation in processes such as inflammation, cellular metabolism, and chemotaxis. HYPOTHESIS: We posited that C11ORF95-RELA acts as an oncogenic TF that aberrantly shapes the tumor epigenome to drive aberrant transcription. Approach: To this end we developed an in utero electroporation (IUE) mouse model of ependymoma to express C11ORF95-RELA during embryonic development. Our IUE approach allowed us to develop C11ORF95-RELA driven tumor models and cell lines. We comprehensively characterized the epigenome and transcriptome of C11ORF95-RELA fusion driven mouse cells by H3K27ac ChIP-seq, ATAC-seq, and RNA-seq. RESULTS This data revealed that: 1) C11ORF95-RELA directly engages ‘open’ chromatin and is enriched at regions with known RELA TF binding sites as well as novel genomic loci/motifs, 2) C11ORF95-RELA preferentially binds to both H3K27ac (active) enhancers and promoters, and 3) Bound C11ORF95-RELA promoter loci are associated with increased transcription of genes shared with human ependymoma. CONCLUSION Our findings shed light on the transcriptional mechanisms of C11ORF95-RELA, and reveal downstream targets that may represent cancer dependency genes and molecular targets.

scholarly journals Identification of Potential Key lncRNAs in the Context of Mouse Myeloid Differentiation by Systematic Transcriptomics Analysis

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 630
Author(s):  
Yongqing Lan ◽  
Meng Li ◽  
Shuangli Mi
Keyword(s):  
Transcription Factor ◽  
Cell Model ◽  
Myeloid Differentiation ◽  
Rna Seq ◽  
Hematopoietic Differentiation ◽  
Granulocytic Differentiation ◽  
Expression Of Genes ◽  
Non Coding Rnas

Hematopoietic differentiation is a well-orchestrated process by many regulators such as transcription factor and long non-coding RNAs (lncRNAs). However, due to the large number of lncRNAs and the difficulty in determining their roles, the study of lncRNAs is a considerable challenge in hematopoietic differentiation. Here, through gene co-expression network analysis over RNA-seq data generated from representative types of mouse myeloid cells, we obtained a catalog of potential key lncRNAs in the context of mouse myeloid differentiation. Then, employing a widely used in vitro cell model, we screened a novel lncRNA, named Gdal1 (Granulocytic differentiation associated lncRNA 1), from this list and demonstrated that Gdal1 was required for granulocytic differentiation. Furthermore, knockdown of Cebpe, a principal transcription factor of granulocytic differentiation regulation, led to down-regulation of Gdal1, but not vice versa. In addition, expression of genes involved in myeloid differentiation and its regulation, such as Cebpa, were influenced in Gdal1 knockdown cells with differentiation blockage. We thus systematically identified myeloid differentiation associated lncRNAs and substantiated the identification by investigation of one of these lncRNAs on cellular phenotype and gene regulation levels. This study promotes our understanding of the regulation of myeloid differentiation and the characterization of roles of lncRNAs in hematopoietic system.

scholarly journals Transcription Factor Co-expression Networks of Adipose RNA-Seq Data Reveal Regulatory Mechanisms of Obesity

2018 ◽  
Vol 19 (4) ◽  
pp. 289-299 ◽  
Author(s):  
Ruta Skinkyte-Juskiene ◽  
Lisette J.A. Kogelman ◽  
Haja N. Kadarmideen
Keyword(s):  
Transcription Factor ◽  
Regulatory Mechanisms ◽  
Rna Seq

scholarly journals Genome-wide RNA-seq analysis indicates that the DAG1 transcription factor promotes hypocotyl elongation acting on ABA, ethylene and auxin signaling

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Riccardo Lorrai ◽  
Francesco Gandolfi ◽  
Alessandra Boccaccini ◽  
Veronica Ruta ◽  
Marco Possenti ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Hypocotyl Elongation ◽  
Auxin Signaling ◽  
Rna Seq ◽  
Genome Wide

scholarly journals Drought tolerance molecular responses of two cultivated varieties Jerusalem artichoke (Helianthus tuberosus L.) as revealed by RNA-Seq

2020 ◽  
Author(s):  
Shipeng Yang ◽  
Lihui Wang ◽  
Qiwen Zhong ◽  
Guangnan Zhang ◽  
Haiwang Zhang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Resistance ◽  
Metabolic Pathways ◽  
Jerusalem Artichoke ◽  
Tibet Plateau ◽  
Helianthus Tuberosus ◽  
Rna Seq ◽  
Concentration Gradients ◽  
Light Reaction ◽  
Metabolic Activities

Abstract Background Jerusalem artichoke (Helianthus tuberosus L.) is a highly stress-resistant crop, especially it grows normally in the desertified land of Qinghai-Tibet Plateau in the past two years, and has become a crop with agricultural, industrial and ecological functions. However, there are few studies on drought resistance of Jerusalem artichoke at present, and studies on the mechanisms of stress resistance of Jerusalem artichoke breeding and fructan are seriously lagging behind. In this study, we selected two differentially resistant cultivars for drought stress experiments with different concentration gradients, the aim was finding DEGs and metabolic pathways associated with drought stress. Results Based on an additional analysis of the metabolic pathways under drought stress using MapMan, the most different types of metabolism included secondary metabolism, light reaction metabolism and cell wall. As a whole, QY1 and QY3 both had a large number of up-regulated genes in the flavor pathway. It was suggested that flavonoids could help Jerusalem artichoke to resist drought stress and maintain normal metabolic activities. In addition, the gene analysis of the abscisic acid (ABA) key metabolic pathway showed that QY3 had more genes in NAC and WRKY than QY1, but QY1 had more genes in response to drought stress as a whole. By combining RNA-Seq and WGCNA, a weighted gene co-expression network was constructed and divided into modules. By analyzing specifically the expressed modules, four modules were found to have the highest correlation with drought. Further research on the genes revealed that all 16 genes related to histone, ABA and protein kinase had the highest significance in these pathways. Conclusions These findings represent the first RNA-Seq analysis of drought stress in Jerusalem artichoke, which is of substantial significance to explore the function of drought resistance in Jerusalem artichoke and the excavation of related genes.

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