scholarly journals Comparative transcriptomics identifies the transcription factors BRANCHED1 and TCP4, as well as the microRNA miR166 as candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae)

2021 ◽  
Author(s):  
Lydia Gramzow ◽  
Katharina Klupsch ◽  
Noe Fernandez Pozo ◽  
Martin Hoelzer ◽  
Manja Marz ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Differentially Expressed Genes ◽  
Small Rnas ◽  
Model System ◽  
Differentially Expressed ◽  
Evolutionary Transition ◽  
Floral Buds ◽  
Genetic Mechanisms ◽  
Transcription Factor 4 ◽  
Synthesis And Degradation

Background: Fruits are the seed-bearing structures of flowering plants and are highly diverse in terms of morphology, texture and maturation. Dehiscent fruits split open upon maturation to discharge their seeds while indehiscent fruits are dispersed as a whole. Indehiscent fruits evolved from dehiscent fruits several times independently in the crucifer family (Brassicaceae). The fruits of Lepidium appelianum, for example, are indehiscent while the fruits of the closely related L. campestre are dehiscent. Here, we investigate the molecular and genetic mechanisms underlying the evolutionary transition from dehiscent to indehiscent fruits using these two Lepidium species as model system. Results: We have sequenced the transcriptomes and small RNAs of floral buds, flowers and fruits of L. appelianum and L. campestre and analyzed differentially expressed genes (DEGs) and differently differentially expressed genes (DDEGs). DEGs are genes that show significantly different transcript levels in the same structures (buds, flowers and fruits) in different species, or in different structures in the same species. DDEGs are genes for which the change in expression level between two structures is significantly different in one species than in the other. Comparing the two species, the highest number of DEGs was found in flowers, followed by fruits and floral buds while the highest number of DDEGs was found in fruits versus flowers followed by flowers versus floral buds. Several gene ontology terms related to cell wall synthesis and degradation were overrepresented in different sets of DEGs highlighting the importance of these processes for fruit opening. Furthermore, the fruit valve identity genes FRUITFUL and YABBY3 were among the DEGs identified. Finally, the microRNA miR166 as well as the TCP transcription factors BRANCHED1 (BRC1) and TCP FAMILY TRANSCRIPTION FACTOR 4 (TCP4) were found to be DDEGs. Conclusions: Our study reveals differences in gene expression between dehiscent and indehiscent fruits and uncovers miR166, BRC1 and TCP4 as possible causes for the evolutionary transition from dehiscent to indehiscent fruits in Lepidium.

scholarly journals Comparative transcriptomics identifies the transcription factors BRANCHED1 and TCP4, as well as the microRNA miR166 as candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium

2021 ◽  
Author(s):  
Lydia Gramzow ◽  
Katharina Klupsch ◽  
Noé Fernández Pozo ◽  
Martin Hölzer ◽  
Manja Marz ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Differentially Expressed Genes ◽  
Small Rnas ◽  
Model System ◽  
Differentially Expressed ◽  
Evolutionary Transition ◽  
Floral Buds ◽  
Genetic Mechanisms ◽  
Transcription Factor 4 ◽  
Synthesis And Degradation

Abstract Background: Fruits are the seed-bearing structures of flowering plants and are highly diverse in terms of morphology, texture and maturation. Dehiscent fruits split open upon maturation to discharge their seeds while indehiscent fruits are dispersed as a whole. Indehiscent fruits evolved from dehiscent fruits several times independently in the crucifer family (Brassicaceae). The fruits of Lepidium appelianum, for example, are indehiscent while the fruits of the closely related L. campestre are dehiscent. Here, we investigate the molecular and genetic mechanisms underlying the evolutionary transition from dehiscent to indehiscent fruits using these two Lepidium species as model system.Results: We have sequenced the transcriptomes and small RNAs of floral buds, flowers and fruits of L. appelianum and L. campestre and analyzed differentially expressed genes (DEGs) and differently differentially expressed genes (DDEGs). DEGs are genes that show significantly different transcript levels in the same structures (buds, flowers and fruits) in different species, or in different structures in the same species. DDEGs are genes for which the change in expression level between two structures is significantly different in one species than in the other. Comparing the two species, the highest number of DEGs was found in flowers, followed by fruits and floral buds while the highest number of DDEGs was found in fruits versus flowers followed by flowers versus floral buds. Several gene ontology terms related to cell wall synthesis and degradation were overrepresented in different sets of DEGs highlighting the importance of these processes for fruit opening. Furthermore, the fruit valve identity genes FRUITFUL and YABBY3 were among the DEGs identified. Finally, the microRNA miR166 as well as the TCP transcription factors BRANCHED1 (BRC1) and TCP FAMILY TRANSCRIPTION FACTOR 4 (TCP4) were found to be DDEGs.Conclusions: Our study reveals differences in gene expression between dehiscent and indehiscent fruits and uncovers miR166, BRC1 and TCP4 as possible causes for the evolutionary transition from dehiscent to indehiscent fruits in Lepidium.

Transcriptome analysis of Tetranychus cinnabarinus responses to an insecticide exposure

2020 ◽  
Vol 25 (7) ◽  
pp. 1329-1342
Author(s):  
Jia Chen ◽  
Xianyan Ye ◽  
Jing Wang ◽  
Bin Xia ◽  
Tianrong Xin
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Degradation Pathway ◽  
Differentially Expressed ◽  
Detoxification Enzymes ◽  
Tetranychus Cinnabarinus ◽  
Glutathione S Transferase ◽  
Chitin Synthesis ◽  
Sublethal Concentrations ◽  
Synthesis And Degradation

Diflubenzuron, a benzoylphenylurea insecticide that interferes with chitin biosynthesis, causes arthropods to moult abnormally and die. However, its mechanism of action in Tetranychus cinnabarinus is still unclear. In order to explore the effects of different sublethal concentrations of diflubenzuron on T. cinnabarinus, we conducted a high-throughput RNA-seq technology to identify the variations in transcriptomic profile of T. cinnabarinus larvae. The results revealed that 470 and 49 differentially expressed genes were identified in LC50-and LC70-treated groups, comparing with the control. We also identified and analyzed the detoxification enzymes involved in the transcritome of T. cinnabarinus, including 34 cytochrome P450 genes, 17 glutathione-s-transferase genes (GSTs), 12 acetylcholinesterase genes (AChEs) and 9 ABC transporter genes. In addition, differentially expressed genes analysis showed that the gene expression levels of detoxification enzymes were generally enhanced. At the same time, seven and eleven genes were involved in chitin synthesis and degradation ways, respectively. The expression level of most genes involved in chitin synthesis and degradation pathway were generally up-regulated after exposure to sublethal concentrations of diflubenzuron. Moreover, for transcriptome validation, the mRNA expression results of ten specially expressed genes by quantitative real-time PCR demonstrated that these gene expression trends were consistent with that of the transcriptome data. Together, all these results suggested that sublethal concentrations of diflubenzuron exposure affected gene expression of major detoxification enzymes and chitin metabolism genes in T. cinnabarinus larvae. These findings may be helpful to further understand the possible molecular mechanism of benzoylphenylurea insecticides in T. cinnabarinus, as well as in other spider mites.

scholarly journals Identification of regulatory networks and hub genes controlling mammary gland development and lactation in dairy goats during the late lactation, dry period, and late gestation stages

2020 ◽  
Author(s):  
Rong Xuan ◽  
Tianle Chao ◽  
Xiaodong Zhao ◽  
Aili Wang ◽  
Yunpeng Chu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Mammary Gland ◽  
Differentially Expressed Genes ◽  
Mammary Gland Development ◽  
Late Gestation ◽  
Differentially Expressed ◽  
Dry Period ◽  
Mammary Gland Tissue ◽  
Three Stages ◽  
Gland Development

Abstract Background From the late lactation to late gestation stages, the mammary gland tissue of goats undergoes a process from involution to remodeling and then to high differentiation of mammary gland tissue. From the perspective of lactation, this is a continuous development process of the goat mammary gland from the termination of lactation to the restoration of lactation. We performed transcriptome sequencing on goat mammary gland tissues at three mammary gland developmental stages to screen for differentially expressed genes that affect mammary gland development and the physiological process of lactation and mapped their expression profiles in three stages. The objective of this study is to reveal the expression characteristics of these genes and their potential function during mammary gland development and lactation. Results We identified 1,381 differentially expressed genes in the mammary gland during three stages and found that the expression level of genes encoding casein, such as alpha-s1-casein (CSN1S1), alpha-s2-casein (CSN1S2), beta-casein (CSN2), and kappa-casein (CSN3), and alpha-lactalbumin (LALBA) were higher in mammary gland tissues during the late lactation stage and late gestation stage than those during the dry period. In addition, we constructed six functional networks related to differentially expressed genes and found that these genes are closely related to mammary gland growth and development, apoptosis, immunity, substance transport, biosynthesis, and metabolism. Finally, we identified 35 differentially expressed transcription factors, which were classified into 16 families, and predicted that transcription factors of the basic leucine zipper domain (bZIP) family and basic helix-loop-helix (bHLH) family regulated the expression levels of genes related to mammary gland development and lactation. Conclusions Among the late lactation, dry period, and late gestation stages, there are differences in the expression levels of genes related to mammary gland growth and development, apoptosis, immunity, basic substance transport, biosynthesis, and metabolism in mammary gland tissues. Some genes in the same family or with similar functions have similar expression patterns. These differentially expressed genes or transcription factors work synergistically to participate in the regulation of mammary gland development and the physiological process of lactation.

scholarly journals A novel insight into nitrogen and auxin signaling in lateral root formation in tea plant [Camellia sinensis (L.) O. Kuntze]

2020 ◽  
Author(s):  
Shunkai Hu ◽  
Mi Zhang ◽  
Yiqing Yang ◽  
Wei Xuan ◽  
Zhongwei Zou ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Transcription Factors ◽  
Differentially Expressed Genes ◽  
Lateral Roots ◽  
Nitrogen Concentration ◽  
Tea Plant ◽  
Differentially Expressed ◽  
Auxin Signaling ◽  
Tea Plants ◽  
Low Nitrogen

Abstract Abstract Background Tea plant (Camellia sinensis) is one of the most popular non-alcoholic beverage worldwide. Lateral roots (LRs) of tea plant are the main organ used for tea plant to absorb soil moisture and nutrients. Lateral roots formation and development are tightly regulated by the nitrogen and auxin signaling pathway. In order to understand the function of auxin and nitrogen signaling in LRs formation and development, transcriptome analysis was applied to investigate the differentially expressed genes involved in lateral roots of tea plants treated with indole-3-butyric acid (IBA), N-1-naphthylphthalamic acid (NPA), low and high nitrogen concentration. Results A total of 296 common differentially expressed genes were mainly identified and annotated to four signaling pathways, such as nitrogen metabolism, plant hormone signal transduction, Glutathione metabolism and transcription factors. RNA-sequencing results revealed that majority of differentially expressed genes play important roles in nitrogen metabolism and hormonal signal transduction. Low nitrogen condition induced the biosynthesis of auxin and accumulation of transcripts, thereby regulating lateral roots formation. Furthermore, metabolism of cytokinin and ethylene biosynthesis were also involved in lateral roots development. Transcription factors like MYB genes also contributed to the lateral roots formation of tea plants through secondary cell wall biosynthesis. Reversed phase ultra performance liquid chromatography (RP-UPLC) results showed that the auxin concentration in lateral roots was increased, while the nitrogen level decreased. Thus, tea plant lateral roots formation could be induced by low nitrogen concentration via auxin biosynthesis and accumulation. Conclusion This study provides new insights into the mechanisms associated with nitrogen and auxin signaling pathways to regulate LRs formation and arises new clues for the efficient utilization of nitrogen in tea plant at the genetic level.

scholarly journals Transgene-associated human growth hormone expression in pancreatic β-cells impairs identification of sex-based gene expression differences

2019 ◽  
Vol 316 (2) ◽  
pp. E196-E209 ◽  
Author(s):  
Jennifer S. Stancill ◽  
Anna B. Osipovich ◽  
Jean-Philippe Cartailler ◽  
Mark A. Magnuson
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Growth Hormone ◽  
Transcription Factors ◽  
Differentially Expressed Genes ◽  
Human Growth ◽  
Differentially Expressed ◽  
Β Cells ◽  
Pancreatic Β Cells ◽  
Male And Female

Fluorescent protein reporter genes are widely used to identify and sort murine pancreatic β-cells. In this study, we compared use of the MIP-GFP transgene, which exhibits aberrant expression of human growth hormone (hGH), with a newly derived Ins2Apple allele that lacks hGH expression on the expression of sex-specific genes. β-Cells from MIP-GFP transgenic mice exhibit changes in the expression of 7,733 genes, or greater than half of their transcriptome, compared with β-cells from Ins2Apple/+ mice. To determine how these differences might affect a typical differential gene expression study, we analyzed the effect of sex on gene expression using both reporter lines. Six hundred fifty-seven differentially expressed genes were identified between male and female β-cells containing the Ins2Apple allele. Female β-cells exhibit higher expression of Xist, Tmed9, Arpc3, Eml2, and several islet-enriched transcription factors, including Nkx2-2 and Hnf4a, whereas male β-cells exhibited a generally higher expression of genes involved in cell cycle regulation. In marked contrast, the same male vs. female comparison of β-cells containing the MIP-GFP transgene revealed only 115 differentially expressed genes, and comparison of the 2 lists of differentially expressed genes revealed only 17 that were common to both analyses. These results indicate that 1) male and female β-cells differ in their expression of key transcription factors and cell cycle regulators and 2) the MIP-GFP transgene may attenuate sex-specific differences that distinguish male and female β-cells, thereby impairing the identification of sex-specific variations.

scholarly journals Transcriptome analysis reveals modulation of the STAT family in PEDV-infected IPEC-J2 cells

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhengzheng Hu ◽  
Yuchen Li ◽  
Heng Du ◽  
Junxiao Ren ◽  
Xianrui Zheng ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Differentially Expressed Genes ◽  
Influenza A ◽  
Molecular Mechanisms ◽  
Host Cells ◽  
Differentially Expressed ◽  
Economic Losses ◽  
Receptor Interaction ◽  
Epithelial Cell Line ◽  
Diarrhea Virus

Abstract Background Porcine epidemic diarrhea virus (PEDV) is a causative agent of serious viral enteric disease in suckling pigs. Such diseases cause considerable economic losses in the global swine industry. Enhancing our knowledge of PEDV-induced transcriptomic responses in host cells is imperative to understanding the molecular mechanisms involved in the immune response. Here, we analyzed the transcriptomic profile of intestinal porcine epithelial cell line J2 (IPEC-J2) after infection with a classical strain of PEDV to explore the host response. Results In total, 854 genes were significantly differentially expressed after PEDV infection, including 716 upregulated and 138 downregulated genes. Functional annotation analysis revealed that the differentially expressed genes were mainly enriched in the influenza A, TNF signaling, inflammatory response, cytokine receptor interaction, and other immune-related pathways. Next, the putative promoter regions of the 854 differentially expressed genes were examined for the presence of transcription factor binding sites using the MEME tool. As a result, 504 sequences (59.02%) were identified as possessing at least one binding site of signal transducer and activator of transcription (STAT), and five STAT transcription factors were significantly induced by PEDV infection. Furthermore, we revealed the regulatory network induced by STAT members in the process of PEDV infection. Conclusion Our transcriptomic analysis described the host genetic response to PEDV infection in detail in IPEC-J2 cells, and suggested that STAT transcription factors may serve as key regulators in the response to PEDV infection. These results further our understanding of the pathogenesis of PEDV.

scholarly journals Network Analyses of Integrated Differentially Expressed Genes in Papillary Thyroid Carcinoma to Identify Characteristic Genes

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 45 ◽  
Author(s):  
Junliang Shang ◽  
Qian Ding ◽  
Shasha Yuan ◽  
Jin-Xing Liu ◽  
Feng Li ◽  
...  
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Differentially Expressed Genes ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Papillary Thyroid ◽  
Topological Properties ◽  
Network Analyses ◽  
Genetic Mechanisms

Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. Identifying characteristic genes of PTC are of great importance to reveal its potential genetic mechanisms. In this paper, we proposed a framework, as well as a measure named Normalized Centrality Measure (NCM), to identify characteristic genes of PTC. The framework consisted of four steps. First, both up-regulated genes and down-regulated genes, collectively called differentially expressed genes (DEGs), were screened and integrated together from four datasets, that is, GSE3467, GSE3678, GSE33630, and GSE58545; second, an interaction network of DEGs was constructed, where each node represented a gene and each edge represented an interaction between linking nodes; third, both traditional measures and the NCM measure were used to analyze the topological properties of each node in the network. Compared with traditional measures, more genes related to PTC were identified by the NCM measure; fourth, by mining the high-density subgraphs of this network and performing Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, several meaningful results were captured, most of which were demonstrated to be associated with PTC. The experimental results proved that this network framework and the NCM measure are useful for identifying more characteristic genes of PTC.

scholarly journals Divergence between motoneurons: gene expression profiling provides a molecular characterization of functionally discrete somatic and autonomic motoneurons

2006 ◽  
Vol 24 (3) ◽  
pp. 276-289 ◽  
Author(s):  
Dapeng Cui ◽  
Kimberly J. Dougherty ◽  
David W. Machacek ◽  
Michael Sawchuk ◽  
Shawn Hochman ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Differentially Expressed Genes ◽  
Expression Profiles ◽  
Cell Types ◽  
Differentially Expressed ◽  
Columnar Cell ◽  
Expression Change ◽  
Affymetrix Microarrays ◽  
Lateral Motor Column ◽  
Combinatorial Codes

Studies in the developing spinal cord suggest that different motoneuron (MN) cell types express very different genetic programs, but the degree to which adult programs differ is unknown. To compare genetic programs between adult MN columnar cell types, we used laser capture microdissection (LCM) and Affymetrix microarrays to create expression profiles for three columnar cell types: lateral and medial MNs from lumbar segments and sympathetic preganglionic motoneurons located in the thoracic intermediolateral nucleus. A comparison of the three expression profiles indicated that ∼7% (813/11,552) of the genes showed significant differences in their expression levels. The largest differences were observed between sympathetic preganglionic MNs and the lateral motor column, with 6% (706/11,552) of the genes being differentially expressed. Significant differences in expression were observed for 1.8% (207/11,552) of the genes when comparing sympathetic preganglionic MNs with the medial motor column. Lateral and medial MNs showed the least divergence, with 1.3% (150/11,552) of the genes being differentially expressed. These data indicate that the amount of divergence in expression profiles between identified columnar MNs does not strictly correlate with divergence of function as defined by innervation patterns (somatic/muscle vs. autonomic/viscera). Classification of the differentially expressed genes with regard to function showed that they underpin all fundamental cell systems and processes, although most differentially expressed genes encode proteins involved in signal transduction. Mining the expression profiles to examine transcription factors essential for MN development suggested that many of the same transcription factors participate in combinatorial codes in embryonic and adult neurons, but patterns of expression change significantly.

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