scholarly journals Tissue-specific transcriptome analyses reveal candidate genes for stilbene, flavonoid and anthraquinone biosynthesis in the medicinal plant Polygonum cuspidatum

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaowei Wang ◽  
Hongyan Hu ◽  
Zhijun Wu ◽  
Haili Fan ◽  
Guowei Wang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Medicinal Plant ◽  
Expression Patterns ◽  
Phenylpropanoid Pathway ◽  
Polygonum Cuspidatum ◽  
Specific Expression ◽  
Tissue Specific ◽  
Factors Associated ◽  
Specific Accumulation ◽  
Different Tissues

Abstract Background Polygonum cuspidatum Sieb. et Zucc. is a well-known medicinal plant whose pharmacological effects derive mainly from its stilbenes, anthraquinones, and flavonoids. These compounds accumulate differentially in the root, stem, and leaf; however, the molecular basis of such tissue-specific accumulation remains poorly understood. Because tissue-specific accumulation of compounds is usually associated with tissue-specific expression of the related biosynthetic enzyme genes and regulators, we aimed to clarify and compare the transcripts expressed in different tissues of P. cuspidatum in this study. Results High-throughput RNA sequencing was performed using three different tissues (the leaf, stem, and root) of P. cuspidatum. In total, 80,981 unigenes were obtained, of which 40,729 were annotated, and 21,235 differentially expressed genes were identified. Fifty-four candidate synthetase genes and 12 transcription factors associated with stilbene, flavonoid, and anthraquinone biosynthetic pathways were identified, and their expression levels in the three different tissues were analyzed. Phylogenetic analysis of polyketide synthase gene families revealed two novel CHS genes in P. cuspidatum. Most phenylpropanoid pathway genes were predominantly expressed in the root and stem, while methylerythritol 4-phosphate and isochorismate pathways for anthraquinone biosynthesis were dominant in the leaf. The expression patterns of synthase genes were almost in accordance with metabolite profiling in different tissues of P. cuspidatum as measured by high-performance liquid chromatography or ultraviolet spectrophotometry. All predicted transcription factors associated with regulation of the phenylpropanoid pathway were expressed at lower levels in the stem than in the leaf and root, but no consistent trend in their expression was observed between the leaf and the root. Conclusions The molecular knowledge of key genes involved in the biosynthesis of P. cuspidatum stilbenes, flavonoids, and anthraquinones is poor. This study offers some novel insights into the biosynthetic regulation of bioactive compounds in different P. cuspidatum tissues and provides valuable resources for the potential metabolic engineering of this important medicinal plant.

scholarly journals Transcriptomic Analysis and Specific Expression of Transcription Factor Genes in the Root and Sporophyll of Dryopteris fragrans (L.) Schott

2020 ◽  
Vol 21 (19) ◽  
pp. 7296
Author(s):  
Lingling Chen ◽  
Dongrui Zhang ◽  
Chunhua Song ◽  
Hemeng Wang ◽  
Xun Tang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Glandular Trichomes ◽  
Transcriptomic Analysis ◽  
Specific Gene ◽  
Specific Expression ◽  
Tissue Specific ◽  
Transcription Factor Genes ◽  
Dryopteris Fragrans ◽  
Different Tissues

Background: Dryopteris fragrans, which is densely covered with glandular trichomes, is considered to be one of the ferns with the most medicinal potential. The transcriptomes from selected tissues of D. fragrans were collected and analyzed for functional and comparative genomic studies. The aim of this study was to determine the transcriptomic characteristics of wild D. fragrans sporangium in tissues from the SR (root), SL (sporophyll), and TRL (sporophyll with glandular trichomes removed). Results: Cluster analysis identified genes that were highly expressed in an organ-specific manner according to read mapping, feature counting, and normalization. The functional map identified gene clusters that can uniquely describe the function of each tissue. We identified a group of three tissue-specific transcription factors targeting the SL, SR, and TRL. In addition, highly expressed transcription factors (TFs) were found in each tissue-specific gene cluster, where ERF and bHLH transcription factors were the two types showing the most distinct expression patterns between the three different tissues. The specific expression of transcription factor genes varied between the different types of tissues. The numbers of transcription factors specifically expressed in the roots and sporophylls were 60 and 30, respectively, while only seven were found for the sporophylls with glandular trichomes removed. The expression of genes known to be associated with the development of glandular trichomes in flowering plants, including MIXTA, ATML1, and MYB106, were also validated and are discussed. In particular, a unigene encoding MIXTA was identified and exhibited the highest expression level in SL in D. fragrans. Conclusions: This study is the first report of global transcriptomic analysis in different tissues of D. fragrans, and the first to discuss these findings in the context of the development of homologous glandular trichomes. These results set the stage for further research on the development, stress resistance, and secondary metabolism of D. fragrans glandular trichomes.

scholarly journals Genome-wide and expression analysis of B-box gene family in pepper

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jing Ma ◽  
Jia-xi Dai ◽  
Xiao-wei Liu ◽  
Duo Lin
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Transient Expression Assay ◽  
Specific Expression ◽  
Tissue Specific ◽  
Duplication Events ◽  
Onion Inner Epidermis

Abstract Background BBX transcription factors are a kind of zinc finger transcription factors with one or two B-box domains, which partilant in plant growth, development and response to abiotic or biotic stress. The BBX family has been identified in Arabidopsis, rice, tomato and some other model plant genomes. Results Here, 24 CaBBX genes were identified in pepper (Capsicum annuum L.), and the phylogenic analysis, structures, chromosomal location, gene expression patterns and subcellular localizations were also carried out to understand the evolution and function of CaBBX genes. All these CaBBXs were divided into five classes, and 20 of them distributed in 11 of 12 pepper chromosomes unevenly. Most duplication events occurred in subgroup I. Quantitative RT-PCR indicated that several CaBBX genes were induced by abiotic stress and hormones, some had tissue-specific expression profiles or differentially expressed at developmental stages. Most of CaBBX members were predicated to be nucleus-localized in consistent with the transient expression assay by onion inner epidermis of the three tested CaBBX members (CaBBX5, 6 and 20). Conclusion Several CaBBX genes were induced by abiotic stress and exogenous phytohormones, some expressed tissue-specific and variously at different developmental stage. The detected CaBBXs act as nucleus-localized transcription factors. Our data might be a foundation in the identification of CaBBX genes, and a further understanding of their biological function in future studies.

scholarly journals Tissue-Specific Expression Patterns of Arabidopsis NF-Y Transcription Factors Suggest Potential for Extensive Combinatorial Complexity

2008 ◽  
Vol 149 (2) ◽  
pp. 625-641 ◽  
Author(s):  
Nicholas Siefers ◽  
Kristen K. Dang ◽  
Roderick W. Kumimoto ◽  
William Edwards Bynum ◽  
Gregory Tayrose ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Expression Patterns ◽  
Combinatorial Complexity ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression

Tissue-specific expression patterns of nuclear receptors

2013 ◽  
Author(s):  
AL Bookout ◽  
Y Jeong ◽  
M Downes ◽  
RT Yu ◽  
RM Evans ◽  
...  
Keyword(s):  
Nuclear Receptors ◽  
Expression Patterns ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression

scholarly journals Regulation of rice root development by a retrotransposon acting as a microRNA sponge

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Jungnam Cho ◽  
Jerzy Paszkowski
Keyword(s):  
Gene Regulation ◽  
Transcription Factors ◽  
Root Development ◽  
Binding Sites ◽  
Transcriptional Control ◽  
Specific Expression ◽  
Ability To Act ◽  
Specific Accumulation ◽  
In Trans ◽  
Microrna Sponge

It is well documented that transposable elements (TEs) can regulate the expression of neighbouring genes. However, their ability to act in trans and influence ectopic loci has been reported rarely. We searched in rice transcriptomes for tissue-specific expression of TEs and found them to be regulated developmentally. They often shared sequence homology with co-expressed genes and contained potential microRNA-binding sites, which suggested possible contributions to gene regulation. In fact, we have identified a retrotransposon that is highly transcribed in roots and whose spliced transcript constitutes a target mimic for miR171. miR171 destabilizes mRNAs encoding the root-specific family of SCARECROW-Like transcription factors. We demonstrate that retrotransposon-derived transcripts act as decoys for miR171, triggering its degradation and thus results in the root-specific accumulation of SCARECROW-Like mRNAs. Such transposon-mediated post-transcriptional control of miR171 levels is conserved in diverse rice species.

scholarly journals Tissue Distribution of ACE2 Protein in Syrian Golden Hamster (Mesocricetus auratus) and Its Possible Implications in SARS-CoV-2 Related Studies

2021 ◽  
Vol 11 ◽  
Author(s):  
Voddu Suresh ◽  
Deepti Parida ◽  
Aliva P. Minz ◽  
Manisha Sethi ◽  
Bhabani S. Sahoo ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Golden Hamster ◽  
Expression Patterns ◽  
Mesocricetus Auratus ◽  
Syrian Golden Hamster ◽  
Surface Epithelium ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Specific Expression Pattern

The Syrian golden hamster (Mesocricetus auratus) has recently been demonstrated as a clinically relevant animal model for SARS-CoV-2 infection. However, lack of knowledge about the tissue-specific expression pattern of various proteins in these animals and the unavailability of reagents like antibodies against this species hampers these models’ optimal use. The major objective of our current study was to analyze the tissue-specific expression pattern of angiotensin-converting enzyme 2, a proven functional receptor for SARS-CoV-2 in different organs of the hamster. Using two different antibodies (MA5-32307 and AF933), we have conducted immunoblotting, immunohistochemistry, and immunofluorescence analysis to evaluate the ACE2 expression in different tissues of the hamster. Further, at the mRNA level, the expression of Ace2 in tissues was evaluated through RT-qPCR analysis. Both the antibodies detected expression of ACE2 in kidney, small intestine, tongue, and liver. Epithelium of proximal tubules of kidney and surface epithelium of ileum expresses a very high amount of this protein. Surprisingly, analysis of stained tissue sections showed no detectable expression of ACE2 in the lung or tracheal epithelial cells. Similarly, all parts of the large intestine were negative for ACE2 expression. Analysis of tissues from different age groups and sex didn’t show any obvious difference in ACE2 expression pattern or level. Together, our findings corroborate some of the earlier reports related to ACE2 expression patterns in human tissues and contradict others. We believe that this study’s findings have provided evidence that demands further investigation to understand the predominant respiratory pathology of SARS-CoV-2 infection and disease.

scholarly journals Development of cDNA normalization system and preliminary transcription analysis of KCS genes in apple tissues

2011 ◽  
Vol 59 (3) ◽  
pp. 9-12 ◽  
Author(s):  
Zsolt Albert ◽  
Cs. Deák ◽  
A. Miskó ◽  
M. Tóth ◽  
I. Papp
Keyword(s):  
Gene Expression ◽  
Expression System ◽  
Expression Patterns ◽  
Housekeeping Genes ◽  
Apple Fruit ◽  
Rt Pcr ◽  
Specific Primers ◽  
Specific Expression ◽  
Transcription Analysis ◽  
Tissue Specific

Wax production is an important aspect of apple (Malus domestica Borkh.) fruit development from both theoretical and practical point of views. The complex molecular mechanism that controls wax biosynthesis is still widely unknown but many studies focused on this topic. We aimed to develop further the experimental framework of these efforts with a description of an improved reference genes expression system. Results in the literature show that similarities exist among the expression of some housekeeping genes of different plant species. Based on these considerations and on gene expression data from Arabidopsis thaliana, some genes in apple were assigned for analysis. EST sequences of apple were used to design specific primers for RT-PCR experiments. Isolation of intact RNA from different apple tissues and performing RT-PCR reaction were also key point in obtaining expression patterns. To monitor DNA contamination of the RNA samples, specific primers were used that amplify intron-containing sequences from the cDNA. We found that actin primers can be used for the detection of intron containing genomic DNA, and tubulin primers are good internal controls in RT-PCR experiments. We were able to make a difference between tissue-specific and tissue-independent gene-expression, furthermore we found tissue specific differences between the expression patterns of candidate genes, that are potentially involved in wax-biosynthesis. Our results show that KCS1 and KCS4 are overexpressed in the skin tissue, this could mean that these genes have skin-specific expression in apple fruit.

scholarly journals Transcription Profiles of Age-at-Maturity-Associated Genes Suggest Cell Fate Commitment Regulation as a Key Factor in the Atlantic Salmon Maturation Process

2019 ◽  
Vol 10 (1) ◽  
pp. 235-246 ◽  
Author(s):  
Johanna Kurko ◽  
Paul V. Debes ◽  
Andrew H. House ◽  
Tutku Aykanat ◽  
Jaakko Erkinaro ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Cell Fate ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Expression Patterns ◽  
Hippo Signaling ◽  
Age At Maturity ◽  
Specific Expression ◽  
Hpg Axis ◽  
Tissue Specific

Despite recent taxonomic diversification in studies linking genotype with phenotype, follow-up studies aimed at understanding the molecular processes of such genotype-phenotype associations remain rare. The age at which an individual reaches sexual maturity is an important fitness trait in many wild species. However, the molecular mechanisms regulating maturation timing processes remain obscure. A recent genome-wide association study in Atlantic salmon (Salmo salar) identified large-effect age-at-maturity-associated chromosomal regions including genes vgll3, akap11 and six6, which have roles in adipogenesis, spermatogenesis and the hypothalamic-pituitary-gonadal (HPG) axis, respectively. Here, we determine expression patterns of these genes during salmon development and their potential molecular partners and pathways. Using Nanostring transcription profiling technology, we show development- and tissue-specific mRNA expression patterns for vgll3, akap11 and six6. Correlated expression levels of vgll3 and akap11, which have adjacent chromosomal location, suggests they may have shared regulation. Further, vgll3 correlating with arhgap6 and yap1, and akap11 with lats1 and yap1 suggests that Vgll3 and Akap11 take part in actin cytoskeleton regulation. Tissue-specific expression results indicate that vgll3 and akap11 paralogs have sex-dependent expression patterns in gonads. Moreover, six6 correlating with slc38a6 and rtn1, and Hippo signaling genes suggests that Six6 could have a broader role in the HPG neuroendrocrine and cell fate commitment regulation, respectively. We conclude that Vgll3, Akap11 and Six6 may influence Atlantic salmon maturation timing via affecting adipogenesis and gametogenesis by regulating cell fate commitment and the HPG axis. These results may help to unravel general molecular mechanisms behind maturation.

scholarly journals EMT-Inducing Transcription Factors, Drivers of Melanoma Phenotype Switching, and Resistance to Treatment

Cancers ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 2154 ◽  
Author(s):  
Yaqi Tang ◽  
Simon Durand ◽  
Stéphane Dalle ◽  
Julie Caramel
Keyword(s):  
Transcription Factors ◽  
Neural Crest ◽  
Epithelial Mesenchymal Transition ◽  
Expression Patterns ◽  
Specific Expression ◽  
Therapeutic Targeting ◽  
Mesenchymal Transition ◽  
Neural Crest Stem Cell ◽  
Resistance To Treatment ◽  
Phenotype Switching

Transcription factors, extensively described for their role in epithelial–mesenchymal transition (EMT-TFs) in epithelial cells, also display essential functions in the melanocyte lineage. Recent evidence has shown specific expression patterns and functions of these EMT-TFs in neural crest-derived melanoma compared to carcinoma. Herein, we present an update of the specific roles of EMT-TFs in melanocyte differentiation and melanoma progression. As major regulators of phenotype switching between differentiated/proliferative and neural crest stem cell-like/invasive states, these factors appear as major drivers of intra-tumor heterogeneity and resistance to treatment in melanoma, which opens new avenues in terms of therapeutic targeting.

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