scholarly journals Comparative transcriptome analysis of Alpinia oxyphylla Miq. reveals tissue-specific expression of flavonoid biosynthesis genes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Lin Yuan ◽  
Kun Pan ◽  
Yonghui Li ◽  
Bo Yi ◽  
Bingmiao Gao
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Genetically Engineered ◽  
Flavonoid Biosynthesis ◽  
Specific Gene ◽  
Specific Expression ◽  
Tissue Specific ◽  
Alpinia Oxyphylla ◽  
Leaf Tissues

Abstract Background Alpinia oxyphylla Miq. is an important edible and medicinal herb, and its dried fruits are widely used in traditional herbal medicine. Flavonoids are one of the main chemical compounds in A. oxyphylla; however, the genetic and molecular mechanisms of flavonoid biosynthesis are not well understood. We performed transcriptome analysis in the fruit, root, and leaf tissues of A. oxyphylla to delineate tissue-specific gene expression and metabolic pathways in this medicinal plant. Results In all, 8.85, 10.10, 8.68, 6.89, and 8.51 Gb clean data were obtained for early-, middle-, and late-stage fruits, leaves, and roots, respectively. Furthermore, 50,401 unigenes were grouped into functional categories based on four databases, namely Nr (47,745 unigenes), Uniprot (49,685 unigenes), KOG (20,153 unigenes), and KEGG (27,285 unigenes). A total of 3110 differentially expressed genes (DEGs) and five distinct clusters with similar expression patterns were obtained, in which 27 unigenes encoded 13 key enzymes associated with flavonoid biosynthesis. In particular, 9 DEGs were significantly up-regulated in fruits, whereas expression of 11 DEGs were highly up-regulated in roots, compared with those in leaves. Conclusion The DEGs and metabolic pathway related to flavonoids biosynthesis were identified in root, leaf, and different stages of fruits from A. oxyphylla. These results provide insights into the molecular mechanism of flavonoid biosynthesis in A. oxyphylla and application of genetically engineered varieties of A. oxyphylla.

scholarly journals Comparative Transcriptome Analysis of Alpinia oxyphylla reveals Tissue-specific Expression of Flavonoid Biosynthesis Genes

2020 ◽  
Author(s):  
Bingmiao Gao
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Genetically Engineered ◽  
Flavonoid Biosynthesis ◽  
Specific Gene ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Alpinia Oxyphylla

Abstract Background: Alpinia oxyphylla is an important edible and medicinal herb, and its dried fruits are widely used in traditional herbal medicine. Flavonoids are one of the main chemical compounds in A. oxyphylla ; however, the genetic and molecular mechanisms of flavonoid biosynthesis are not well understood. Methods: We performed transcriptome analysis in the fruit, root, and leaf tissues of A. oxyphylla to delineate tissue-specific gene expression and metabolic pathways in this medicinal plant. Results: In all, 8.85, 10.10, 8.68, 6.89, and 8.51 Gb clean data were obtained for early-, middle-, and late-stage fruits, leaves, and roots, respectively. Furthermore, 50,401 unigenes were grouped into functional categories based on four databases, namely Nr (47,745 unigenes), Uniprot (49,685 unigenes), KOG (20,153 unigenes), and KEGG (27,285 unigenes). A total of 3,110 differentially expressed genes and five distinct clusters with similar expression patterns were obtained, in which 27 unigenes encoded 13 key enzymes (such as CHS, CHI, F3H, FLS, ANS ) associated with flavonoid biosynthesis. Conclusion: The tissue-specific expression of the genes corresponds to accumulation of flavonoids in these tissues.These results provide insights into the molecular mechanism of flavonoid biosynthesis in A. oxyphylla and application of genetically engineered varieties of A. oxyphylla .

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 A non-coding genetic variant maximally associated with serum urate levels is functionally linked to HNF4A-dependent PDZK1 expression

2018 ◽  
Author(s):  
Sarada Ketharnathan ◽  
Megan Leask ◽  
James Boocock ◽  
Amanda J. Phipps-Green ◽  
Jisha Antony ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepg2 Cells ◽  
Molecular Mechanisms ◽  
Genetic Variant ◽  
Fluorescent Protein ◽  
Serum Urate ◽  
Specific Gene ◽  
Specific Expression ◽  
Enhancer Activity ◽  
Tissue Specific

ABSTRACTSeveral dozen genetic variants associate with serum urate levels, but the precise molecular mechanisms by which they affect serum urate are unknown. Here we tested for functional linkage of the maximally-associated genetic variant rs1967017 at the PDZK1 locus to elevated PDZK1 expression.We performed expression quantitative trait locus (eQTL) and likelihood analyses followed by gene expression assays. Zebrafish were used to determine the ability of rs1967017 to direct tissue-specific gene expression. Luciferase assays in HEK293 and HepG2 cells measured the effect of rs1967017 on transcription amplitude.PAINTOR analysis revealed rs1967017 as most likely to be causal and rs1967017 was an eQTL for PDZK1 in the intestine. The region harboring rs1967017 was capable of directly driving green fluorescent protein expression in the kidney, liver and intestine of zebrafish embryos, consistent with a conserved ability to confer tissue-specific expression. The urate-increasing T-allele of rs1967017 strengthens a binding site for the transcription factor HNF4A. siRNA depletion of HNF4A reduced endogenous PDZK1 expression in HepG2 cells. Luciferase assays showed that the T-allele of rs1967017 gains enhancer activity relative to the urate-decreasing C-allele, with T-allele enhancer activity abrogated by HNF4A depletion. HNF4A physically binds the rs1967017 region, suggesting direct transcriptional regulation of PDZK1 by HNF4A.With other reports our data predict that the urate-raising T-allele of rs1967017 enhances HNF4A binding to the PDZK1 promoter, thereby increasing PDZK1 expression. As PDZK1 is a scaffold protein for many ion channel transporters, increased expression can be predicted to increase activity of urate transporters and alter excretion of urate.

scholarly journals Tissue-specific gene expression in the pituitary: the glycoprotein hormone alpha-subunit gene is regulated by a gonadotrope-specific protein.

1992 ◽  
Vol 12 (5) ◽  
pp. 2143-2153 ◽  
Author(s):  
F Horn ◽  
J J Windle ◽  
K M Barnhart ◽  
P L Mellon
Keyword(s):  
Molecular Mechanisms ◽  
Regulatory Element ◽  
Alpha Subunit ◽  
Specific Factor ◽  
Specific Gene ◽  
Homeodomain Protein ◽  
Subunit Gene ◽  
Glycoprotein Hormone ◽  
Specific Expression ◽  
Tissue Specific

The molecular mechanisms for the development of multiple distinct endocrine cell types in the anterior pituitary have been an area of intensive investigation. Though the homeodomain protein Pit-1/GHF-1 is known to be involved in differentiation of the somatotrope and lactotrope lineages, which produce growth hormone and prolactin, respectively, little is known of the transcriptional regulators important for the gonadotrope cell lineage, which produces the glycoprotein hormones luteinizing hormone and follicle-stimulating hormone. Using transgenic mice and transfection into a novel gonadotrope lineage cell line, we have identified a regulatory element that confers gonadotrope-specific expression to the glycoprotein hormone alpha-subunit gene. A tissue-specific factor that binds to this element is purified and characterized as a 54-kDa protein which is present uniquely in cells of the gonadotrope lineage and is not Pit-1/GHF-1. The human and equine alpha-subunit genes are also expressed in placental cells. However, the previously characterized placental transcription factors designated TSEB and alpha-ACT are not found in the pituitary gonadotrope cells, indicating that independent mechanisms confer expression of these genes in the two different tissues.

Detection of genes with tissue-specific expression patterns using Akaike’s information criterion procedure

2003 ◽  
Vol 12 (3) ◽  
pp. 251-259 ◽  
Author(s):  
Koji Kadota ◽  
Shin-Ichiro Nishimura ◽  
Hidemasa Bono ◽  
Shugo Nakamura ◽  
Yoshihide Hayashizaki ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Information Criterion ◽  
Cell Types ◽  
Specific Gene ◽  
Akaike's Information Criterion ◽  
Expression Array ◽  
Specific Expression ◽  
Tissue Specific ◽  
Significance Level ◽  
Akaike’S Information Criterion

We applied a method based on Akaike’s information criterion (AIC) to detect genes whose expression profile is considerably different in some tissue(s) than in others. Such observations are detected as outliers, and the method we used was originally developed to detect outliers. The main advantage of the method is that objective decisions are possible because the procedure is independent of a significance level. We applied the method to 48 expression ratios corresponding to various tissues in each of 14,610 clones obtained from the RIKEN Expression Array Database (READ; http://read.gsc.riken.go.jp ). As a result, for several tissues (e.g., muscle, heart, and tongue tissues that contain similar cell types) we objectively obtained specific clones without any “thresholding.” Our study demonstrates the feasibility of the method for detecting tissue-specific gene expression patterns.

Tissue-specific gene expression in the pituitary: the glycoprotein hormone alpha-subunit gene is regulated by a gonadotrope-specific protein

1992 ◽  
Vol 12 (5) ◽  
pp. 2143-2153
Author(s):  
F Horn ◽  
J J Windle ◽  
K M Barnhart ◽  
P L Mellon
Keyword(s):  
Molecular Mechanisms ◽  
Regulatory Element ◽  
Alpha Subunit ◽  
Specific Factor ◽  
Specific Gene ◽  
Homeodomain Protein ◽  
Subunit Gene ◽  
Glycoprotein Hormone ◽  
Specific Expression ◽  
Tissue Specific

The molecular mechanisms for the development of multiple distinct endocrine cell types in the anterior pituitary have been an area of intensive investigation. Though the homeodomain protein Pit-1/GHF-1 is known to be involved in differentiation of the somatotrope and lactotrope lineages, which produce growth hormone and prolactin, respectively, little is known of the transcriptional regulators important for the gonadotrope cell lineage, which produces the glycoprotein hormones luteinizing hormone and follicle-stimulating hormone. Using transgenic mice and transfection into a novel gonadotrope lineage cell line, we have identified a regulatory element that confers gonadotrope-specific expression to the glycoprotein hormone alpha-subunit gene. A tissue-specific factor that binds to this element is purified and characterized as a 54-kDa protein which is present uniquely in cells of the gonadotrope lineage and is not Pit-1/GHF-1. The human and equine alpha-subunit genes are also expressed in placental cells. However, the previously characterized placental transcription factors designated TSEB and alpha-ACT are not found in the pituitary gonadotrope cells, indicating that independent mechanisms confer expression of these genes in the two different tissues.

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 ◽  
Author(s):  
Johanna Kurko ◽  
Paul V. Debes ◽  
Andrew 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

AbstractDespite 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 on adipogenesis and gametogenesis by regulating cell fate commitment and the HPG axis. These results may help to unravel general molecular mechanisms behind maturation.

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 Comparative Transcriptome Analysis Reveals Key Genes and Pathways Involved in Prickle Development in Eggplant

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 341
Author(s):  
Lei Zhang ◽  
Haoyun Sun ◽  
Tao Xu ◽  
Tianye Shi ◽  
Zongyun Li ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Morphological Analysis ◽  
Molecular Mechanisms ◽  
Flavonoid Biosynthesis ◽  
Phenotypic Characterization ◽  
Comparative Transcriptome ◽  
Hub Genes ◽  
Breeding Programs ◽  
Comparative Transcriptome Analysis ◽  
Key Pathways

Eggplant is one of the most important vegetables worldwide. Prickles on the leaves, stems and fruit calyxes of eggplant may cause difficulties during cultivation, harvesting and transportation, and therefore is an undesirable agronomic trait. However, limited knowledge about molecular mechanisms of prickle morphogenesis has hindered the genetic improvement of eggplant. In this study, we performed the phenotypic characterization and transcriptome analysis on prickly and prickleless eggplant genotypes to understand prickle development at the morphological and molecular levels. Morphological analysis revealed that eggplant prickles were multicellular, lignified and layered organs. Comparative transcriptome analysis identified key pathways and hub genes involved in the cell cycle as well as flavonoid biosynthetic, photosynthetic, and hormone metabolic processes during prickle development. Interestingly, genes associated with flavonoid biosynthesis were up-regulated in developing prickles, and genes associated with photosynthesis were down-regulated in developing and matured prickles. It was also noteworthy that several development-related transcription factors such as bHLH, C2H2, MYB, TCP and WRKY were specifically down- or up-regulated in developing prickles. Furthermore, four genes were found to be differentially expressed within the Pl locus interval. This study provides new insights into the regulatory molecular mechanisms underlying prickle morphogenesis in eggplant, and the genes identified might be exploited in breeding programs to develop prickleless eggplant cultivars.

scholarly journals Methylation of the Cyclin A1 Promoter Correlates with Gene Silencing in Somatic Cell Lines, while Tissue-Specific Expression of Cyclin A1 Is Methylation Independent

2000 ◽  
Vol 20 (9) ◽  
pp. 3316-3329 ◽  
Author(s):  
Carsten Müller ◽  
Carol Readhead ◽  
Sven Diederichs ◽  
Gregory Idos ◽  
Rong Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Promoter Methylation ◽  
Cpg Island ◽  
Trichostatin A ◽  
Specific Gene ◽  
Cyclin A1 ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression

ABSTRACT Gene expression in mammalian organisms is regulated at multiple levels, including DNA accessibility for transcription factors and chromatin structure. Methylation of CpG dinucleotides is thought to be involved in imprinting and in the pathogenesis of cancer. However, the relevance of methylation for directing tissue-specific gene expression is highly controversial. The cyclin A1 gene is expressed in very few tissues, with high levels restricted to spermatogenesis and leukemic blasts. Here, we show that methylation of the CpG island of the human cyclin A1 promoter was correlated with nonexpression in cell lines, and the methyl-CpG binding protein MeCP2 suppressed transcription from the methylated cyclin A1 promoter. Repression could be relieved by trichostatin A. Silencing of a cyclin A1 promoter-enhanced green fluorescent protein (EGFP) transgene in stable transfected MG63 osteosarcoma cells was also closely associated with de novo promoter methylation. Cyclin A1 could be strongly induced in nonexpressing cell lines by trichostatin A but not by 5-aza-cytidine. The cyclin A1 promoter-EGFP construct directed tissue-specific expression in male germ cells of transgenic mice. Expression in the testes of these mice was independent of promoter methylation, and even strong promoter methylation did not suppress promoter activity. MeCP2 expression was notably absent in EGFP-expressing cells. Transcription from the transgenic cyclin A1 promoter was repressed in most organs outside the testis, even when the promoter was not methylated. These data show the association of methylation with silencing of the cyclin A1 gene in cancer cell lines. However, appropriate tissue-specific repression of the cyclin A1 promoter occurs independently of CpG methylation.

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