scholarly journals Co-expression and Transcriptome Analysis of Marchantia polymorpha Transcription Factors Supports Class C ARFs as Independent Actors of an Ancient Auxin Regulatory Module

2018 ◽  
Vol 9 ◽  
Author(s):  
Eduardo Flores-Sandoval ◽  
Facundo Romani ◽  
John L. Bowman
Keyword(s):  
Transcription Factors ◽  
Transcriptome Analysis ◽  
Marchantia Polymorpha ◽  
Regulatory Module ◽  
Class C

scholarly journals Transcriptome Analysis of Marchantin Biosynthesis from the Liverwort Marchantia polymorpha

2017 ◽  
Vol 12 (8) ◽  
pp. 1934578X1701200
Author(s):  
Hironobu Takahashi ◽  
Yoshinori Asakawa
Keyword(s):  
Gene Expression ◽  
Transcriptome Analysis ◽  
Transcriptome Sequencing ◽  
Biological Activities ◽  
Digital Gene Expression ◽  
Marchantia Polymorpha ◽  
Rna Seq ◽  
Gene Expression Analyses

Marchantin A, the first characterized macrocyclic bis(bibenzyls) found in the liverwort Marchantia polymorpha shows interesting biological activities such as antifungal, antimicrobial, cytotoxic, antioxidant and muscle relaxing activity. Previously, Zenk et al. reported the phenylpropane/polymalonate pathway in the biosynthesis of the marchantins in M. polymorpha. To clear this pathway, transcriptome sequencing and digital gene expression analyses of M. polymorpha were carried out by using Illumina RNA-seq system.

Analysis of the transcription factors and their regulatory roles during a step-by-step differentiation of induced pluripotent stem cells into hepatocyte-like cells

2019 ◽  
Vol 15 (6) ◽  
pp. 383-398 ◽  
Author(s):  
Yannick Tauran ◽  
Stéphane Poulain ◽  
Myriam Lereau-Bernier ◽  
Mathieu Danoy ◽  
Marie Shinohara ◽  
...  
Keyword(s):  
Stem Cells ◽  
Transcription Factors ◽  
Induced Pluripotent Stem Cells ◽  
Transcriptome Analysis ◽  
Pluripotent Stem Cells ◽  
Original Method ◽  
Induced Pluripotent

Human induced pluripotent stem cells have been investigated through a sequential in vitro step-by-step differentiation into hepatocyte-like cells using nanoCAGE, an original method for promoters, transcription factors, and transcriptome analysis.

scholarly journals Transcriptome analysis of Pueraria candollei var. mirifica for gene discovery in the biosyntheses of isoflavones and miroestrol

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Nithiwat Suntichaikamolkul ◽  
Kittitya Tantisuwanichkul ◽  
Pinidphon Prombutara ◽  
Khwanlada Kobtrakul ◽  
Julie Zumsteg ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Transcriptome Analysis ◽  
De Novo ◽  
Biosynthetic Genes ◽  
Pueraria Candollei ◽  
Isoflavone Synthase ◽  
Young Leaves ◽  
Plausible Mechanism ◽  
Polymerase Chain ◽  
R2r3 Myb

Abstract Background Pueraria candollei var. mirifica, a Thai medicinal plant used traditionally as a rejuvenating herb, is known as a rich source of phytoestrogens, including isoflavonoids and the highly estrogenic miroestrol and deoxymiroestrol. Although these active constituents in P. candollei var. mirifica have been known for some time, actual knowledge regarding their biosynthetic genes remains unknown. Results Miroestrol biosynthesis was reconsidered and the most plausible mechanism starting from the isoflavonoid daidzein was proposed. A de novo transcriptome analysis was conducted using combined P. candollei var. mirifica tissues of young leaves, mature leaves, tuberous cortices, and cortex-excised tubers. A total of 166,923 contigs was assembled for functional annotation using protein databases and as a library for identification of genes that are potentially involved in the biosynthesis of isoflavonoids and miroestrol. Twenty-one differentially expressed genes from four separate libraries were identified as candidates involved in these biosynthetic pathways, and their respective expressions were validated by quantitative real-time reverse transcription polymerase chain reaction. Notably, isoflavonoid and miroestrol profiling generated by LC-MS/MS was positively correlated with expression levels of isoflavonoid biosynthetic genes across the four types of tissues. Moreover, we identified R2R3 MYB transcription factors that may be involved in the regulation of isoflavonoid biosynthesis in P. candollei var. mirifica. To confirm the function of a key-isoflavone biosynthetic gene, P. candollei var. mirifica isoflavone synthase identified in our library was transiently co-expressed with an Arabidopsis MYB12 transcription factor (AtMYB12) in Nicotiana benthamiana leaves. Remarkably, the combined expression of these proteins led to the production of the isoflavone genistein. Conclusions Our results provide compelling evidence regarding the integration of transcriptome and metabolome as a powerful tool for identifying biosynthetic genes and transcription factors possibly involved in the isoflavonoid and miroestrol biosyntheses in P. candollei var. mirifica.

scholarly journals Analogous and Diverse Functions of APSES-Type Transcription Factors in the Morphogenesis of the Entomopathogenic Fungus Metarhizium rileyi

2020 ◽  
Vol 86 (8) ◽  
Author(s):  
Caiyan Xin ◽  
Jinping Zhang ◽  
Siji Nian ◽  
Guangxi Wang ◽  
Zhongkang Wang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Transcriptome Analysis ◽  
Entomopathogenic Fungus ◽  
Regulatory Mechanisms ◽  
Sequencing Analysis ◽  
Fungal Virulence ◽  
Content Type ◽  
Dimorphic Transition ◽  
Metarhizium Rileyi ◽  
Fungal Morphogenesis

ABSTRACT APSES-type transcription factors (TFs) have analogous and diverse functions in the regulation of fungal morphogenesis processes. However, little is known about these functions in microsclerotium formation. In this study, we characterized two orthologous APSES genes (MrStuA and MrXbp) in the entomopathogenic fungus Metarhizium rileyi. Deletion of either MrStuA or MrXbp impaired dimorphic transition, conidiation, fungal virulence, and microsclerotium formation. Compared with the wild-type strain, ΔMrStuA and ΔMrXbp mutants were hypersensitive to thermal and oxidative stress. Furthermore, transcriptome sequencing analysis revealed that MrStuA and MrXbp independently regulate their own distinctive subsets of signaling pathways during dimorphic transition and microsclerotium formation, but they also show an overlapping regulation of genes during these two distinct morphogenesis processes. These results provide a global insight into vital roles of MrStuA and MrXbp in M. rileyi and aid in dissection of the interacting regulatory mechanisms of dimorphism transition and microsclerotium development. IMPORTANCE Transcription factors (TFs) are core components of the signaling pathway and play an important role in transcriptional regulation of gene expression during fungal morphogenesis processes. A prevailing theory suggests an interplay between different TFs regulating microsclerotial differentiation; however, the persisting issue remains that these interplay mechanisms are not clear. Here, we analyzed two members of the APSES-type TFs in Metarhizium rileyi using a gene deletion strategy and transcriptome analysis. Mutants were significantly impaired in microsclerotium formation and dimorphic transition. Transcriptome analysis provided evidence for interacting regulatory mechanisms by the two TFs in microsclerotium formation and dimorphic transition. Furthermore, we investigated their overlapping roles in mediating the expression of genes required for different fungal morphogenesis processes. Characterization of TFs in this study will aid in dissecting the interplay between regulatory mechanisms in fungal morphogenesis processes.

scholarly journals A proximal tissue-specific module and a distal negative regulatory module control apolipoprotein(a) gene transcription

2004 ◽  
Vol 379 (1) ◽  
pp. 151-159 ◽  
Author(s):  
Sarita NEGI ◽  
Saurabh K. SINGH ◽  
Nirupma PATI ◽  
Vikas HANDA ◽  
Ruchi CHAUHAN ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Gene Transcription ◽  
Hela Cells ◽  
Hepg2 Cells ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Tissue Specific ◽  
Apolipoprotein A ◽  
Regulatory Module ◽  
Specific Manner

The apo(a) [apolipoprotein(a)] gene is responsible for variations in plasma lipoprotein(a), high levels of which are a risk factor for atherosclerosis and myocardial infarction. The apo(a) promoter stimulates the expression of reporter genes in HepG2 cells, but not in HeLa cells. In the present study, we demonstrate that the 1.4 kb apo(a) promoter comprises two composite regulatory regions: a distal negative regulatory module (positions −1432 to −716) and a proximal tissue-specific module (−716 to −616). The distal negative regulatory module contains two strong negative regulatory regions [polymorphic PNR (pentanucleotide repeat region) and NREβ (negative regulatory element β)], which sandwich the postive regulatory region PREβ (positive regulatory element β). The PNR was shown to bind to transcription factors in a tissue-specific manner, whereas the ubiquitous transcription factors hepatocyte nuclear factor 3α and GATA binding protein 4 bound to NREβ to repress gene transcription. The proximal tissue-specific module contains two regulatory elements: an activating region (PREα) that activates transcription in HepG2 cells, and NREα, which is responsible for repressing the apo(a) gene in HeLa cells. NREα binds to a HeLa-specific repressor. These multiple regulatory elements might work co-operatively to finely regulate apo(a) gene expression. Although the tissue-specific module is required for apo(a) gene activation and repression in a tissue-specific manner, the combinatorial interplay of the distal and proximal regulators might define the complex pathway(s) of apo(a) gene regulation.

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