scholarly journals Transcriptome analysis reveals regulatory networks and hub genes in flavonoid metabolism of Rosa roxburghii

2021 ◽  
Author(s):  
Huiqing Yan ◽  
Xiaolong Huang ◽  
Zongmin Wu ◽  
Yanjing Liu ◽  
Yin Yi ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Transcription Factors ◽  
Regulatory Networks ◽  
Anthocyanin Content ◽  
Flavonoid Pathway ◽  
Flavonoid Metabolism ◽  
Coa Ligase ◽  
Black Module ◽  
Rosa Roxburghii Tratt ◽  
Rosa Roxburghii

Rosa roxburghii Tratt, the most popular fruit that blooms in the southwest of China, is rich in flavonoids. However, the regulatory network and critical genes involved in the metabolism of flavonoid compounds in R. roxburghii are still unknown. In this study, we revealed that flavonoid, anthocyanin and catechin accumulated at different levels in various tissues of R. roxburghii . We further obtained and analyzed differentially expressed genes (DEGs) involved in flavonoid metabolism from five samples of R. roxburghii by transcriptome sequencing. A total of 1 130 DEGs were identified, including 166 flavonoid pathway biosynthesis genes, 622 transcription factors, 301 transporters, and 221 cytochrome P450 proteins. A weighted gene co-expression network analysis (WGCNA) of the DEGs uncovered different co-expression networks. In terms of biosynthesis enzymes, cytochrome P450 CYP749A22 and CYP72A219 were highlighted in regulation flavonoids content. Anthocyanin 3-O-glucosyltransferase and F3’H were the top two critical enzymes for anthocyanin content. In contrast, caffeic acid 3-O-methyltransferase, 4-coumarate-CoA ligase, and shikimate O-hydroxycinnamoyl transferase were essential for catechin accumulation. Additionally, the eigengene network of the “black” module had high correlations with total flavonoid (r= 0.9, p=5e-06). There were 26 eigengenes in the “black” module, including six flavonoid biosynthesis, 14 TFs and six transporters. Among them, besides cytochrome P450 proteins ( DN136557_c0_g1 , DN135573_c0_g1 and DN145971_c4_g1 ), isoflavone-hydroxylase ( DN143321_c3_g1 ) was crucial for total flavonoids content based on the high degree of connectivity. The transcription factors RrWRKY45 ( DN142829_c1_g5 ), RrTCP20 ( DN146443_c1_g1) and RrERF118 ( DN141507_c3_g2) were significantly correlated with flavonoids in R. roxburghii . The present transcriptomic and biochemical data on metabolites should encourage further investigation on functional genomics and breeding of R. roxburghii with strong pharmaceutical potential.

Transcriptional Control of Parturition: Insights from Gene Regulation Studies in the Myometrium

2021 ◽  
Author(s):  
Nawrah Khader ◽  
Virlana M Shchuka ◽  
Oksana Shynlova ◽  
Jennifer A Mitchell
Keyword(s):  
Transcription Factors ◽  
Regulatory Networks ◽  
Transcriptional Control ◽  
Progesterone Receptors ◽  
Activator Protein 1 ◽  
Transcriptional Regulatory Networks ◽  
Regulatory Pathways ◽  
Transcriptional Regulatory ◽  
Mechanistic Basis ◽  
Labour Onset

Abstract The onset of labour is a culmination of a series of highly coordinated and preparatory physiological events that take place throughout the gestational period. In order to produce the associated contractions needed for fetal delivery, smooth muscle cells in the muscular layer of the uterus (i.e. myometrium) undergo a transition from quiescent to contractile phenotypes. Here, we present the current understanding of the roles transcription factors play in critical labour-associated gene expression changes as part of the molecular mechanistic basis for this transition. Consideration is given to both transcription factors that have been well-studied in a myometrial context, i.e. activator protein 1 (AP-1), progesterone receptors (PRs), estrogen receptors (ERs), and nuclear factor kappa B (NF-κB), as well as additional transcription factors whose gestational event-driving contributions have been demonstrated more recently. These transcription factors may form pregnancy- and labour- associated transcriptional regulatory networks in the myometrium to modulate the timing of labour onset. A more thorough understanding of the transcription factor-mediated, labour-promoting regulatory pathways holds promise for the development of new therapeutic treatments that can be used for the prevention of preterm labour in at-risk women.

scholarly journals Comprehensive network modeling from single cell RNA sequencing of human and mouse reveals well conserved transcription regulation of hematopoiesis

BMC Genomics ◽  
2020 ◽  
Vol 21 (S11) ◽  
Author(s):  
Shouguo Gao ◽  
Zhijie Wu ◽  
Xingmin Feng ◽  
Sachiko Kajigaya ◽  
Xujing Wang ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Transcription Factors ◽  
Single Cell ◽  
Rna Sequencing ◽  
Transcription Regulation ◽  
Regulatory Networks ◽  
Stem Cell Differentiation ◽  
Hematopoietic Stem ◽  
Single Cell Rna Sequencing ◽  
Human And Mouse

Abstract Background Presently, there is no comprehensive analysis of the transcription regulation network in hematopoiesis. Comparison of networks arising from gene co-expression across species can facilitate an understanding of the conservation of functional gene modules in hematopoiesis. Results We used single-cell RNA sequencing to profile bone marrow from human and mouse, and inferred transcription regulatory networks in each species in order to characterize transcriptional programs governing hematopoietic stem cell differentiation. We designed an algorithm for network reconstruction to conduct comparative transcriptomic analysis of hematopoietic gene co-expression and transcription regulation in human and mouse bone marrow cells. Co-expression network connectivity of hematopoiesis-related genes was found to be well conserved between mouse and human. The co-expression network showed “small-world” and “scale-free” architecture. The gene regulatory network formed a hierarchical structure, and hematopoiesis transcription factors localized to the hierarchy’s middle level. Conclusions Transcriptional regulatory networks are well conserved between human and mouse. The hierarchical organization of transcription factors may provide insights into hematopoietic cell lineage commitment, and to signal processing, cell survival and disease initiation.

scholarly journals Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jifang Zhang ◽  
Jian Zhao ◽  
Qunyun Tan ◽  
Xiaojun Qiu ◽  
Shiyong Mei
Keyword(s):  
Transcription Factors ◽  
Raphanus Sativus ◽  
Regulatory Networks ◽  
Anthocyanin Biosynthesis ◽  
Comparative Transcriptome ◽  
Structural Genes ◽  
Key Genes ◽  
Transcript Profiles ◽  
Species Specific ◽  
Anthocyanin Biosynthetic Genes

AbstractRadish (Raphanus sativus) is an important vegetable worldwide that exhibits different flesh and skin colors. The anthocyanins responsible for the red and purple coloring in radishes possess nutritional value and pharmaceutical potential. To explore the structural and regulatory networks related to anthocyanin biosynthesis and identify key genes, we performed comparative transcriptome analyses of the skin and flesh of six colored radish accessions. The transcript profiles showed that each accession had a species-specific transcript profile. For radish pigmentation accumulation, the expression levels of anthocyanin biosynthetic genes (RsTT4, RsC4H, RsTT7, RsCCOAMT, RsDFR, and RsLDOX) were significantly upregulated in the red- and purple-colored accessions, but were downregulated or absent in the white and black accessions. The correlation test, combined with metabolome (PCC > 0.95), revealed five structural genes (RsTT4, RsDFR, RsCCOAMT, RsF3H, and RsBG8L) and three transcription factors (RsTT8-1, RsTT8-2, and RsPAR1) to be significantly correlated with flavonoids in the skin of the taproot. Four structural genes (RsBG8L, RsDFR, RsCCOAMT, and RsLDOX) and nine transcription factors (RsTT8-1, RsTT8-2, RsMYB24L, RsbHLH57, RsPAR2L, RsbHLH113L, RsOGR3L, RsMYB24, and RsMYB34L) were found to be significantly correlated with metabolites in the flesh of the taproot. This study provides a foundation for future studies on the gene functions and genetic diversity of radish pigmentation and should aid in the cultivation of new valuable radish varieties.

scholarly journals The interplay of microRNAs and transcription factors in autophagy regulation in nonalcoholic fatty liver disease

2021 ◽  
Author(s):  
Yumi Kim ◽  
Da-Hye Lee ◽  
So-Hyun Park ◽  
Tae-Il Jeon ◽  
Chang Hwa Jung
Keyword(s):  
Transcription Factors ◽  
Liver Disease ◽  
Fatty Liver ◽  
Nonalcoholic Fatty Liver Disease ◽  
Posttranscriptional Regulation ◽  
Fatty Liver Disease ◽  
Regulatory Networks ◽  
Nonalcoholic Fatty Liver ◽  
Autophagy Pathway ◽  
Cytoplasmic Processes

AbstractThe autophagy-lysosomal degradation system has an important role in maintaining liver homeostasis by removing unnecessary intracellular components. Impaired autophagy has been linked to nonalcoholic fatty liver disease (NAFLD), which includes hepatitis, steatosis, fibrosis, and cirrhosis. Thus, gaining an understanding of the mechanisms that regulate autophagy and how autophagy contributes to the development and progression of NAFLD has become the focus of recent studies. Autophagy regulation has been thought to be primarily regulated by cytoplasmic processes; however, recent studies have shown that microRNAs (miRNAs) and transcription factors (TFs) also act as key regulators of autophagy by targeting autophagy-related genes. In this review, we summarize the miRNAs and TFs that regulate the autophagy pathway in NAFLD. We further focus on the transcriptional and posttranscriptional regulation of autophagy and discuss the complex regulatory networks involving these regulators in autophagy. Finally, we highlight the potential of targeting miRNAs and TFs involved in the regulation of autophagy for the treatment of NAFLD.

Botanical characteristics, phytochemistry and related biological activities of Rosa roxburghii Tratt fruit and the potential use in functional foods: a review

2021 ◽  
Author(s):  
Litao Wang ◽  
Mu-Jie Lv ◽  
Juan-Yan An ◽  
Xiao-Hong Fan ◽  
Ming-Zhu Dong ◽  
...  
Keyword(s):  
Climate Change ◽  
Functional Foods ◽  
Biological Activities ◽  
Supply And Demand ◽  
Arable Land ◽  
Rosa Roxburghii Tratt ◽  
Botanical Characteristics ◽  
Rosa Roxburghii ◽  
Global Population ◽  
Potential Use

With increasing global population, the reduction of arable land and climate change and incongruity between food supply and demand has become increasingly severe. Nowadays, with the elementary nutrients required for...

Structural characterization of a novel acidic polysaccharide from Rosa roxburghii Tratt fruit and its α-glucosidase inhibitory activity

2018 ◽  
Vol 9 (7) ◽  
pp. 3974-3985 ◽  
Author(s):  
Lei Wang ◽  
Chun Chen ◽  
Bin Zhang ◽  
Qiang Huang ◽  
Xiong Fu ◽  
...  
Keyword(s):  
Structural Characterization ◽  
Inhibitory Activity ◽  
Acidic Polysaccharide ◽  
Rosa Roxburghii Tratt ◽  
Rosa Roxburghii

An acidic polysaccharide (RTFP-3) extracted from Rosa roxburghii Tratt fruit can inhibit the activity of α-glucosidase.

scholarly journals Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638

Life ◽  
2018 ◽  
Vol 8 (4) ◽  
pp. 40 ◽  
Author(s):  
Antonia Denis ◽  
Mario Alberto Martínez-Núñez ◽  
Silvia Tenorio-Salgado ◽  
Ernesto Perez-Rueda
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Regulatory Networks ◽  
Pyrococcus Furiosus ◽  
Structural Domain ◽  
Transcriptional Regulatory Networks ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Transcriptional Regulatory ◽  
Cellular Domain

In recent years, there has been a large increase in the amount of experimental evidence for diverse archaeal organisms, and these findings allow for a comprehensive analysis of archaeal genetic organization. However, studies about regulatory mechanisms in this cellular domain are still limited. In this context, we identified a repertoire of 86 DNA-binding transcription factors (TFs) in the archaeon Pyrococcus furiosus DSM 3638, that are clustered into 32 evolutionary families. In structural terms, 45% of these proteins are composed of one structural domain, 41% have two domains, and 14% have three structural domains. The most abundant DNA-binding domain corresponds to the winged helix-turn-helix domain; with few alternative DNA-binding domains. We also identified seven regulons, which represent 13.5% (279 genes) of the total genes in this archaeon. These analyses increase our knowledge about gene regulation in P. furiosus DSM 3638 and provide additional clues for comprehensive modeling of transcriptional regulatory networks in the Archaea cellular domain.

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