scholarly journals Morphological observation, RNA-Seq quantification, and expression profiling: novel insight into grafting-responsive carotenoid biosynthesis in watermelon grafted onto pumpkin rootstock

2016 ◽  
Author(s):  
Guang Liu ◽  
Xingping Yang ◽  
Jinhua Xu ◽  
Man Zhang ◽  
Qian Hou ◽  
...  
Keyword(s):  
Expression Profiling ◽  
Carotenoid Biosynthesis ◽  
Morphological Observation ◽  
Rna Seq ◽  
Insight Into

scholarly journals NKL Homeobox Gene VENTX Is Part of a Regulatory Network in Human Conventional Dendritic Cells

2021 ◽  
Vol 22 (11) ◽  
pp. 5902
Author(s):  
Stefan Nagel ◽  
Claudia Pommerenke ◽  
Corinna Meyer ◽  
Hans G. Drexler
Keyword(s):  
Dendritic Cells ◽  
Transcription Factors ◽  
Cell Lines ◽  
Expression Profiling ◽  
Regulatory Network ◽  
Homeobox Gene ◽  
Leukemia Cell Line ◽  
Specific Gene ◽  
Rna Seq ◽  
And Function

Recently, we documented a hematopoietic NKL-code mapping physiological expression patterns of NKL homeobox genes in human myelopoiesis including monocytes and their derived dendritic cells (DCs). Here, we enlarge this map to include normal NKL homeobox gene expressions in progenitor-derived DCs. Analysis of public gene expression profiling and RNA-seq datasets containing plasmacytoid and conventional dendritic cells (pDC and cDC) demonstrated HHEX activity in both entities while cDCs additionally expressed VENTX. The consequent aim of our study was to examine regulation and function of VENTX in DCs. We compared profiling data of VENTX-positive cDC and monocytes with VENTX-negative pDC and common myeloid progenitor entities and revealed several differentially expressed genes encoding transcription factors and pathway components, representing potential VENTX regulators. Screening of RNA-seq data for 100 leukemia/lymphoma cell lines identified prominent VENTX expression in an acute myelomonocytic leukemia cell line, MUTZ-3 containing inv(3)(q21q26) and t(12;22)(p13;q11) and representing a model for DC differentiation studies. Furthermore, extended gene analyses indicated that MUTZ-3 is associated with the subtype cDC2. In addition to analysis of public chromatin immune-precipitation data, subsequent knockdown experiments and modulations of signaling pathways in MUTZ-3 and control cell lines confirmed identified candidate transcription factors CEBPB, ETV6, EVI1, GATA2, IRF2, MN1, SPIB, and SPI1 and the CSF-, NOTCH-, and TNFa-pathways as VENTX regulators. Live-cell imaging analyses of MUTZ-3 cells treated for VENTX knockdown excluded impacts on apoptosis or induced alteration of differentiation-associated cell morphology. In contrast, target gene analysis performed by expression profiling of knockdown-treated MUTZ-3 cells revealed VENTX-mediated activation of several cDC-specific genes including CSFR1, EGR2, and MIR10A and inhibition of pDC-specific genes like RUNX2. Taken together, we added NKL homeobox gene activities for progenitor-derived DCs to the NKL-code, showing that VENTX is expressed in cDCs but not in pDCs and forms part of a cDC-specific gene regulatory network operating in DC differentiation and function.

scholarly journals Transcriptome Sequencing and Biochemical Analysis of Perianths and Coronas Reveal Flower Color Formation in Narcissus pseudonarcissus

2018 ◽  
Vol 19 (12) ◽  
pp. 4006 ◽  
Author(s):  
Xi Li ◽  
Dongqin Tang ◽  
Hui Du ◽  
Yimin Shi
Keyword(s):  
Flower Color ◽  
Carotenoid Biosynthesis ◽  
Carotenoid Content ◽  
Rna Seq ◽  
Color Formation ◽  
Light Yellow ◽  
Color Fading ◽  
Narcissus Pseudonarcissus ◽  
Bulbous Plant ◽  
Β Carotene

Narcissus pseudonarcissus is an important bulbous plant with white or yellow perianths and light yellow to orange-red coronas, but little is known regarding the biochemical and molecular basis related to flower color polymorphisms. To investigate the mechanism of color formation, RNA-Seq of flower of two widely cultured cultivars (‘Slim Whitman’ and ‘Pinza’) with different flower color was performed. A total of 84,463 unigenes were generated from the perianths and coronas. By parallel metabolomic and transcriptomic analyses, we provide an overview of carotenoid biosynthesis, degradation, and accumulation in N. pseudonarcissus. The results showed that the content of carotenoids in the corona was higher than that in the perianth in both cultivars. Accordingly, phytoene synthase (PSY) transcripts have a higher abundance in the coronas than that in perianths. While the expression levels of carotenoid biosynthetic genes, like GGPPS, PSY, and LCY-e, were not significantly different between two cultivars. In contrast, the carotenoid degradation gene NpCCD4 was highly expressed in white-perianth cultivars, but was hardly detected in yellow-perianth cultivars. Silencing of NpCCD4 resulted in a significant increase in carotenoid accumulation, especially in all-trans-β-carotene. Therefore, we presume that NpCCD4 is a crucial factor that causes the low carotenoid content and color fading phenomenon of ‘Slim Whitman’ by mediating carotenoid turnover. Our findings provide mass RNA-seq data and new insights into carotenoid metabolism in N. pseudonarcissus.

scholarly journals Gene identification using RNA-seq in two sweetpotato genotypes and the use of mining to analyze carotenoid biosynthesis

2017 ◽  
Vol 109 ◽  
pp. 189-195 ◽  
Author(s):  
Z. Qin ◽  
A. Li ◽  
F. Hou ◽  
Q. Wang ◽  
S. Dong ◽  
...  
Keyword(s):  
Carotenoid Biosynthesis ◽  
Gene Identification ◽  
Rna Seq

scholarly journals RNA-Seq Approach for Genetic Improvement of Meat Quality in Pig and Evolutionary Insight into the Substrate Specificity of Animal Carbonyl Reductases

PLoS ONE ◽  
2012 ◽  
Vol 7 (9) ◽  
pp. e42198 ◽  
Author(s):  
Won Yong Jung ◽  
Seul Gi Kwon ◽  
Minky Son ◽  
Eun Seok Cho ◽  
Yuno Lee ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Meat Quality ◽  
Genetic Improvement ◽  
Rna Seq ◽  
Insight Into

Digital expression profiling of a grape-bud EST collection leads to new insight into molecular events during grape-bud dormancy release

Plant Science ◽  
2007 ◽  
Vol 173 (4) ◽  
pp. 446-457 ◽  
Author(s):  
Tsvika Keilin ◽  
Xuequn Pang ◽  
Jaganatha Venkateswari ◽  
Tamar Halaly ◽  
Omer Crane ◽  
...  
Keyword(s):  
Expression Profiling ◽  
Bud Dormancy ◽  
Dormancy Release ◽  
Molecular Events ◽  
Digital Expression ◽  
Bud Dormancy Release ◽  
Insight Into

scholarly journals A Transcriptomic Analysis of Gonads from the Low-Temperature-Induced Masculinization of Takifugu rubripes

Animals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 3419
Author(s):  
He Zhou ◽  
Yuqing Sun ◽  
Xin Li ◽  
Ziyu Zhou ◽  
Kexin Ma ◽  
...  
Keyword(s):  
Low Temperature ◽  
Transcriptome Sequencing ◽  
Average Length ◽  
Gonadal Development ◽  
Temperature Treatment ◽  
Takifugu Rubripes ◽  
Rna Seq ◽  
Low Temperature Treatment ◽  
Cultured Fish ◽  
Insight Into

The phenotypic sex of fish is usually plastic. Low-temperature treatment induces the masculinization of Takifugu rubripes, resulting in pseudo-males (PM) with the physiological sex of a male (M) and genetic sex of a female (F). For a comparison of gonadal transcriptomes, we collected gonads from three groups of T. rubripes (F, M, and PM) for high-throughput transcriptome sequencing. The results provided 467,640,218 raw reads (70.15 Gb) and a total of 436,151,088 clean reads (65.43 Gb), with an average length of 150 bp. Only 79 differentially expressed genes (DEGs) were identified between F and PM, whereas 12,041 and 11,528 DEGs were identified between F and M, and PM and M, respectively. According to the functional annotation of DEGs, 13 DEGs related to gonadal development were screened (LOC101066759, dgat1, limk1, fbxl3, col6a3, fgfr3, dusp22b, svil, abhd17b, srgap3, tmem88b, bud4, and mustn10) which might participate in formating PM. A quantitative PCR of the DEGs confirmed the reliability of the RNA-seq. Our results provide an important contribution to the genome sequence resources for T. rubripes and insight into the molecular mechanism of masculinization in a cultured fish subject to low-temperature treatment.

scholarly journals Dysregulated Pyrimidine Biosynthesis Contributes to 5-FU Resistance in SCLC Patient-Derived Organoids but Response to a Novel Polymeric Fluoropyrimidine, CF10

Cancers ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 788 ◽  
Author(s):  
William H. Gmeiner ◽  
Lance D. Miller ◽  
Jeff W. Chou ◽  
Anthony Dominijanni ◽  
Lysette Mutkus ◽  
...  
Keyword(s):  
Drug Target ◽  
Pyrimidine Biosynthesis ◽  
Cancer Drug ◽  
Rna Seq ◽  
Novel Approach ◽  
Anti Cancer ◽  
New Treatments ◽  
Insight Into ◽  
Sclc Patient ◽  
Identify Gene Expression

Chemo-immunotherapy is central to the treatment of small cell lung cancer (SCLC). Despite modest progress made with the addition of immunotherapy, current cytotoxic regimens display minimal survival benefit and new treatments are needed. Thymidylate synthase (TS) is a well-validated anti-cancer drug target, but conventional TS inhibitors display limited clinical efficacy in refractory or recurrent SCLC. We performed RNA-Seq analysis to identify gene expression changes in SCLC biopsy samples to provide mechanistic insight into the potential utility of targeting pyrimidine biosynthesis to treat SCLC. We identified systematic dysregulation of pyrimidine biosynthesis, including elevated TYMS expression that likely contributes to the lack of efficacy for current TS inhibitors in SCLC. We also identified E2F1-3 upregulation in SCLC as a potential driver of TYMS expression that may contribute to tumor aggressiveness. To test if TS inhibition could be a viable strategy for SCLC treatment, we developed patient-derived organoids (PDOs) from human SCLC biopsy samples and used these to evaluate both conventional fluoropyrimidine drugs (e.g., 5-fluorouracil), platinum-based drugs, and CF10, a novel fluoropyrimidine polymer with enhanced TS inhibition activity. PDOs were relatively resistant to 5-FU and while moderately sensitive to the front-line agent cisplatin, were relatively more sensitive to CF10. Our studies demonstrate dysregulated pyrimidine biosynthesis contributes to drug resistance in SCLC and indicate that a novel approach to target these pathways may improve outcomes.

scholarly journals Author Correction: De novo assembly of the Platycladus orientalis (L.) Franco transcriptome provides insight into the development and pollination mechanism of female cone based on RNA-Seq data

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Wei Zhou ◽  
Qi Chen ◽  
Xiao-Bing Wang ◽  
Tyler O. Hughes ◽  
Jian-Jun Liu ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
De Novo ◽  
Rna Seq ◽  
Female Cone ◽  
Pollination Mechanism ◽  
Platycladus Orientalis ◽  
Insight Into

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