Microarray based global transcriptome profiling reveals involvement of non-Hsa21 genes and microRNAs in molecular mechanism of Down syndrome pathogenesis

Dendrobium nestor is a famous orchid species in the Orchidaceae family. There is a diversity of flower colorations in the Dendrobium species, but knowledge of the genes involved and molecular mechanism underlying the flower color formation in D. nestor is less studied. Therefore, we performed transcriptome profiling using Illumina sequencing to facilitate thorough studies of the purple color formation in petal samples collected at three developmental stages, namely—flower bud stage (F), half bloom stage (H), and full bloom stage (B) in D. nestor. In addition, we identified key genes and their biosynthetic pathways as well as the transcription factors (TFs) associated with purple flower color formation. We found that the phenylpropanoid–flavonoid–anthocyanin biosynthesis genes such as phenylalanine ammonia lyase, chalcone synthase, anthocyanidin synthase, and UDP-flavonoid glucosyl transferase, were largely up-regulated in the H and B samples as compared to the F samples. This upregulation might partly account for the accumulation of anthocyanins, which confer the purple coloration in these samples. We further identified several differentially expressed genes related to phytohormones such as auxin, ethylene, cytokinins, salicylic acid, brassinosteroid, and abscisic acid, as well as TFs such as MYB and bHLH, which might play important roles in color formation in D. nestor flower. Sturdy upregulation of anthocyanin biosynthetic structural genes might be a potential regulatory mechanism in purple color formation in D. nestor flowers. Several TFs were predicted to regulate the anthocyanin genes through a K-mean clustering analysis. Our study provides valuable resource for future studies to expand our understanding of flower color development mechanisms in D. nestor.

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Global transcriptome profiling analysis reveals insight into saliva-responsive genes in alfalfa

Plant Cell Reports ◽

10.1007/s00299-015-1903-9 ◽

2015 ◽

Vol 35 (3) ◽

pp. 561-571 ◽

Cited By ~ 18

Author(s):

Wenxian Liu ◽

Zhengshe Zhang ◽

Shuangyan Chen ◽

Lichao Ma ◽

Hucheng Wang ◽

...

Keyword(s):

Transcriptome Profiling ◽

Global Transcriptome ◽

Profiling Analysis ◽

Insight Into

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Transcriptome profiling analysis of muscle tissue reveals potential candidate genes affecting water holding capacity in Chinese Simmental beef cattle

Scientific Reports ◽

10.1038/s41598-021-91373-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Lili Du ◽

Tianpeng Chang ◽

Bingxing An ◽

Mang Liang ◽

Xinghai Duan ◽

...

Keyword(s):

Beef Cattle ◽

Candidate Genes ◽

Molecular Mechanism ◽

Meat Quality ◽

Relevant Literature ◽

Transcriptome Profiling ◽

Water Holding Capacity ◽

Potential Candidate ◽

Protein Protein Interaction ◽

Water Holding

AbstractWater holding capacity (WHC) is an important sensory attribute that greatly influences meat quality. However, the molecular mechanism that regulates the beef WHC remains to be elucidated. In this study, the longissimus dorsi (LD) muscles of 49 Chinese Simmental beef cattle were measured for meat quality traits and subjected to RNA sequencing. WHC had significant correlation with 35 kg water loss (r = − 0.99, p < 0.01) and IMF content (r = 0.31, p < 0.05), but not with SF (r = − 0.20, p = 0.18) and pH (r = 0.11, p = 0.44). Eight individuals with the highest WHC (H-WHC) and the lowest WHC (L-WHC) were selected for transcriptome analysis. A total of 865 genes were identified as differentially expressed genes (DEGs) between two groups, of which 633 genes were up-regulated and 232 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that DEGs were significantly enriched in 15 GO terms and 96 pathways. Additionally, based on protein–protein interaction (PPI) network, animal QTL database (QTLdb), and relevant literature, the study not only confirmed seven genes (HSPA12A, HSPA13, PPARγ, MYL2, MYPN, TPI, and ATP2A1) influenced WHC in accordance with previous studies, but also identified ATP2B4, ACTN1, ITGAV, TGFBR1, THBS1, and TEK as the most promising novel candidate genes affecting the WHC. These findings could offer important insight for exploring the molecular mechanism underlying the WHC trait and facilitate the improvement of beef quality.

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Molecular mechanism of temperature-dependent sex determination and differentiation in Chinese alligator revealed by developmental transcriptome profiling

Science Bulletin ◽

10.1016/j.scib.2018.01.004 ◽

2018 ◽

Vol 63 (4) ◽

pp. 209-212 ◽

Cited By ~ 5

Author(s):

Jian-Qing Lin ◽

Qi Zhou ◽

Hai-Qiong Yang ◽

Li-Ming Fang ◽

Ke-Yi Tang ◽

...

Keyword(s):

Sex Determination ◽

Molecular Mechanism ◽

Transcriptome Profiling ◽

Temperature Dependent ◽

Chinese Alligator

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Transcriptome and mebabolomic profiling: the effect of LED light quality on morphological traits, and phenylpropanoid-derived compounds accumulation in Sarcandra glabra seedlings

10.21203/rs.3.rs-26873/v1 ◽

2020 ◽

Author(s):

Dejin Xie ◽

Lingyan Chen ◽

Chengcheng Zhou ◽

Muhammad Waqqas Khan Tarin ◽

Deming Yang ◽

...

Keyword(s):

Leaf Area ◽

Molecular Mechanism ◽

Red Light ◽

Chinese Herb ◽

Leaf Tissue ◽

Transcriptome Profiling ◽

Accumulation Pattern ◽

Phenylpropanoid Biosynthesis ◽

Myb Proteins ◽

Almost All

Abstract Background Sarcandra glabra is an evergreen and traditional Chinese herb, having medicinal significance as anti-oxidant, anti-bacterial, anti-inflammatory, and anti-tumor. Recently, China has initiated to establish cultivation of this plant in greenhouse under artificial light-emitting diodes (LED). However, little is known regarding the effects of the different LED lights on plant growth, accumulation pattern of secondary metabolites, and the molecular mechanism of Sarcandra glabra. Results Compared to white light (WL), the red light (RL) increased the height and decreased the stem diameter and leaf area, while blue light (BL) suppressed the height and leaf area. According to our transcriptome profiling, some differentially expressed genes (DEGs) were enriched in the phenylpropanoid biosynthesis. We identified 46 unigenes encoding for almost all known enzymes involved in phenylpropanoid biosynthesis, while the expression level of RNA-seq and qPCR were largely consistent. Meanwhile, we found 53 unigenes encoding R2R3-MYB proteins and 53 unigenes encoding bHLH proteins that several of them were related to flavonoids biosynthesis. Based on metabolomic profiling, a total of 454 metabolites were detected and the distribution of chemicals varied significantly. While flavonoids, phenolic acids, and tannins were mainly located in leaves; Organic acids, lignans and coumarins, and terpenoids were much more abundant in WG (root tissue under WL). Meanwhile, the yields of most flavonoids from BY (leaf tissue under BL) and the synthesis of primarily targeted compounds was lower than in WY (leaf tissue under WL) and RY (leaf tissue under RL). Instead, the leaves grown under RL exhibited a greater production of bioactive phytochemicals such as esculetin, fraxetin, esculin, and scopoletin. Conclusion These results provide further insight into the molecular mechanism of metabolites accumulation patterns in S. glabra under different light conditions, enabling the development of optimum breeding conditions for this plant.

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Musashi-2 controls cell fate, lineage bias, and TGF-β signaling in HSCs

Journal of Experimental Medicine ◽

10.1084/jem.20130736 ◽

2014 ◽

Vol 211 (1) ◽

pp. 71-87 ◽

Cited By ~ 87

Author(s):

Sun-Mi Park ◽

Raquel P. Deering ◽

Yuheng Lu ◽

Patrick Tivnan ◽

Steve Lianoglou ◽

...

Keyword(s):

Cell Fate ◽

Rna Binding ◽

Asymmetric Cell Division ◽

Cell Function ◽

Rna Binding Protein ◽

Transcriptome Profiling ◽

Hematopoietic Stem ◽

Rna Translation ◽

Important Regulator ◽

Global Transcriptome

Hematopoietic stem cells (HSCs) are maintained through the regulation of symmetric and asymmetric cell division. We report that conditional ablation of the RNA-binding protein Msi2 results in a failure of HSC maintenance and engraftment caused by a loss of quiescence and increased commitment divisions. Contrary to previous studies, we found that these phenotypes were independent of Numb. Global transcriptome profiling and RNA target analysis uncovered Msi2 interactions at multiple nodes within pathways that govern RNA translation, stem cell function, and TGF-β signaling. Msi2-null HSCs are insensitive to TGF-β–mediated expansion and have decreased signaling output, resulting in a loss of myeloid-restricted HSCs and myeloid reconstitution. Thus, Msi2 is an important regulator of the HSC translatome and balances HSC homeostasis and lineage bias.

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