scholarly journals Transcriptome Analysis of Improved Wool Production in Skin-Specific Transgenic Sheep Overexpressing Ovine β-Catenin

2019 ◽  
Vol 20 (3) ◽  
pp. 620 ◽  
Author(s):  
Jiankui Wang ◽  
Kai Cui ◽  
Zu Yang ◽  
Tun Li ◽  
Guoying Hua ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Wnt Signaling Pathway ◽  
Hair Follicles ◽  
Rna Seq ◽  
Wool Production ◽  
Evolutionarily Conserved ◽  
Transgenic Sheep ◽  
Wool Follicle ◽  
Polymerase Chain ◽  
Canonical Wnt

β-Catenin is an evolutionarily conserved molecule in the canonical Wnt signaling pathway, which controls decisive steps in embryogenesis and functions as a crucial effector in the development of hair follicles. However, the molecular mechanisms underlying wool production have not been fully elucidated. In this study, we investigated the effects of ovine β-catenin on wool follicles of transgenic sheep produced by pronuclear microinjection with a skin-specific promoter of human keratin14 (k14). Both polymerase chain reaction and Southern blot analysis showed that the sheep carried the ovine β-catenin gene and that the β-catenin gene could be stably inherited. To study the molecular responses to high expression of β-catenin, high-throughput RNA-seq technology was employed using three transgenic sheep and their wild-type siblings. These findings suggest that β-catenin normally plays an important role in wool follicle development by activating the downstream genes of the Wnt pathway and enhancing the expression of keratin protein genes and keratin-associated protein genes.

scholarly journals Integrated Physiological and Transcriptomic Analyses Responses to Altitude Stress in Oat (Avena sativa L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Yu Jinqiu ◽  
Li Bing ◽  
Song Tingting ◽  
He Jinglei ◽  
KongLing Zelai ◽  
...  
Keyword(s):  
High Altitude ◽  
Avena Sativa ◽  
Molecular Mechanisms ◽  
Rna Seq ◽  
High Altitudes ◽  
Genome Wide ◽  
New Findings ◽  
Polymerase Chain ◽  
Transcriptomic Changes ◽  
Stressful Environments

Oat is an annual gramineous forage grass with the remarkable ability to survive under various stressful environments. However, understanding the effects of high altitude stresses on oats is poor. Therefore, the physiological and the transcriptomic changes were analyzed at two sites with different altitudes, low (ca. 2,080 m) or high (ca. 2,918 m), respectively. Higher levels of antioxidant enzyme activity, reactive oxygen and major reductions in photosynthesis-related markers were suggested for oats at high altitudes. Furthermore, oat yields were severely suppressed at the high altitude. RNA-seq results showed that 11,639 differentially expressed genes were detected at both the low and the high altitudes in which 5,203 up-regulated and 6,436 down-regulated. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment tests were conducted and a group of major high altitude-responsive pigment metabolism genes, photosynthesis, hormone signaling, and cutin, suberine and wax biosynthesis were excavated. Using quantitative real-time polymerase chain response, we also confirmed expression levels of 20 DEGs (qRT-PCR). In summary, our study generated genome-wide transcript profile and may be useful for understanding the molecular mechanisms of Avena sativa L. in response to high altitude stress. These new findings contribute to our deeper relevant researches on high altitude stresses and further exploring new candidategenes for adapting plateau environment oat molecular breeding.

scholarly journals Identification and characterization of circRNAs in the skin during the wool follicle development of Aohan fine wool sheep

2019 ◽  
Author(s):  
Ranran Zhao ◽  
Nan Liu ◽  
Fuhui Han ◽  
Hegang Li ◽  
Jifeng Liu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Circular Rnas ◽  
Follicle Development ◽  
Rna Seq ◽  
Ampk Signaling ◽  
Wool Follicle ◽  
Solid Foundation ◽  
Sheep Shoulder ◽  
Competitive Endogenous Rna

Abstract Background Aohan fine wool sheep (AFWS) is an early fine wool variety breed cultivated in China. The wool has excellent quality and good textile performance. Investigating the molecular mechanisms that regulate wool growth is important for improving wool quality and yield. Circular RNAs (circRNAs) are non-coding RNAs which are widely expressed and can act as a competitive endogenous RNA (ceRNA) to bind to miRNA. Although circRNA has been studied in many fields, research in sheep wool follicles is limited. To understand the regulation of circRNA in the growth of fine wool sheep, we used RNA-seq to identify circRNAs in sheep shoulder skin at three stages, embryonic day 90 (E90d), embryonic day 120 (E120d), and Birth.Results We identified 8,753circRNAs and found that 1,351 were differentially expressed. We also analyzed the classification and characteristic of the circRNAs in sheep shoulder skin. GO and KEGG were used for source genes of circRNAs, and these were mainly enriched in cellular component organization, regulation of primary metabolic process, tight junctions, and the cGMP-PKG and AMPK signaling pathways. In addition, we predicted interactions between 17 circRNAs and 8 miRNAs using miRanda ( http://www.microrna.org/microrna/home.do ). Based on the significant pathways, we speculate the circ-0005720, circ-0001754, circ-0008036, circ-0004032, circ-0005174, circ-0005519, circ-0007826 may play an important role in regulating wool follicle growth in AFWS. 5 circRNAs were randomly selected to validate the results of the RNA-seq by qRT-PCR.Conclusion Our results provide more information about circRNAs in regulating wool follicle development in AFWS and provide a solid foundation for future experiments.

scholarly journals Transcriptome analysis of two Pogostemon cablin chemotypes reveals genes related to patchouli alcohol biosynthesis

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12025
Author(s):  
Wuping Yan ◽  
Zhouchen Ye ◽  
Shijia Cao ◽  
Guanglong Yao ◽  
Jing Yu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Differentially Expressed ◽  
Perennial Herb ◽  
Pcr Analysis ◽  
Biosynthetic Pathways ◽  
Rna Seq ◽  
Patchouli Alcohol ◽  
Pogostemon Cablin ◽  
Polymerase Chain ◽  
Distribution Frequency

Pogostemon cablin, a medicinally and economically important perennial herb, is cultivated around the world due to its medicinal and aromatic properties. Different P. cablin cultivars exhibit different morphological traits and patchouli oil components and contents (especially patchouli alcohol (PA) and pogostone (PO)). According to the signature constituent of the leaf, P. cablin was classified into two different chemotypes, including PA-type and PO-type. To better understand the molecular mechanisms of PA biosynthesis, the transcriptomes of Chinese-cultivated P. cablin cv. PA-type “Nanxiang” (NX) and PO-type “Paixiang” (PX) were analyzed and compared with ribonucleic acid sequencing (RNA-Seq) technology. We obtained a total of 36.83 G clean bases from the two chemotypes, compared them with seven databases and revealed 45,394 annotated unigenes. Thirty-six candidate unigenes participating in the biosynthesis of PA were found in the P. cablin transcriptomes. Overall, 8,390 differentially expressed unigenes were identified between the chemotypes, including 2,467 upregulated and 5,923 downregulated unigenes. Furthermore, six and nine differentially expressed genes (DEGs) were mapped to the terpenoid backbone biosynthetic and sesquiterpenoid and triterpenoid biosynthetic pathways, respectively. One key sesquiterpene synthase gene involved in the sesquiterpenoid and triterpenoid biosynthetic pathways, encoding patchoulol synthase variant 1, was significantly upregulated in NX. Additionally, GC-MS analysis of the two chemotypes in this study showed that the content of PA in NX was significantly higher than that of PX, while the content of PO showed the opposite phenotype. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that the DEG expression tendency was consistent with the transcriptome sequencing results. Overall, 23 AP2/ERF, 13 bHLH, 11 MYB, 11 NAC, three Trihelix, 10 WRKY and three bZIP genes that were differentially expressed may act as regulators of terpenoid biosynthesis. Altogether, 8,314 SSRs were recognized within 6,825 unigenes, with a distribution frequency of 18.32%, among which 1,202 unigenes contained more than one SSR. The transcriptomic characteristics of the two P. cablin chemotypes are comprehensively reported in this study, and these results will contribute to a better understanding of the molecular mechanism of PA biosynthesis. Our transcriptome data also provide a valuable genetic resource for further studies on P. cablin.

scholarly journals Transcriptome profiling reveals transcriptional and alternative splicing regulation in the early embryonic development of hair follicles in the cashmere goat

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Yanjun Zhang ◽  
Lele Wang ◽  
Zhen Li ◽  
Dong Chen ◽  
Wenjing Han ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Molecular Mechanisms ◽  
Transcriptome Profiling ◽  
Hair Follicles ◽  
Splicing Regulation ◽  
Cashmere Goat ◽  
Rna Seq ◽  
Three Stages ◽  
Functional Pathways ◽  
First Time

AbstractThe undercoat fiber of the cashmere goat, from the secondary hair follicle (HF), possesses commercial value. However, very few studies have focused on the molecular details of primary and secondary HF initiation and development in goat embryos. In this study, skin samples at embryonic day 45, 55, and 65 (E45, E55, and E65) were collected and prepared for RNA sequencing (RNA-seq). We found that the HF probably initiated from E55 to E65 by analyzing the functional pathways of differentially expressed genes (DEGs). Most key genes in canonical signaling pathways, including WNT, TGF-β, FGF, Hedgehog, NOTCH, and other factors showed clear expression changes from E55 to E65. We, for the first time, explored alternative splicing (AS) alterations, which showed distinct patterns among these three stages. Functional pathways of AS-regulated genes showed connections to HF development. By comparing the published RNA-seq samples from the E60, E120, and newborn (NB) stages, we found the majority of WNT/β-catenin signaling genes were important in the initiation of HF development, while other factors including FOXN1, GATA3, and DLX3 may have a consistent influence on HF development. Our investigation supported the time points of embryonic HF initiation and identified genes that have potential functions of embryonic HF initiation and development. We further explored the potential regulatory roles of AS in HF initiation, which extended our knowledge about the molecular mechanisms of HF development.

scholarly journals Chibby cooperates with 14-3-3 to regulate β-catenin subcellular distribution and signaling activity

2008 ◽  
Vol 181 (7) ◽  
pp. 1141-1154 ◽  
Author(s):  
Feng-Qian Li ◽  
Adaobi Mofunanya ◽  
Kimberley Harris ◽  
Ken-Ichi Takemaru
Keyword(s):  
Transcriptional Activation ◽  
Nuclear Export ◽  
Molecular Mechanisms ◽  
Affinity Purification ◽  
Nuclear Accumulation ◽  
Binding Motif ◽  
Transcriptional Coactivator ◽  
Evolutionarily Conserved ◽  
Canonical Wnt ◽  
Affinity Purification Mass Spectrometry

β-Catenin functions in both cell–cell adhesion and as a transcriptional coactivator in the canonical Wnt pathway. Nuclear accumulation of β-catenin is the hallmark of active Wnt signaling and is frequently observed in human cancers. Although β-catenin shuttles in and out of the nucleus, the molecular mechanisms underlying its translocation remain poorly understood. Chibby (Cby) is an evolutionarily conserved molecule that inhibits β-catenin–mediated transcriptional activation. Here, we identified 14-3-3ε and 14-3-3ζ as Cby-binding partners using affinity purification/mass spectrometry. 14-3-3 proteins specifically recognize serine 20 within the 14-3-3–binding motif of Cby when phosphorylated by Akt kinase. Notably, 14-3-3 binding results in sequestration of Cby into the cytoplasm. Moreover, Cby and 14-3-3 form a stable tripartite complex with β-catenin, causing β-catenin to partition into the cytoplasm. Our results therefore suggest a novel paradigm through which Cby acts in concert with 14-3-3 proteins to facilitate nuclear export of β-catenin, thereby antagonizing β-catenin signaling.

scholarly journals Identification and characterization of circRNAs in the skin during wool follicle development in Aohan fine wool sheep

2020 ◽  
Author(s):  
Ranran Zhao ◽  
Nan Liu ◽  
Fuhui Han ◽  
Hegang Li ◽  
Jifeng Liu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Future Research ◽  
Circular Rnas ◽  
Follicle Development ◽  
Rna Seq ◽  
Ampk Signaling ◽  
Competitive Endogenous Rnas ◽  
Wool Follicle ◽  
Sheep Shoulder

Abstract Background: Aohan fine wool sheep (AFWS) is a historically bred fine wool sheep, cultivated in China. The wool has excellent quality and good textile performance. Investigating the molecular mechanisms that regulate wool growth is important to improve wool quality and yield. Circular RNAs (circRNAs) are non-coding RNAs that are widely expressed, and can act as a competitive endogenous RNAs (ceRNAs) to bind to miRNAs. Although circRNAs have been studied in many fields, research on their activity in sheep wool follicles is limited. To understand the regulation of circRNAs in the growth of fine wool in sheep, we used RNA-seq to identify circRNAs in sheep shoulder skin samples at three developmental stages: embryonic day 90 (E90d), embryonic day 120 (E120d), and at birth (Birth). Results: We identified 8,753 circRNAs and found that 918 were differentially-expressed. We then analyzed the classification and characteristic of the circRNAs in sheep shoulder skin. Using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), we identified the source genes of circRNAs, which were mainly enriched in cellular component organization, regulation of primary metabolic processes, tight junctions, and the cGMP-PKG and AMPK signaling pathways. In addition, we predict interactions between 17 circRNAs and eight miRNAs, using miRanda software. Based on the significant pathways, we speculate that circ_0005720, circ_0001754, circ_0008036, circ_0004032, circ_0005174, circ_0005519, circ_0007826 might play an important role in regulating wool follicle growth in AFWS. Seven circRNAs were randomly selected, and have validated the results of the RNA-seq by qRT-PCR. Conclusion: Our results provide more information about circRNAs in regulating wool follicle development in AFWS, and establish a solid foundation for future research.

scholarly journals Identification and characterization of circRNAs in the skin during wool follicle development in Aohan fine wool sheep

2020 ◽  
Author(s):  
Ranran Zhao ◽  
Nan Liu ◽  
Fuhui Han ◽  
Hegang Li ◽  
Jifeng Liu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Future Research ◽  
Circular Rnas ◽  
Follicle Development ◽  
Rna Seq ◽  
Ampk Signaling ◽  
Competitive Endogenous Rnas ◽  
Wool Follicle ◽  
Sheep Shoulder

Abstract Background: Aohan fine wool sheep (AFWS) is a historically bred fine wool sheep, cultivated in China. The wool has excellent quality and good textile performance. Investigating the molecular mechanisms that regulate wool growth is important to improve wool quality and yield. Circular RNAs (circRNAs) are non-coding RNAs that are widely expressed, and can act as a competitive endogenous RNAs (ceRNAs) to bind to miRNAs. Although circRNAs have been studied in many fields, research on their activity in sheep wool follicles is limited. To understand the regulation of circRNAs in the growth of fine wool in sheep, we used RNA-seq to identify circRNAs in sheep shoulder skin samples at three developmental stages: embryonic day 90 (E90d), embryonic day 120 (E120d), and at birth (Birth). Results: We identified 8,753 circRNAs and found that 918 were differentially-expressed. We then analyzed the classification and characteristic of the circRNAs in sheep shoulder skin. Using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), we identified the source genes of circRNAs, which were mainly enriched in cellular component organization, regulation of primary metabolic processes, tight junctions, and the cGMP-PKG and AMPK signaling pathways. In addition, we predict interactions between 17 circRNAs and eight miRNAs, using miRanda software. Based on the significant pathways, we speculate that circ_0005720, circ_0001754, circ_0008036, circ_0004032, circ_0005174, circ_0005519, circ_0007826 might play an important role in regulating wool follicle growth in AFWS. Seven circRNAs were randomly selected, and have validated the results of the RNA-seq by qRT-PCR. Conclusion: Our results provide more information about circRNAs in regulating wool follicle development in AFWS, and establish a solid foundation for future research.

Transcriptome analysis of a Triticum aestivum landrace (Roshan) in response to salt stress conditions

2021 ◽  
pp. 1-14
Author(s):  
Jamshid Azimian ◽  
Eslam Majidi Hervan ◽  
Amin Azadi ◽  
Mohammad Reza Bakhtiarizadeh ◽  
Reza Azizinezhad
Keyword(s):  
Salt Stress ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Kegg Pathways ◽  
Go Enrichment ◽  
Meristem Maintenance ◽  
Polymerase Chain ◽  
Gene Expression Levels

Abstract In order to better understand the molecular mechanisms associated with salinity tolerance, transcriptome analysis of a local salt-tolerant wheat landrace (i.e. Roshan) was performed under salt stress. Transcriptome sequencing yielded 137,508,542 clean reads using the Illumina HiSeq 2000 platform. The results of two alignment programs, i.e. STAR and HISAT2, were used separately to perform the analysis of differentially expressed genes (DEGs) using DESeq2. Finally, a total of 17,897 DEGs were identified by DESeq2. Moreover, gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses identified 108 GO terms and 62 significant KEGG pathways, of which ‘metabolic process’ and ‘metabolic pathways’ were the most abundant enriched term and pathway, respectively. Additionally, key salinity-tolerant genes, including asparagine synthetase, were also identified in the present study. Out of 87 identified families of transcription factors, GAI‐RGA ‐ and ‐SCR (GRAS) was one of the most important, which participates in signal transduction, and meristem maintenance and development. Eventually, to validate the gene expression levels, six DEGs were selected for a quantitative real-time polymerase chain reaction, and the results were in line with those of RNA-Seq. The findings of the current study can guide future genetic and molecular studies and allow a better understanding and improvement of salt tolerance in wheat.

scholarly journals Transcriptome and Metabolome Analyses of the Flowers and Leaves of Chrysanthemum dichrum

2021 ◽  
Vol 12 ◽  
Author(s):  
Hua Liu ◽  
Xiaoxi Chen ◽  
Hạixia Chen ◽  
Jie Lu ◽  
Dongliang Chen ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Average Length ◽  
Expression Patterns ◽  
Rna Seq ◽  
Flower Buds ◽  
The Family ◽  
Polymerase Chain ◽  
Chrysanthemum Dichrum

Chrysanthemum dichrum is an important wild species in the family Asteraceae. However, because of a lack of genetic information, there has been relatively little research conducted on the molecular mechanisms in C. dichrum. There is no report describing the transcriptome and metabolome of C. dichrum flowers and leaves at different developmental stages. In this study, high-throughput sequencing and RNA-seq analyses were used to investigate the transcriptome of C. dichrum leaves, flower buds, and blooming flowers. Additionally, these three tissues also underwent a metabolomics analysis. A total of 447,313,764 clean reads were assembled into 77,683 unigenes, with an average length of 839 bp. Of the 44,204 annotated unigenes, 42,189, 28,531, 23,420, and 17,599 were annotated using the Nr, Swiss-Prot, KOG, and KEGG databases, respectively. Furthermore, 31,848 differentially expressed genes (DEGs) were detected between the leaves and flower buds, whereas 23,197 DEGs were detected between the leaves and blooming flowers, and 11,240 DEGs were detected between the flower buds and blooming flowers. Finally, a quantitative real-time Polymerase Chain Reaction (qRT-PCR) assay was conducted to validate the identified DEGs. The metabolome data revealed several abundant metabolites in C. dichrum leaves, flower buds, and blooming flowers, including raffinose, 1-kestose, asparagine, glutamine, and other medicinal compounds. The expression patterns of significant DEGs revealed by the transcriptome analysis as well as the data for the differentially abundant metabolites in three C. dichrum tissues provide important genetic and metabolic information relevant for future investigations of the molecular mechanisms in C. dichrum. Moreover, the results of this study may be useful for the molecular breeding, development, and application of C. dichrum resources.

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