Identification, characterization and expression profiling of circular RNAs in the early cotton fiber developmental stages

Genomics ◽  
2021 ◽  
Vol 113 (1) ◽  
pp. 356-365
Author(s):  
HARON Salih ◽  
Xiao Wang ◽  
Baojun Chen ◽  
Yinhua Jia ◽  
Wenfang Gong ◽  
...  
Keyword(s):  
Cotton Fiber ◽  
Expression Profiling ◽  
Developmental Stages ◽  
Circular Rnas

scholarly journals Expression Profiling and Functional Analysis of Circular RNAs in Inner Mongolian Cashmere Goat Hair Follicles

2021 ◽  
Vol 12 ◽  
Author(s):  
Fangzheng Shang ◽  
Yu Wang ◽  
Rong Ma ◽  
Zhengyang Di ◽  
Zhihong Wu ◽  
...  
Keyword(s):  
Hair Follicle ◽  
Signaling Pathway ◽  
Expression Profiling ◽  
Regulatory Network ◽  
Expression Profiles ◽  
Circular Rna ◽  
Hair Follicles ◽  
Luciferase Reporter ◽  
Circular Rnas ◽  
Cashmere Goats

BackgroundInner Mongolian cashmere goats have hair of excellent quality and high economic value, and the skin hair follicle traits of cashmere goats have a direct and important effect on cashmere yield and quality. Circular RNA has been studied in a variety of tissues and cells.ResultIn this study, high-throughput sequencing was used to obtain the expression profiles of circular RNA (circRNA) in the hair follicles of Inner Mongolian cashmere goats at different embryonic stages (45, 55, 65, and 75 days). A total of 21,784 circRNAs were identified. At the same time, the differentially expressed circRNA in the six comparison groups formed in the four stages were: d75vsd45, 59 upregulated and 33 downregulated DE circRNAs; d75vsd55, 61 upregulated and 102 downregulated DE circRNAs; d75vsd65, 32 upregulated and 33 downregulated DE circRNAs; d65vsd55, 67 upregulated and 169 downregulated DE circRNAs; d65vsd45, 96 upregulated and 63 downregulated DE circRNAs; and d55vsd45, 76 upregulated and 42 downregulated DE circRNAs. Six DE circRNA were randomly selected to verify the reliability of the sequencing results by quantitative RT-PCR. Subsequently, the circRNA corresponding host genes were analyzed by the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The results showed that the biological processes related to hair follicle growth and development enriched by GO mainly included hair follicle morphogenesis and cell development, and the signaling pathways related to hair follicle development included the Notch signaling pathway and NF-κB signaling pathway. We combined the DE circRNA of d75vsd45 with miRNA and mRNA databases (unpublished) to construct the regulatory network of circRNA–miRNA–mRNA, and formed a total of 102 pairs of circRNA–miRNA and 126 pairs of miRNA–mRNA interactions. The binding relationship of circRNA3236–chi-miR-27b-3p and circRNA3236–chi-miR-16b-3p was further verified by dual-luciferase reporter assays, and the results showed that circRNA3236 and chi-miR-27b-3p, and circRNA3236 and chi-miR-16b-3p have a targeted binding relationship.ConclusionTo summarize, we established the expression profiling of circRNA in the fetal skin hair follicles of cashmere goats, and found that the host gene of circRNA may be involved in the development of hair follicles of cashmere goats. The regulatory network of circRNA–miRNA–mRNA was constructed and preliminarily verified using DE circRNAs.

Gene Expression Profiling of Cells, Tissues, and Developmental Stages of the Nematode C. elegans

2003 ◽  
Vol 68 (0) ◽  
pp. 159-170 ◽  
Author(s):  
S.J. MCKAY ◽  
R. JOHNSEN ◽  
J. KHATTRA ◽  
J. ASANO ◽  
D.L. BAILLIE ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Developmental Stages ◽  
C Elegans

scholarly journals Expression Profiling of Mammalian Male Meiosis and Gametogenesis Identifies Novel Candidate Genes for Roles in the Regulation of Fertility

2004 ◽  
Vol 15 (3) ◽  
pp. 1031-1043 ◽  
Author(s):  
Ulrich Schlecht ◽  
Philippe Demougin ◽  
Reinhold Koch ◽  
Leandro Hermida ◽  
Christa Wiederkehr ◽  
...  
Keyword(s):  
Germ Cell ◽  
Germ Cells ◽  
Expression Profiling ◽  
Large Scale ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Control Cell ◽  
Cell Types ◽  
Male Meiosis ◽  
Cell Expression

We report a comprehensive large-scale expression profiling analysis of mammalian male germ cells undergoing mitotic growth, meiosis, and gametogenesis by using high-density oligonucleotide microarrays and highly enriched cell populations. Among 11,955 rat loci investigated, 1268 were identified as differentially transcribed in germ cells at subsequent developmental stages compared with total testis, somatic Sertoli cells as well as brain and skeletal muscle controls. The loci were organized into four expression clusters that correspond to somatic, mitotic, meiotic, and postmeiotic cell types. This work provides information about expression patterns of ∼200 genes known to be important during male germ cell development. Approximately 40 of those are included in a group of 121 transcripts for which we report germ cell expression and lack of transcription in three somatic control cell types. Moreover, we demonstrate the testicular expression and transcriptional induction in mitotic, meiotic, and/or postmeiotic germ cells of 293 as yet uncharacterized transcripts, some of which are likely to encode factors involved in spermatogenesis and fertility. This group also contains potential germ cell-specific targets for innovative contraceptives. A graphical display of the data is conveniently accessible through the GermOnline database at http://www.germonline.org .

scholarly journals Functions of Circular RNAs Involved in Animal Skeletal Muscle Development – A Review

2020 ◽  
Vol 20 (1) ◽  
pp. 3-10
Author(s):  
Patricia Adu-Asiamah ◽  
Qiying Leng ◽  
Haidong Xu ◽  
Jiahui Zheng ◽  
Zhihui Zhao ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Growth And Development ◽  
Molecular Mechanisms ◽  
Muscle Development ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Vital Role ◽  
Circular Rnas ◽  
Cell Proliferation And Differentiation ◽  
Mirna Sponges

AbstractCircular RNAs (circRNAs) have been identified in the skeletal muscle of numerous species of animals. Their abundance, diversity, and their dynamic expression patterns have been revealed in various developmental stages and physiological conditions in skeletal muscles. Recently, studies have made known that circRNAs widely participate in muscle cell proliferation and differentiation. They are also involved in other life processes such as functioning as microRNA (miRNA) sponges, regulators of splicing and transcription, and modifiers of parental gene expression with emerging pieces of evidence indicating a high chance of playing a vital role in several cells and tissues, especially the muscles. Other research has emphatically stated that the growth and development of skeletal muscle are regulated by proteins as well as non-coding RNAs, which involve circRNAs. Therefore, circRNAs have been considered significant biological regulators for understanding the molecular mechanisms of myoblasts. Here, we discuss how circRNAs are abundantly expressed in muscle (myoblast) and their critical roles in growth and development.

scholarly journals Flavonoids Accumulation in Fruit Peel and Expression Profiling of Related Genes in Purple (Passiflora edulis f. edulis) and Yellow (Passiflora edulis f. flavicarpa) Passion Fruits

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2240
Author(s):  
Meng Shi ◽  
Muhammad Moaaz Ali ◽  
Yinying He ◽  
Songfeng Ma ◽  
Hafiz Muhammad Rizwan ◽  
...  
Keyword(s):  
Expression Profiling ◽  
Developmental Stages ◽  
Antioxidant Defense System ◽  
Ultra Performance Liquid Chromatography ◽  
Passion Fruit ◽  
Total Flavonoids ◽  
Fruit Peel ◽  
Passiflora Edulis ◽  
Flavonoid Metabolism ◽  
Fruit Samples

Flavonoids play a key role as a secondary antioxidant defense system against different biotic and abiotic stresses, and also act as coloring compounds in various fruiting plants. In this study, fruit samples of purple (Passiflora edulis f. edulis) and yellow (Passiflora edulis f. flavicarpa) passion fruit were collected at five developmental stages (i.e., fruitlet, green, veraison, maturation, and ripening stage) from an orchard located at Nanping, Fujian, China. The contents of flavonoid, anthocyanin, proanthocyanin, and their metabolites were determined using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS), activities of key enzymes involved in flavonoid metabolism were measured, and expression profiling of related genes was done using quantitative real-time PCR (qRT-PCR). The results revealed that total flavonoids, anthocyanins, and procyanidins were found to be increased in the fruit peel of both cultivars with fruit maturity. Total flavonoids, anthocyanins, procyanidins, flavonoid metabolites (i.e., rutin, luteolin, and quercetin), and anthocyanin metabolites (i.e., cyanidin-3-O-glucoside chloride, peonidin-3-O-glucoside, and pelargonidin-3-O-glucoside) were found abundant in the peel of purple passion fruit, as compared to yellow passion fruit. Principle component analysis showed that the enzymes, i.e., C4H, 4CL, UFGT, and GST were maybe involved in the regulation of flavonoids metabolism in the peel of passion fruit cultivars. Meanwhile, PePAL4, Pe4CL2,3, PeCHS2, and PeGST7 may play an important role in flavonoid metabolism in fruit peel of the passion fruit. This study provides new insights for future elucidation of key mechanisms regulating flavonoids biosynthesis in passion fruit.

scholarly journals Genome-wide identification and expression profiling of glutathione S-transferase family under multiple abiotic and biotic stresses in Medicago truncatula L.

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0247170
Author(s):  
Md. Soyib Hasan ◽  
Vishal Singh ◽  
Shiful Islam ◽  
Md. Sifatul Islam ◽  
Raju Ahsan ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Expression Profiling ◽  
Developmental Stages ◽  
Functional Characterization ◽  
Drought Treatment ◽  
Specific Expression ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Genome Wide

Glutathione transferases (GSTs) constitute an ancient, ubiquitous, multi-functional antioxidant enzyme superfamily that has great importance on cellular detoxification against abiotic and biotic stresses as well as plant development and growth. The present study aimed to a comprehensive genome-wide identification and functional characterization of GST family in one of the economically important legume plants—Medicago truncatula. Here, we have identified a total of ninety-two putative MtGST genes that code for 120 proteins. All these members were classified into twelve classes based on their phylogenetic relationship and the presence of structural conserved domain/motif. Among them, 7 MtGST gene pairs were identified to have segmental duplication. Expression profiling of MtGST transcripts revealed their high level of organ/tissue-specific expression in most of the developmental stages and anatomical tissues. The transcripts of MtGSTU5, MtGSTU8, MtGSTU17, MtGSTU46, and MtGSTU47 showed significant up-regulation in response to various abiotic and biotic stresses. Moreover, transcripts of MtGSTU8, MtGSTU14, MtGSTU28, MtGSTU30, MtGSTU34, MtGSTU46 and MtGSTF8 were found to be highly upregulated in response to drought treatment for 24h and 48h. Among the highly stress-responsive MtGST members, MtGSTU17 showed strong affinity towards its conventional substrates reduced glutathione (GSH) and 1‐chloro‐2,4‐dinitrobenzene (CDNB) with the lowest binding energy of—5.7 kcal/mol and -6.5 kcal/mol, respectively. Furthermore, the substrate-binding site residues of MtGSTU17 were found to be highly conserved. These findings will facilitate the further functional and evolutionary characterization of GST genes in Medicago.

scholarly journals Significance of Sex Differences in ncRNAs Expression and Function in Pregnancy and Related Complications

Biomedicines ◽  
2021 ◽  
Vol 9 (11) ◽  
pp. 1509
Author(s):  
Rosaria Varì ◽  
Beatrice Scazzocchio ◽  
Tiziana Filardi ◽  
Anna Citarella ◽  
Maria Bellenghi ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Noncoding Rnas ◽  
Circular Rnas ◽  
Sexually Dimorphic ◽  
Fetal Sex ◽  
Complex Interactions ◽  
Physiological Processes ◽  
Different Types ◽  
And Function ◽  
In Pregnancy

In the era of personalized medicine, fetal sex-specific research is of utmost importance for comprehending the mechanisms governing pregnancy and pregnancy-related complications. In recent times, noncoding RNAs (ncRNAs) have gained increasing attention as critical players in gene regulation and disease pathogenesis, and as candidate biomarkers in human diseases as well. Different types of ncRNAs, including microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), participate in every step of pregnancy progression, although studies taking into consideration fetal sex as a central variable are still limited. To date, most of the available data have been obtained investigating sex-specific placental miRNA expression. Several studies revealed that miRNAs regulate the (patho)-physiological processes in a sexually dimorphic manner, ensuring normal fetal development, successful pregnancy, and susceptibility to diseases. Moreover, the observation that ncRNA profiles differ according to cells, tissues, and developmental stages of pregnancy, along with the complex interactions among different types of ncRNAs in regulating gene expression, strongly indicates that more studies are needed to understand the role of sex-specific ncRNA in pregnancy and associated disorders.

scholarly journals Microarray Analysis And Functional Prediction Of Differentially-Expressed Circular RNAs In Acquired Middle Ear Choleateatoma

2021 ◽  
Author(s):  
Shumin Xie ◽  
Li Jin ◽  
Tuanfang Yin ◽  
Jihao Ren ◽  
Wei Liu
Keyword(s):  
Microarray Analysis ◽  
Middle Ear ◽  
Expression Profiling ◽  
Normal Skin ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Functional Prediction ◽  
High Confidence ◽  
Network Analyses ◽  
Middle Ear Cholesteatoma

Abstract Background: Middle ear cholesteatoma is characterized by hyper-proliferation of keratinocytes. Circular RNA (circRNA) plays an essential role in the pathogenesis of many proliferative diseases. However, the role of circRNA in the etiopathogenesis of middle ear cholesteatoma is rarely investigated so far. Our aim was to investigate the differential expression profiling of circRNAs between acquired middle ear cholesteatoma and normal skin, and to indentify potential circRNAs contributing to the etiopathogenesis of middle ear cholesteatoma. Microarray analysis and functional prediction were performed to investigate the circRNA expression profiling between middle ear cholesteatoma and normal skin. Validation of differentially expressed circRNAs was conducted by qRT-PCR. Prediction of m6A modification was also carried out. Results: Microarray analysis displayed that totally 93 up-regulated and 85 down-regulated circRNAs were identified in middle ear cholesteatoma. Through validation, expressions of hsa_circRNA_104327 and hsa_circRNA_404655 were significantly higher, while hsa_circRNA_000319 was significantly down-regulated in cholesteatoma. GO classification, KEGG pathway, and ceRNA network analyses suggested that these differentially expressed circRNAs might play importantant roles in the etiopathogenesis of middle ear cholesteatoma. Prediction of m6A modification exhibited that hsa_circRNA_000319 possessed 4 m6A sites with very high confidence, and hsa_circRNA_404655 had 3 m6A sites with high confidence.Conclusions: Our study indicated possible roles of differentially expressed circRNAs in the etiopathogenesis of middle ear cholesteatoma. Targeting on these differentially expressed circRNAs may provide a new and effective treatment for middle ear cholesteatoma in the future.

scholarly journals A genome-wide circular RNA transcriptome in Rat

2021 ◽  
Author(s):  
Disha Sharma ◽  
Paras Sehgal ◽  
Sridhar Sivasubbu ◽  
Vinod Scaria
Keyword(s):  
Developmental Stages ◽  
Donor Site ◽  
Model Organism ◽  
Circular Rna ◽  
Model Organisms ◽  
Circular Rnas ◽  
Acceptor Site ◽  
Tissue Samples ◽  
A Genome ◽  
The Difference

AbstractBackgroundCircular RNAs are a novel class of non-coding RNAs that backsplice from 5’ donor site and 3’ acceptor site to form a circular structure. A number of circRNAs have been discovered in model organisms including human, mouse, Drosophila, among other organisms. There are a few candidate-based studies on circular RNAs in rat, a well studied model organism. The availability of a recent dataset of transcriptomes encompassing 11 tissues, 4 developmental stages and 2 genders motivated us to explore the landscape of circular RNAs in the organism.MethodologyIn order to understand the difference among different pipelines, we have used the same bodymap RNA sequencing dataset. A number of pipelines have been published to identify the backsplice junctions for the discovery of circRNAs but studies comparing these tools have suggested that a combination of tools would be a better approach to identify high-confidence circular RNAs. We employed 5 different combinations of tools including tophat_CIRCexplorer2, segemehl_CIRCexplorer2, star_CIRCexplorer, Bowtie2_findcirc and Bowtie2_findcirc (noHisat2) to identify circular RNAs from the dataset.ResultsOur analysis identified a number of tissue-specific, developmental stage specific and gender specific circular RNAs. We further independently validated 16 circRNA junctions out of 24 selected candidates in 5 tissue samples. We additionally estimated the quantitative expression of 5 circRNA candidates using real-time PCR and our analysis suggests 3 candidates as tissue-enrichedConclusionThis study is one of the most comprehensive studies that provides a circular RNA transcriptome as well as to understand the difference among different computational pipelines in Rat.

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