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

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.

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

10.21203/rs.2.15954/v2 ◽

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

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

10.21203/rs.2.15954/v1 ◽

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.

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Comparative Transcriptomic Analysis of Riptortus pedestris (Hemiptera: Alydidae) to Characterize Wing Formation across All Developmental Stages

Insects ◽

10.3390/insects12030226 ◽

2021 ◽

Vol 12 (3) ◽

pp. 226

Author(s):

Siying Fu ◽

Yujie Duan ◽

Siqi Wang ◽

Yipeng Ren ◽

Wenjun Bu

Keyword(s):

Molecular Mechanisms ◽

Developmental Stages ◽

Average Length ◽

Transcriptome Assembly ◽

Expression Profiles ◽

Economic Losses ◽

Future Research ◽

Economic Damage ◽

Wing Formation ◽

Riptortus Pedestris

Riptortus pedestris (Hemiptera: Alydidae) is a major agricultural pest in East Asia that causes considerable economic losses to the soybean crop each year. However, the molecular mechanisms governing the growth and development of R. pedestris have not been fully elucidated. In this study, the Illumina HiSeq6000 platform was employed to perform de novo transcriptome assembly and determine the gene expression profiles of this species across all developmental stages, including eggs, first-, second-, third-, fourth-, and fifth-instar nymphs, and adults. In this study, a total of 60,058 unigenes were assembled from numerous raw reads, exhibiting an N50 length of 2126 bp and an average length of 1199 bp, and the unigenes were annotated and classified with various databases, such as the Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Gene Ontology (GO). Furthermore, various numbers of differentially expressed genes (DEGs) were calculated through pairwise comparisons of all life stages, and some of these DEGs were associated with immunity, metabolism, and development by GO and KEGG enrichment. In addition, 35,158 simple sequence repeats (SSRs) and 715,604 potential single nucleotide polymorphisms (SNPs) were identified from the seven transcriptome libraries of R. pedestris. Finally, we identified and summarized ten wing formation-related signaling pathways, and the molecular properties and expression levels of five wing development-related genes were analyzed using quantitative real-time PCR for all developmental stages of R. pedestris. Taken together, the results of this study may establish a foundation for future research investigating developmental processes and wing formation in hemimetabolous insects and may provide valuable data for pest control efforts attempting to reduce the economic damage caused by this pest.

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Comparative Transcriptome Analysis Reveals Regulatory Networks during the Maize Ear Shank Elongation Process

International Journal of Molecular Sciences ◽

10.3390/ijms22137029 ◽

2021 ◽

Vol 22 (13) ◽

pp. 7029

Author(s):

Cai-Yun Xiong ◽

Qing-You Gong ◽

Hu Pei ◽

Chang-Jian Liao ◽

Rui-Chun Yang ◽

...

Keyword(s):

Regulatory Networks ◽

Molecular Mechanisms ◽

Developmental Stages ◽

Rna Seq ◽

Short Branch ◽

Transcriptional Dynamics ◽

New Varieties ◽

Elongation Process ◽

Temporal Expression Pattern ◽

Maize Ear

In maize, the ear shank is a short branch that connects the ear to the stalk. The length of the ear shank mainly affects the transportation of photosynthetic products to the ear, and also influences the dehydration of the grain by adjusting the tightness of the husks. However, the molecular mechanisms of maize shank elongation have rarely been described. It has been reported that the maize ear shank length is a quantitative trait, but its genetic basis is still unclear. In this study, RNA-seq was performed to explore the transcriptional dynamics and determine the key genes involved in maize shank elongation at four different developmental stages. A total of 8145 differentially expressed genes (DEGs) were identified, including 729 transcription factors (TFs). Some important genes which participate in shank elongation were detected via function annotation and temporal expression pattern analyses, including genes related to signal transduction hormones (auxin, brassinosteroids, gibberellin, etc.), xyloglucan and xyloglucan xyloglucosyl transferase, and transcription factor families. The results provide insights into the genetic architecture of maize ear shanks and developing new varieties with ideal ear shank lengths, enabling adjustments for mechanized harvesting in the future.

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Evaluation of Appropriate Reference Genes For Investigating Gene Expression in Chlorops oryzae (Diptera: Chloropidae)

Journal of Economic Entomology ◽

10.1093/jee/toz142 ◽

2019 ◽

Vol 112 (5) ◽

pp. 2207-2214 ◽

Cited By ~ 1

Author(s):

Ping Tian ◽

Lin Qiu ◽

Ailin Zhou ◽

Guo Chen ◽

Hualiang He ◽

...

Keyword(s):

Gene Expression ◽

Ribosomal Protein ◽

Reference Genes ◽

Molecular Mechanisms ◽

Developmental Stages ◽

Quantitative Polymerase Chain Reaction ◽

Housekeeping Genes ◽

Future Research ◽

Economic Damage ◽

Physiological Processes

Abstract Reverse transcription quantitative polymerase chain reaction (PCR) has become an invaluable technique for analyzing gene expression in many insects. However, this approach requires the use of stable reference genes to normalize the data. Chlorops oryzae causes significant economic damage to rice crops throughout Asia. The lack of suitable reference genes has hindered research on the molecular mechanisms underlying many physiological processes of this species. In this study, we used quantitative real-time PCR to evaluate the expression of eight C. oryzae housekeeping genes glyceraldehyde-3-phosphate dehydrogenase (GAPDH), β-actin (βACT), beta-tubulin (βTUB), Delta Elongation factor-1 (EF1δ), ribosomal protein S11 (RPS11), RPS15, C-terminal-Binding Protein (CtBP), and ribosomal protein 49 (RP49) in different developmental stages and tissues in both larvae and adults. We analyzed the data with four different software packages: geNorm, NormFinder, BestKeeper, and RefFinder and compared the results obtained with each method. The results indicate that PRS15 and RP49 can be used as stable reference genes for quantifying gene expression in different developmental stages and larval tissues. GAPDH and βACT, which have been considered stable reference genes by previous studies, were the least stable of the candidate genes with respect to larval tissues. GAPDH was, however, the most stable reference gene for adult tissues. We verified the candidate reference genes identified and found that the expression levels of Cadherins (Cads) changed when different reference genes were used to normalize gene expression. This study provides a valuable foundation for future research on gene function, and investigating the molecular basis of physiological processes, in C. oryzae.

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P5398CircRNAs deregulation in heart failure patients

European Heart Journal ◽

10.1093/eurheartj/ehz746.0358 ◽

2019 ◽

Vol 40 (Supplement_1) ◽

Author(s):

S Greco ◽

A Made' ◽

M Longo ◽

R Tikhomirov ◽

S Castelvecchio ◽

...

Keyword(s):

Molecular Mechanisms ◽

Rna Binding ◽

Rna Binding Proteins ◽

Functional Characterization ◽

Enrichment Analysis ◽

Host Gene ◽

Circular Rnas ◽

Amplification Efficiency ◽

Rna Seq ◽

Bioinformatics Pipeline

Abstract Background Circular RNAs (circRNAs) are an emerging class of noncoding RNAs stemming from the splicing and circularization of pre-mRNAs exons. CircRNAs can regulate transcription and splicing, sequester microRNAs acting as “sponge” and inducing the respective targets, and bind to RNA binding proteins. Recently, they have been found deregulated in dilated cardiomyopathies (DCM), one of the cardiovascular diseases with the worst rate of morbidity and mortality, and whose molecular mechanisms are only partially known. Purpose Therein, we will evaluate in ischemic DCM patients the modulation of 17 circRNAs, 14 out of them obtained from literature data on DCM ischemic or not, while the other 3 were circRNAs not characterized in the heart previously. The study aims to identify circRNAs candidates for further functional characterization in DCM. In addition, as differential expression (DE) analysis is not easily performed for circRNAs in RNA-seq datasets, the validated circRNAs will be used to set up the most specific and sensitive bioinformatics pipeline for circRNA-DE analysis. Methods We designed divergent and convergent specific primers for 17 circRNAs and their host gene, respectively, and their amplification efficiency was measured by RT-qPCR. Transcripts expression was measured in left ventricle biopsies of 12 patients affected by non end-stage ischemic HF and of 12 matched controls. Results We identified cPVT1, cANKRD17, cBPTF as DE, and validated the modulation of 5 out of the 14 DCM-related circRNAs (cHIPK3, cALPK2, cPCMTD1, cNEBL, cSLC8A1), while cPDRM5, cTTN1 showed opposite modulation, which may be due to the specific disease condition. All of them were modulated differently from the respective host gene. CircRNA/miRNA interactions were predicted using Starbase 3.0. Next, mRNAs-targets of the identified miRNAs were predicted by mirDIP 4.1 and intersected with gene expression datasets of the same patients, previously obtained by microarray analysis. We found that cBPTF and cANKRD17 might sponge 12 and 2 miRNAs, respectively. Enrichment analysis of the relevant targets identified several important pathways implicated in DCM, such as MAPK, FoxO, EGFR, VEGF and Insulin/IGF pathways. In addition, deep RNA-Seq analysis that is currently ongoing and the validated circRNAs will be used to optimize the bioinformatics pipeline for circRNA DE analysis. Conclusions We identified a subset of circRNAs deregulated in ischemic HF potentially implicated in HF pathogenesis.

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

Annals of Animal Science ◽

10.2478/aoas-2019-0053 ◽

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.

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RNA-Seq Profiling of Circular RNAs During Development of Hindgut in Rat Embryos With Ethylenethiourea-Induced Anorectal Malformations

Frontiers in Genetics ◽

10.3389/fgene.2021.605015 ◽

2021 ◽

Vol 12 ◽

Author(s):

Si Ying Li ◽

Chen Yi Wang ◽

Yun Xia Xiao ◽

Xiao Bing Tang ◽

Zheng Wei Yuan ◽

...

Keyword(s):

Molecular Mechanisms ◽

Transforming Growth Factor ◽

Quantitative Polymerase Chain Reaction ◽

Anorectal Malformations ◽

Normal Group ◽

Differentially Expressed ◽

Mitogen Activated Protein Kinase ◽

Circular Rnas ◽

Rna Seq ◽

Pregnant Rats

Anorectal malformations (ARMs) are among the most common congenital terminal digestive tract malformations. Circular RNAs (circRNAs), a novel type of endogenous non-coding RNAs, play roles in the development of the digestive system; however, their contributions to the pathogenesis of ARMs are not well-established. In this study, we explored the mechanism underlying ethylenethiourea (ETU)-induced ARMs by profiling circRNA expression via RNA-seq and constructing a regulatory circRNA-miRNA-mRNA network. Nine pregnant rats were gavage-fed a single dose of 125 mg/kg 1% ETU (ARM group) on gestational day 10 (GD10), and another 9 pregnant rats received a similar dose of saline (normal group) as a control. Embryos were obtained by cesarean section on the key time-points of anorectal development (GD14, GD15, and GD16). Hindgut samples isolated from the fetuses were evaluated by high-throughput sequencing and differentially expressed circRNAs were validated by reverse transcription-quantitative polymerase chain reaction, agarose gel electrophoresis, and Sanger cloning and sequencing. A total of 18295 circRNAs were identified in the normal and ARM groups. Based on the 425 differentially expressed circRNAs (|Fc| > 2, p < 0.05), circRNA-miRNA and miRNA-mRNA pairs were predicted using miREAP, miRanda, and TargetScan. A total of 55 circRNAs (14 up- and 41 downregulated in the ARM group compared to the normal group) were predicted to bind to 195 miRNAs and 947 mRNAs. Competing endogenous RNA networks and a Kyoto Encyclopedia of Genes and Genomes analysis revealed that novel_circ_001042 had the greatest connectivity and was closely related to ARM-associated signaling pathways, such as the Wingless Type MMTV integration site family, mitogen-activated protein kinase, and transforming growth factor-β pathways. These results provide original insight into the roles of circRNAs in ARMs and provide a valuable resource for further analyses of molecular mechanisms and signaling networks.

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Identification and characterization of ERV transcripts in goat embryos

Reproduction ◽

10.1530/rep-18-0336 ◽

2019 ◽

pp. 115-126

Author(s):

Ruizhi Deng ◽

Chengquan Han ◽

Lu Zhao ◽

Qing Zhang ◽

Beifen Yan ◽

...

Keyword(s):

Embryonic Development ◽

Molecular Mechanisms ◽

Developmental Stages ◽

Expression Patterns ◽

Developmental Rate ◽

Endogenous Retroviruses ◽

Early Embryonic Development ◽

Rna Seq ◽

Embryonic Genome ◽

Genome Activation

Endogenous retroviruses (ERVs), which are abundant in mammalian genomes, can modulate the expression of nearby genes, and their expression is dynamic and stage-specific during early embryonic development in mice and humans. However, the functions and mechanisms of ERV elements in regulating embryonic development remain unclear. Here, we utilized several methods to determine the contribution of ERVs to the makeup and regulation of transcripts during embryonic genome activation (EGA). We constructed an ERV library and embryo RNA-seq library (IVF_2c and IVF_8c) of goat to serve as our research basis. The GO and KEGG analysis of nearby ERV genes revealed that some ERV elements may be associated with embryonic development. RNA-seq results were consistent with the features of EGA. To obtain the transcripts derived from the ERV sequences, we blasted the ERV sequences with embryonic transcripts and identified three lncRNAs and one mRNA that were highly expressed in IVF-8c rather than in IVF-2c (q-value <0.05). Then, we validated the expression patterns of nine ERV-related transcripts during early developmental stages and knocked down three high-expression transcripts in EGA. The knockdown of lncRNA TCONS_00460156 or mRNA HSD17B11 significantly decreased the developmental rate of IVF embryos. Our findings suggested that some transcripts from ERVs are essential for the early embryonic development of goat, and analyzing the ERV expression profile during goat EGA may help elucidate the molecular mechanisms of ERV in regulating embryonic development.

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Analysis of Transcriptome and miRNAome in the Muscle of Bamei Pigs at Different Developmental Stages

Animals ◽

10.3390/ani10071198 ◽

2020 ◽

Vol 10 (7) ◽

pp. 1198 ◽

Cited By ~ 2

Author(s):

Guofang Wu ◽

Lin Ma ◽

Lei Wang ◽

Jiping Zhou ◽

Yuhong Ma ◽

...

Keyword(s):

Skeletal Muscle ◽

Meat Quality ◽

Molecular Mechanisms ◽

Target Genes ◽

Developmental Stages ◽

Enrichment Analysis ◽

Rna Seq ◽

Developmental Processes ◽

Citrate Cycle ◽

Molecular Approaches

The growth of skeletal muscle involves complex developmental processes that play an important part in the determinization of pork quality. The investigation of skeletal muscle mRNA or miRNA profiles is especially important for finding molecular approaches to improve meat quality in pig breeding. Therefore, we studied the transcriptome (mRNA and miRNA) profiles of skeletal muscle with RNA-Seq in three developmental stages of pigs: 65-day embryonic (E65), postnatal 0 days (natal) and 10 months (adult). We found 10,035, 9050 and 4841 differentially expressed (DE) genes for natal vs. E65, adult vs. E65 and adult vs. natal, 55, 101 and 85 DE miRNA for natal vs. E65, adult vs. E65 and adult vs. natal, respectively. In addition, the target genes of DE miRNA that was in a negative correlation with the corresponding miRNA in the same comparison group were selected for enrichment analysis. Gene Ontology terms were mainly classified into developmental processes. Pathway analysis revealed enrichment in the Rap1 signaling pathway, citrate cycle and oxidative phosphorylation and carbon. Finally, RT-PCR was employed for validating the level of expression of 11 DE miRNA and 14 DEGs. The transcriptome profiles of skeletal muscle from the different developmental stages of the Bamei pigs were obtained. From these data, hundreds of DE miRNA and mRNA, and the miRNA–mRNA regulatory network can provide valuable insights into further understanding of key molecular mechanisms and improving the meat quality in pig breeding.

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