scholarly journals Deciphering the miRNA transcriptome of breast muscle from the embryonic to post-hatching periods in chickens

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jie Liu ◽  
Fuwei Li ◽  
Xin Hu ◽  
Dingguo Cao ◽  
Wei Liu ◽  
...  
Keyword(s):  
Protein Turnover ◽  
Muscle Development ◽  
Expression Profiles ◽  
Target Function ◽  
Chicken Muscle ◽  
Differentially Expressed Mirnas ◽  
Mirna Expression Level ◽  
Series Expression ◽  
Cellular Turnover ◽  
Short Time

Abstract Background miRNAs play critical roles in growth and development. Various studies of chicken muscle development have focused on identifying miRNAs that are important for embryo or adult muscle development. However, little is known about the role of miRNAs in the whole muscle development process from embryonic to post-hatching periods. Here, we present a comprehensive investigation of miRNA transcriptomes at 12-day embryo (E12), E17, and day 1 (D1), D14, D56 and D98 post-hatching stages. Results We identified 337 differentially expressed miRNAs (DE-miRNAs) during muscle development. A Short Time-Series Expression Miner analysis identified two significantly different expression profiles. Profile 4 with downregulated pattern contained 106 DE-miRNAs, while profile 21 with upregulated pattern contained 44 DE-miRNAs. The DE-miRNAs with the upregulated pattern mainly played regulatory roles in cellular turnover, such as pyrimidine metabolism, DNA replication, and cell cycle, whereas DE-miRNAs with the downregulated pattern directly or indirectly contributed to protein turnover metabolism such as glycolysis/gluconeogenesis, pyruvate metabolism and biosynthesis of amino acids. Conclusions The main functional miRNAs during chicken muscle development differ between embryonic and post-hatching stages. miRNAs with an upregulated pattern were mainly involved in cellular turnover, while miRNAs with a downregulated pattern mainly played a regulatory role in protein turnover metabolism. These findings enrich information about the regulatory mechanisms involved in muscle development at the miRNA expression level, and provide several candidates for future studies concerning miRNA-target function in regulation of chicken muscle development.

scholarly journals Deciphering the microRNA transcriptome of skeletal muscle during porcine development

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1504 ◽  
Author(s):  
Miaomiao Mai ◽  
Long Jin ◽  
Shilin Tian ◽  
Rui Liu ◽  
Wenyao Huang ◽  
...  
Keyword(s):  
Muscle Development ◽  
Model Organism ◽  
Muscle Disease ◽  
Porcine Muscle ◽  
Development Stages ◽  
Age Related ◽  
Series Expression ◽  
Pig Muscle ◽  
Short Time

MicroRNAs (miRNAs) play critical roles in many important biological processes, such as growth and development in mammals. Various studies of porcine muscle development have mainly focused on identifying miRNAs that are important for fetal and adult muscle development; however, little is known about the role of miRNAs in middle-aged muscle development. Here, we present a comprehensive investigation of miRNA transcriptomes across five porcine muscle development stages, including one prenatal and four postnatal stages. We identified 404 known porcine miRNAs, 118 novel miRNAs, and 101 miRNAs that are conserved in other mammals. A set of universally abundant miRNAs was found across the distinct muscle development stages. This set of miRNAs may play important housekeeping roles that are involved in myogenesis. A short time-series expression miner analysis indicated significant variations in miRNA expression across distinct muscle development stages. We also found enhanced differentiation- and morphogenesis-related miRNA levels in the embryonic stage; conversely, apoptosis-related miRNA levels increased relatively later in muscle development. These results provide integral insight into miRNA function throughout pig muscle development stages. Our findings will promote further development of the pig as a model organism for human age-related muscle disease research.

scholarly journals Chromosome mapping of five differently expressed miRNAs in porcine skeletal muscle development (Brief Report)

2010 ◽  
Vol 53 (6) ◽  
pp. 734-736
Author(s):  
H. B. He ◽  
S. H. Zhao ◽  
X. Y. Li
Keyword(s):  
Skeletal Muscle ◽  
Muscle Development ◽  
Expression Profiles ◽  
Chromosome Mapping ◽  
Differentially Expressed ◽  
Skeletal Muscle Development ◽  
Regulate Gene Expression ◽  
Mirna Expression Profiles ◽  
Differentially Expressed Mirnas ◽  
Regulatory Rnas

Abstract. MicroRNAs (miRNAs) are a class of short, non-coding regulatory RNAs, which are approximately 22 nucleotides in length. Typically, miRNAs negatively regulate gene expression by binding with the 3' untranslated region (UTR) of its regulatory target mRNAs. MicroRNAs are known to play diverse roles in fundamental biological processes, such as proliferation, differentiation and apoptosis (Bartel 2004, 2009). It has been reported that miR-1, miR-133, miR-181 and miR-206 play important roles in skeletal muscle proliferation and hypertrophy (Callis et al. 2007, McCarthy -Esser 2007). We have detected porcine miRNA expression profiles during different stage of skeletal muscle development and a total of 140 miRNAs were differentially expressed (HUANG et al. 2008). In this study, we mapped five differentially expressed miRNAs (mir-29c, mir-103-1, mir-127, mir-193b and mir-218-1) using the radiation hybrid (IMpRH) panel (YERLE et al. 1998).

Sequencing and characterization of lncRNAs in the breast muscle of Gushi and Arbor Acres chickens

Genome ◽  
2018 ◽  
Vol 61 (5) ◽  
pp. 337-347 ◽  
Author(s):  
Tuanhui Ren ◽  
Zhuanjian Li ◽  
Yu Zhou ◽  
Xuelian Liu ◽  
Ruili Han ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Muscle Development ◽  
Target Genes ◽  
Expression Profiles ◽  
Economic Value ◽  
Muscle Quality ◽  
Specific Expression ◽  
Chicken Muscle ◽  
Molecular Regulatory Mechanisms

Chicken muscle quality is one of the most important factors determining the economic value of poultry, and muscle development and growth are affected by genetics, environment, and nutrition. However, little is known about the molecular regulatory mechanisms of long non-coding RNAs (lncRNAs) in chicken skeletal muscle development. Our study aimed to better understand muscle development in chickens and thereby improve meat quality. In this study, Ribo-Zero RNA-Seq was used to investigate differences in the expression profiles of muscle development related genes and associated pathways between Gushi (GS) and Arbor Acres (AA) chickens. We identified two muscle tissue specific expression lncRNAs. In addition, the target genes of these lncRNAs were significantly enriched in certain biological processes and molecular functions, as demonstrated by Gene Ontology (GO) analysis, and these target genes participate in five signaling pathway, as revealed by an analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Taken together, these data suggest that different lncRNAs might be involved in regulating chicken muscle development and growth and provide new insight into the molecular mechanisms of lncRNAs.

scholarly journals Integrative Analyses of Biochemical Properties and Transcriptome Reveal the Dynamic Changes in Leaf Senescence of Tobacco (Nicotiana tabacum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Binghui Zhang ◽  
Jiahan Yang ◽  
Gang Gu ◽  
Liao Jin ◽  
Chengliang Chen ◽  
...  
Keyword(s):  
Leaf Senescence ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Biochemical Properties ◽  
Dynamic Changes ◽  
Software Analysis ◽  
Nicotiana Tabacum L ◽  
Series Expression ◽  
Functional Investigation ◽  
Short Time

Leaf senescence is an important process of growth and development in plant, and it is a programmed decline controlled by a series of genes. In this study, the biochemical properties and transcriptome at five maturity stages (M1∼M5) of tobacco leaves were analyzed to reveal the dynamic changes in leaf senescence of tobacco. A total of 722, 1,534, 3,723, and 6,933 genes were differentially expressed (DEG) between M1 and M2, M1 and M3, M1 and M4, and M1 and M5, respectively. Significant changes of nitrogen, sugars, and the DEGs related to metabolite accumulation were identified, suggesting the importance of energy metabolism during leaf senescence. Gene Ontology (GO) analysis found that DEGs were enriched in biosynthetic, metabolic, photosynthesis, and redox processes, and especially, the nitrogen metabolic pathways were closely related to the whole leaf senescence process (M1∼M5). All the DEGs were grouped into 12 expression profiles according to their distinct expression patterns based on Short Time-series Expression Miner (STEM) software analysis. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis found that these DEGs were enriched in pathways of carbon metabolism, starch and sucrose metabolism, nitrogen metabolism, and photosynthesis among these expression profiles. A total of 30 core genes were examined by Weight Gene Co-expression Network Analysis (WGCNA), and they appeared to play a crucial role in the regulatory of tobacco senescence. Our results provided valuable information for further functional investigation of leaf senescence in plants.

scholarly journals Male-Biased gga-miR-2954 Regulates Myoblast Proliferation and Differentiation of Chicken Embryos by Targeting YY1

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1325
Author(s):  
Xiuxue Dong ◽  
Yu Cheng ◽  
Lingyun Qiao ◽  
Xin Wang ◽  
Cuiping Zeng ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Development ◽  
Expression Profiles ◽  
Myoblast Differentiation ◽  
Mammalian Skeletal Muscle ◽  
Loss Of Function ◽  
Skeletal Muscle Development ◽  
Chicken Muscle ◽  
Proliferation And Differentiation ◽  
Myoblast Proliferation

Previous studies have shown that gga-miR-2954 was highly expressed in the gonads and other tissues of male chickens, including muscle tissue. Yin Yang1 (YY1), which has functions in mammalian skeletal muscle development, was predicted to be a target gene of gga-miR-2954. The purpose of this study was to investigate whether gga-miR-2954 plays a role in skeletal muscle development by targeting YY1, and evaluate its function in the sexual dimorphism development of chicken muscle. Here, all the temporal and spatial expression profiles in chicken embryonic muscles showed that gga-miR-2954 is highly expressed in males and mainly localized in cytoplasm. Gga-miR-2954 exhibited upregulated expression of in vitro myoblast differentiation stages. Next, through the overexpression and loss-of-function experiments performed in chicken primary myoblasts, we found that gga-miR-2954 inhibited myoblast proliferation but promoted differentiation. During myogenesis, gga-miR-2954 could suppress the expression of YY1, which promoted myoblast proliferation and inhibited the process of myoblast cell differentiation into multinucleated myotubes. Overall, these findings reveal a novel role of gga-miR-2954 in skeletal muscle development through its function of the myoblast proliferation and differentiation by suppressing the expression of YY1. Moreover, gga-miR-2954 may contribute to the sex difference in chicken muscle development.

scholarly journals Dynamic assessing silica particle-induced pulmonary fibrosis and associated regulation of long non-coding RNA expression in Wistar rats

2021 ◽  
Vol 43 (1) ◽  
Author(s):  
Linlin Sai ◽  
Xuejie Qi ◽  
Gongchang Yu ◽  
Juan Zhang ◽  
Yuxin Zheng ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Expression Patterns ◽  
Inflammatory Cells ◽  
Severe Form ◽  
Temporal Expression ◽  
Non Coding Rna ◽  
Series Expression ◽  
Short Time ◽  
Derived Data ◽  
Long Non Coding Rna

Abstract Background Exposure to respirable crystalline silica (RCS) can induce accelerated silicosis (AS), a form of silicosis that is more progressive and severe form of silicosis. In this project we aimed to assess processes of silicosis in rats exposed to RCS with focus on the regulation of long noncoding RNAs (lncRNAs). Results The results showed that RCS induced acute inflammatory response as indicated by the appearance of inflammatory cells in the lung from the first day and peaked on day 7 of exposure. The fibroblasts appeared along with the inflammatory cells decreasing gradually on day 14. Extensive fibrosis appeared in the lung tissue, and silicon nodules were getting larger on day 28. Interestingly, the number of altered lncRNAs increased with the exposure time with 193, 424, 455, 421 and 682 lncRNAs on day 1, 7, 14, 21, and 28 after exposure, respectively. We obtained 285 lncRNAs with five significant temporal expression patterns whose expressions might correlate with severity of silicosis. KEGG analysis showed that lncRNAs from short time-series expression miner (STEM)-derived data mainly involved in 17 pathways such as complement and coagulation cascades. Conclusions The differential expression profiles of lncRNAs may be potential biomarkers in silicosis through modulating expressions of their relevant genes in lungs of rat and thus warrant further investigation.

Identification of differentially expressed microRNAs in outgrowth embryos compared with blastocysts and non-outgrowth embryos in mice

2019 ◽  
Vol 31 (4) ◽  
pp. 645 ◽  
Author(s):  
Jihyun Kim ◽  
Jaewang Lee ◽  
Jin Hyun Jun
Keyword(s):  
Bioinformatics Analysis ◽  
Preimplantation Embryo ◽  
Expression Profiles ◽  
In Silico Analysis ◽  
Differentially Expressed ◽  
Recurrent Implantation Failure ◽  
Preimplantation Embryo Development ◽  
Mirna Expression Profiles ◽  
Differentially Expressed Mirnas ◽  
Silico Analysis

Recurrent implantation failure (RIF) is one of the main causes for the repeated failure of IVF, and the major reason for RIF is thought to be a miscommunication between the embryo and uterus. However, the exact mechanism underlying embryo–uterus cross-talk is not fully understood. The aim of the present study was to identify differentially expressed microRNAs (miRNAs) among blastocysts, non-outgrowth and outgrowth embryos in mice using microarray analysis. A bioinformatics analysis was performed to predict the potential mechanisms of implantation. The miRNA expression profiles differed significantly between non-outgrowth and outgrowth embryos. In all, 3163 miRNAs were detected in blastocysts and outgrowth embryos. Of these, 10 miRNA candidates (let-7b, miR-23a, miR-27a, miR-92a, miR-183, miR-200c, miR-291a, miR-425, miR-429 and miR-652) were identified as significant differentially expressed miRNAs of outgrowth embryos by in silico analysis. The expression of the miRNA candidates was markedly changed during preimplantation embryo development. In particular, let-7b-5p, miR-200c-3p and miR-23a-3p were significantly upregulated in outgrowth embryos compared with non-outgrowth blastocysts. Overall, differentially expressed miRNAs in outgrowth embryos compared with blastocysts and non-outgrowth embryos could be involved in embryo attachment, and interaction between the embryo proper and maternal endometrium during the implantation process.

scholarly journals Comprehensive Proteomic Characterization of the Pectoralis Major at Three Chronological Ages in Beijing-You Chicken

2021 ◽  
Vol 12 ◽  
Author(s):  
Jian Zhang ◽  
Jing Cao ◽  
Ailian Geng ◽  
Haihong Wang ◽  
Qin Chu ◽  
...  
Keyword(s):  
Meat Quality ◽  
Muscle Development ◽  
Expression Profiles ◽  
Pectoralis Major ◽  
Breast Muscle ◽  
Differentially Expressed ◽  
Chronological Age ◽  
Chicken Breast ◽  
Group 13 ◽  
Oocyte Meiosis

Chronological age is one of the important factors influencing muscle development and meat quality in chickens. To evaluate the protein expression profiles during skeletal muscle development, we performed a tandem mass tag (TMT)-based quantitative proteomic strategy in pectoralis major (breast muscle) of Beijing-You chicken (BYC) at the chronological age of 90, 120, and 150 days. Each chronological age contained 3 pooling samples or 15 birds (five birds per pooling sample). A total of 1,413 proteins were identified in chicken breast muscle with FDR < 1% and 197 of them were differentially expressed (fold change ≥1.2 or ≤0.83 and p < 0.05). There were 110 up- and 71 down-regulated proteins in 120 d vs 90 d group, 13 up- and 10 down-regulated proteins in 150 d vs 120 d group. The proteomic profiles of BYC at 120 d were very similar to those at 150 d and highly different from those at 90 d, suggesting that 120 d might be an important chronological age for BYC. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that these differentially expressed proteins were mainly involved in the pathway of glycolysis/gluconeogenesis, adrenergic signaling in cardiomyocytes, focal adhesion, oocyte meiosis and phagosome. Furthermore, some DEPs were quantified using parallel reaction monitoring (PRM) to validate the results from TMT analysis. In summary, these results provided some candidate protein-coding genes for further functional validation and contribute to a comprehensive understanding of muscle development and age-dependent meat quality regulation by proteins in chickens.

scholarly journals Copy Number Variation in SOX6 Contributes to Chicken Muscle Development

Genes ◽  
2018 ◽  
Vol 9 (1) ◽  
pp. 42 ◽  
Author(s):  
Shudai Lin ◽  
Xiran Lin ◽  
Zihao Zhang ◽  
Mingya Jiang ◽  
Yousheng Rao ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Muscle Development ◽  
Chicken Muscle ◽  
Number Variation

Breed Differences In The Expression Levels Of Gga-Mir-222a In Laying Hens Influenced H2S Production By Regulating Methionine Synthase Genes In Gut Bacteria

2020 ◽  
Author(s):  
Sicheng Xing ◽  
Chunbo Huang ◽  
Ruiting Wu ◽  
Yiwen Yang ◽  
Jingyuan Chen ◽  
...  
Keyword(s):  
Laying Hens ◽  
Expression Profiles ◽  
Gas Production ◽  
Methionine Synthase ◽  
Differentially Expressed ◽  
Cecal Content ◽  
Differentially Expressed Mirnas ◽  
Microbial Genes ◽  
H2s Production

Abstract Background: The microbiota in the cecum of laying hens was critical for host digestion metabolism and odor gas production. Recent studies have suggested that host miRNAs could regulate gene expression in the gut microbiota. The expression profiles of host-derived miRNAs in the cecal content of two laying hen breeds, Hy-line Gray and Lohmann Pink, which have dissimilar H2S production were characterized, and their possible effects on H2S production by regulating the expression of related genes in the microbiota were demonstrated. Results: The differential expression of microbial serine O-acetyltransferase, methionine synthase, aspartate aminotransferase, methionine-gamma-lyase and adenylylsulfate kinase between the two breeds resulted in lower H2S production in the Hy-line hens. The results also demonstrated miRNA exosomes in the cecal content of laying hens and the potential miRNA-target relationships between 9 differentially expressed miRNAs and 9 differentially expressed microbial genes related to H2S production were investigated, among which gga-miR-222a targeted two methionine synthase genes, Odosp_3416 and BF9343_2953. An in vitro fermentation experiment showed that gga-miR-222a upregulated the expression of these genes, which increased methionine concentrations but decreased H2S production and soluble sulfide concentrations, indicating the potential of host-derived gga-miR-222a to reduce H2S emission in laying hens. Conclusion: These findings identify both a physiologic role by which miRNA shapes the cecal microbiota of laying hens and a strategy to use host miRNAs to manipulate the microbiome and actively expressed key microbial genes to reduce H2S emission and breed environmentally friendly laying hens.

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