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

Liu, Jie; Li, Fuwei; Hu, Xin; Cao, Deliang; Liu, Wei; Han, Haitang; Zhou, Yan; Lei, Qiuxia

doi:10.1186/s12864-021-07374-y

Cited by 17 publications

(17 citation statements)

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“…Increasing evidence indicates that circRNAs can sequester relevant miRNAs through MREs to post-transcriptionally regulate gene expression. We identified 587 miRNAs in breast muscle at E12, E17, D1, D14, D56, and D98 in a previous study [ 28 ] (Table S 8 ). To investigate ceRNA regulation in muscle and identify muscle-related circRNAs, we identified putative miRNA-circRNA and miRNA-mRNA interactions using the 587 miRNAs and transcripts identified in profiles 3, 14, and 16.…”

Section: Resultsmentioning

confidence: 99%

“…The main mechanism of circRNA may be in acting as miRNA sponges to modulate post-transcriptional regulation [ 31 ]. Our previous studies have explored mRNA and miRNA expression at the same time points as the present research [ 11 , 28 ]. Therefore, we performed circRNA-miRNA-mRNA regulatory network construction using the circRNAs and mRNAs with the same expression pattern and the 587 miRNAs identified in the chicken muscle in our previous studies.…”

Section: Discussionmentioning

confidence: 99%

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Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

Lei

Han

et al. 2022

BMC Genomics

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Background The growth and development of skeletal muscle are regulated by protein-coding genes and non-coding RNA. Circular RNA (circRNA) is a type of non-coding RNA involved in a variety of biological processes, especially in post-transcriptional regulation. To better understand the regulatory mechanism of circRNAs during the development of muscle in chicken, we performed RNA-seq with linear RNA depletion for chicken breast muscle in 12 (E 12) and17 (E 17) day embryos, and 1 (D 1), 14 (D 14), 56 (D 56), and 98 (D 98) days post-hatch. Results We identified 5755 differentially expressed (DE)-circRNAs during muscle development. We profiled the expression of DE-circRNAs and mRNAs (identified in our previous study) at up to six time points during chicken muscle development and uncovered a significant profile (profile 16) for circRNA upregulation during aging in muscle tissues. To investigate competing endogenous RNA (ceRNA) regulation in muscle and identify muscle-related circRNAs, we constructed a circRNA-miRNA-mRNA regulatory network using the circRNAs and mRNAs from profile 16 and miRNAs identified in our previous study, which included 361 miRNAs, 68 circRNAs, 599 mRNAs, and 31,063 interacting pairs. Functional annotation showed that upregulated circRNAs might contribute to glycolysis/gluconeogenesis, biosynthesis of amino acids, pyruvate metabolism, carbon metabolism, glycogen and sucrose metabolism through the ceRNA network, and thus affected postnatal muscle development by regulating muscle protein deposition. Of them, circRNA225 and circRNA226 from the same host gene might be key circRNAs that could regulate muscle development by interacting with seven common miRNAs and 207 mRNAs. Our experiments also demonstrated that there were interactions among circRNA225, gga-miR-1306-5p, and heat shock protein alpha 8 (HSPA8). Conclusions Our results suggest that adequate supply of nutrients such as energy and protein after hatching may be a key factor in ensuring chicken yield, and provide several candidate circRNAs for future studies concerning ceRNA regulation during chicken muscle development.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

Lei

Han

et al. 2022

BMC Genomics

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“…Raw data were subjected to standardized analysis (Liu et al, 2021; Ma et al, 2018). Adapter dimers, low‐quality reads, junk reads, common RNA families (mRNA, rRNA, tRNA, snRNA, and snoRNA), and repeats were removed by using the ACGT101‐miR program (LC Sciences).…”

Section: Methodsmentioning

confidence: 99%

Up‐regulation of miR‐335 and miR‐674‐3p in the rostral ventrolateral medulla contributes to stress‐induced hypertension

Zhang

Xing

Chen

et al. 2022

Journal of Neurochemistry

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The rostral ventrolateral medulla (RVLM) is known as the vasomotor center that plays a crucial role in mediating the development of stress-induced hypertension (SIH).MicroRNAs (miRNAs) are involved in many different biological processes and diseases.However, studies that evaluated the roles of miRNAs in the RVLM during SIH do not exist. Here, we performed RNA sequencing to explore the genome-wide miRNA profiles in RVLM in an SIH rat model established by administering electric foot-shocks and noises. The function of miRNAs in blood pressure regulation was determined in vivo via the intra-RVLM microinjection of the agomir or antagomir. Furthermore, the underlying mechanisms of miRNAs on SIH were investigated through in vitro and in vivo experiments, like gain-of-function. We discovered 786 miRNA transcripts among which 4 were differentially expressed. The over-expression of miR-335 and miR-674-3p in RVLM dramatically increased the heart rate (HR), arterial blood pressure (ABP), systolic blood pressure (SBP), diastolic blood pressure (DBP), and mean arterial pressure (MAP) levels of normotensive rats, whereas the knockdown of miR-335 and miR-674-3p in RVLM markedly reduced the HR, ABP, SBP, DBP, and MAP levels of SIH rats. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation revealed that miR-335 and miR-674-3p participated in regulating the development of SIH from different aspects, like apoptosis-multiple species pathway. Sphk1, whose expression was markedly decreased in SIH, was identified as a novel target of miR-335. MiR-335 over-expression substantially reduced the expression of Sphk1 and promoted neural apoptosis, and its inhibition had opposite effects. Re-introduction of Sphk1 dramatically abrogated the apoptosis induced by miR-335. This study provides the first systematic dissection of the RVLM miRNA landscape in SIH. MiR-335 and miR-674-3p act as SIH promoters, and the identified miR-335/Sphk1/apoptosis axis represents one of the possible mechanisms. These miRNAs can be exploited as potential targets for the molecular-based therapy of SIH.

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“…MiRNAs play important role in the regulation of cellular signal networks in both normal and diseased conditions. In eukaryotes, 2/3 of the coding genes are regulated by miRNAs [11], which participate in the regulation of many physiological processes [12], such as development, cell division, proliferation, and metabolism, and play an essential role in the in ammatory response [13], immune-related pathway [14], tumorigenesis [15] and so on. A growing number of studies have shown that host miRNAs modulate target gene expression at the post-transcriptional level by inhibiting translation and promoting degradation of target genes, and play an important role in against parasite infection [16,17].…”

Section: Introductionmentioning

confidence: 99%

MicroRNA expression profile of Chicken cecal in different stages during Histomonas meleagridis infection

Zhang

Chen

et al. 2022

Preprint

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Background: Histomonas meleagridis is an anaerobic, intercellular parasite, which infects gallinaceous birds such as turkeys and chickens. In recent years, the reemergence of Histomoniasis has caused serious economic losses as drugs to treat the disease have been banned. At present, H. meleagridis research focuses on virulence, gene expression analysis, and the innate immunity of the host. However, there are no studies on the differentially expressed miRNAs (DEMs) associated with the host inflammatory and immune responses induced by H. meleagridis. In this research, high-throughput sequencing was used to analyze the expression profile of cecal miRNA at 10 and 15 days post-infection (DPI) in chickens infected with Chinese JSYZ-F strain H. meleagridis.Results: Compared with the controls, 94 and 127 DEMs were found in cecal of infected chickens at 10 DPI (CE vs CC) and 15 DPI (CEH vs CCH), respectively, of which 60 DEMs were shared at two-time points. Gene Ontology (GO) functional enrichment analysis of the target genes of DEMs indicated that 881 and 1027 GO terms were significantly enriched at 10 and 15 DPI, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the target genes of DEMs demonstrated that 5 and 3 KEGG pathways were significantly enriched at 10 and 15 DPI, respectively. The integrated analysis of miRNA–gene network revealed that the DEMs played important roles in the host inflammatory and immune responses to H. meleagridis infection by dynamically regulating expression levels of inflammation and immune-related cytokines. Conclusion: This article not only suggested that host miRNA expression was dynamically altered by H. meleagridis and host but also revealed differences in the regulation of T cell involved in host responses to different times H. meleagridis infection. This article contributes to future research into miRNA-target interactions during H. meleagridis infection in chickens and provides new ideas for H. meleagridis treatment and control.

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

Cited by 17 publications

References 57 publications

Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

Up‐regulation of miR‐335 and miR‐674‐3p in the rostral ventrolateral medulla contributes to stress‐induced hypertension

MicroRNA expression profile of Chicken cecal in different stages during Histomonas meleagridis infection

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