MicroRNAs mediate liver transcriptome changes upon soy diet intervention in mice

Șeclăman, Edward; Bălăcescu, Loredana; Bălăcescu, Ovidiu; Bejinar, Cristina; Udrescu, Mihai; Marian, Cătălin; Sîrbu, Ioan Ovidiu; Anghel, Andrei

doi:10.1111/jcmm.14140

Cited by 5 publications

(6 citation statements)

References 36 publications

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“…The interactions between the high-confidence viral circRNAs and the DEmiRNAs were predicted using TarPmiR ( http://hulab.ucf.edu/research/projects/miRNA/TarPmiR/ ) [ 47 ] with default parameters. Further analysis considers only the interactions with definite binding probabilities ( P = 1) and binding energies ≤ −20 kcal/mol according to Seclaman’s study [ 48 ].…”

Section: Methodsmentioning

confidence: 99%

Identification and characterization of circRNAs encoded by MERS-CoV, SARS-CoV-1 and SARS-CoV-2

Cai

He³

et al. 2020

Briefings in Bioinformatics

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The life-threatening coronaviruses MERS-CoV, SARS-CoV-1 and SARS-CoV-2 (SARS-CoV-1/2) have caused and will continue to cause enormous morbidity and mortality to humans. Virus-encoded noncoding RNAs are poorly understood in coronaviruses. Data mining of viral-infection-related RNA-sequencing data has resulted in the identification of 28 754, 720 and 3437 circRNAs encoded by MERS-CoV, SARS-CoV-1 and SARS-CoV-2, respectively. MERS-CoV exhibits much more prominent ability to encode circRNAs in all genomic regions than those of SARS-CoV-1/2. Viral circRNAs typically exhibit low expression levels. Moreover, majority of the viral circRNAs exhibit expressions only in the late stage of viral infection. Analysis of the competitive interactions of viral circRNAs, human miRNAs and mRNAs in MERS-CoV infections reveals that viral circRNAs up-regulated genes related to mRNA splicing and processing in the early stage of viral infection, and regulated genes involved in diverse functions including cancer, metabolism, autophagy, viral infection in the late stage of viral infection. Similar analysis in SARS-CoV-2 infections reveals that its viral circRNAs down-regulated genes associated with metabolic processes of cholesterol, alcohol, fatty acid and up-regulated genes associated with cellular responses to oxidative stress in the late stage of viral infection. A few genes regulated by viral circRNAs from both MERS-CoV and SARS-CoV-2 were enriched in several biological processes such as response to reactive oxygen and centrosome localization. This study provides the first glimpse into viral circRNAs in three deadly coronaviruses and would serve as a valuable resource for further studies of circRNAs in coronaviruses.

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Section: Methodsmentioning

confidence: 99%

Identification and characterization of circRNAs encoded by MERS-CoV, SARS-CoV-1 and SARS-CoV-2

Cai

He³

et al. 2020

Briefings in Bioinformatics

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“…Thus far, miRNA expression has been studied in the liver tissues of buffalos ( Rha and Gyeol Yoo, 2015 ), dairy cows ( Bu et al, 2017 ), mice ( Seclaman et al, 2019 ), rats ( Wang et al, 2017 ), pigeons ( Wang et al, 2020 ), pigs ( Kai et al, 2019 ), chickens ( Xu et al, 2019 ), and geese ( Zheng et al, 2015 ). RNA-Seq was used to construct 41 pairs of ceRNA networks on liver tissue from three Holstein cows, which provide new insight into resolving bovine lipid metabolism ( Liang et al, 2017 ).…”

Section: Discussionmentioning

confidence: 99%

MiRNA-Seq reveals key MicroRNAs involved in fat metabolism of sheep liver

Fei

Jin²,

Yuan³

et al. 2023

Front. Genet.

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There is a genetic difference between Hu sheep (short/fat-tailed sheep) and Tibetan sheep (short/thin-tailed sheep) in tail type, because of fat metabolism. Previous studies have mainly focused directly on sheep tail fat, which is not the main organ of fat metabolism. The function of miRNAs in sheep liver fat metabolism has not been thoroughly elucidated. In this study, miRNA-Seq was used to identify miRNAs in the liver tissue of three Hu sheep (short/fat-tailed sheep) and three Tibetan sheep (short/thin-tailed sheep) to characterize the differences in fat metabolism of sheep. In our study, Hu sheep was in a control group, we identified 11 differentially expressed miRNAs (DE miRNAs), including six up-regulated miRNAs and five down-regulated miRNAs. Miranda and RNAhybrid were used to predict the target genes of DE miRNAs, obtaining 3,404 target genes. A total of 115 and 67 GO terms as well as 54 and 5 KEGG pathways were significantly (padj < 0.05) enriched for predicted 3,109 target genes of up-regulated and 295 target genes of down-regulated miRNAs, respectively. oar-miR-432 was one of the most up-regulated miRNAs between Hu sheep and Tibetan sheep. And SIRT1 is one of the potential target genes of oar-miR-432. Furthermore, functional validation using the dual-luciferase reporter assay indicated that the up-regulated miRNA; oar-miR-432 potentially targeted sirtuin 1 (SIRT1) expression. Then, the oar-miR-432 mimic transfected into preadipocytes resulted in inhibited expression of SIRT1. This is the first time reported that the expression of SIRT1 gene was regulated by oar-miR-432 in fat metabolism of sheep liver. These results could provide a meaningful theoretical basis for studying the fat metabolism of sheep.

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“…A long-term soy diet was associated with strong upregulation of 13 microR-NAs, including the well-known tumor suppressor miR-29a-3p. Seclaman et al examined the liver of soy-fed male mice [46] and described the transcriptome impact of upregulated miR-145a-5p and miR-455-3p. Interestingly, the transcriptome analysis identified iron metabolism and xenobiotic/fatty acid metabolizing pathways as coordinately regulated by the two microRNAs.…”

Section: Discussionmentioning

confidence: 99%

“…Taken together, these findings indicate that the soy diet induces significant gene expression responses in different experimental models, an effect that could be modulated at both transcriptional and post-transcriptional levels. The best-known transcriptional factors mediating soy transcriptional effects are RICTOR (rapamycin-insensitive companion of TOR, complex 2) and SREBF1 (sterol regulatory element-binding transcription factor 1) [45,46]. The soy-induced suppression of these two transcription factors protects against insulin resistance and fatty liver [93,94].…”

Section: Discussionmentioning

confidence: 99%

“…CEBPD (CCAAT/enhancer-binding protein delta), a transcriptional regulator that acts as a tumor suppressor, is strongly induced by soy-diet, which might explain the repression of multiple oncogene targets [39]. On the other hand, the impact on microRNA expression indicates that soy-induced gene regulation also involves post-transcriptional mechanisms [46,47].…”

Section: Discussionmentioning

confidence: 99%

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Dietary Soy Impact on Host Transcriptome Profile—A Review

et al. 2021

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Whether eaten, drank, or taken in the form of supplements, soybean has been a part of the human diet for centuries. The dietary use of soybean has been extensively proven to be beneficial for human health, protecting against a wide range of chronic diseases. However, our knowledge regarding the impact of soy intake on global gene expression is still incomplete. The present review summarizes and compares data describing the transcriptional changes in several tissues from two different phyla (fish and mammals) upon soybean diet supplementation. We performed comparative STRING-based pathway enrichment analysis of both individual and aggregated soy-induced transcriptome data in fish and mammals and identified the signaling pathways common between the two datasets. We hypothesize that these pathways represent a conserved transcriptome response to the soy-enriched dietary challenge.

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MicroRNAs mediate liver transcriptome changes upon soy diet intervention in mice

Cited by 5 publications

References 36 publications

Identification and characterization of circRNAs encoded by MERS-CoV, SARS-CoV-1 and SARS-CoV-2

Identification and characterization of circRNAs encoded by MERS-CoV, SARS-CoV-1 and SARS-CoV-2

MiRNA-Seq reveals key MicroRNAs involved in fat metabolism of sheep liver

Dietary Soy Impact on Host Transcriptome Profile—A Review

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