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Prediction and Experimental Verification of a Hierarchical Transcription Factor Regulatory Network of Porcine Myoglobin (Mb).

ABSTRACT: Myoglobin is a key chemical component that determines meat's color and affects consumers' purchase intentions. In this work, we firstly identified the promoter sequence of the Mb gene from the primary assembly of high-throughput genome sequencing in pigs, and predicted its potential transcription factors by LASAGNA. Through the data mining of the mRNA expression profile of longissimus dorsi muscle of different pig breeds, we constructed a hierarchical interplay network of Mb-TFs (Myoglobin-Transcription Factors), consisting of 16 adaptive transcription factors and 23 secondary transcription factors. The verification of gene expression in longissimus dorsi muscle showed that the Mb mRNA and encoded protein were significantly (p < 0.05) more abundant in Bama pigs than Yorkshire pigs. The qRT-PCR (Real-Time Quantitative Reverse Transcription PCR) validation on genes of the Mb-TFs network showed that FOS, STAT3, STAT1, NEFL21, NFE2L2 and MAFB were significant positive regulatory core transcription factors of Mb-TFs network in Bama pigs, whereas ATF3 was the secondary transcription factor most responsible for the activation of the above transcription factors. Our study provides a new strategy to unravel the mechanism of pork color formation, based on public transcriptome and genome data analysis.

SUBMITTER: Yuan D

PROVIDER: S-EPMC8698129 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Rhizoma Drynariae has been widely used for the treatment of osteoarthritis (OA), but its potential targets and molecular mechanisms remain to be further explored. Targets of Rhizoma Drynariae and OA were predicted by relevant databases, and a protein-protein interaction (PPI) network was constructed to identify key targets. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed to obtain related pathways and then select significant pathways associated with OA. The OA chondrocyte model was established by inflammatory factor-induced SW1353 chondrocytes, and molecular docking was conducted to verify the above theoretical prediction. The results showed that a total of 86 Rhizoma Drynariae-OA interaction targets were identified, among which IL-6 and AKT1 were the key targets in the PPI network. Luteolin was the most critical component of Rhizoma Drynariae. KEGG results indicated that the effects of Rhizoma Drynariae on OA are associated with the PI3K/AKT, TNF, IL-17, apoptosis, and HIF-1 signaling pathway. The PI3K/AKT pathway can activate the downstream NF-κB pathway and further regulate the transcription and expression of downstream IL-6, IL-17, HIF-1α, Bax, and TNF, suggesting that the PI3K/AKT/NF-κB pathway is the critical pathway in the treatment of OA with Rhizoma Drynariae. Active components of Rhizoma Drynariae and key proteins of the PI3K/AKT/NF-κB signaling pathway were subjected to molecular docking, whose results showed that luteolin and IKK-α played a critical role. In vitro experiments indicated that both aqueous extracts of Rhizoma Drynariae (AERD) and luteolin inhibited the expression of IL-6 and HIF-1α and suppressed the activation of PI3K/AKT/NF-κB, IL-17, and TNF pathways. The measurement of mitochondrial membrane potential (Δψm) indicated that AERD and luteolin can decrease the LPS-induced early apoptotic cells. Luteolin had a more prominent inhibitory effect than AERD in the abovementioned in vitro experiments. In conclusion, the therapeutic mechanism of Rhizoma Drynariae against OA may be closely related to the inhibition of the PI3K/AKT/NF-κB pathway and downstream pathways, and luteolin plays a vital role in the treatment.

Dataset Information

Prediction and Experimental Verification of a Hierarchical Transcription Factor Regulatory Network of Porcine Myoglobin (Mb).

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