Comprehensive Analysis of Differentially Expressed Profiles of mRNA 5-Methylcytosine Modification in Metabolic Dysfunction-Associated Steatotic Liver Disease
Abstract
1. Introduction
2. Materials and Methods
2.1. Animal Studies and Sample Collection
2.2. Liver Lipid Analysis and Biochemical Assessment
2.3. RNA Isolation and Preparation
2.4. RNA-BS-Seq, RNA-Seq, and Data Analysis
2.5. RT-qPCR Validation
2.6. Statistical Analysis
3. Results
3.1. db/db Mice as a Model of MASLD
3.2. Overview of m5C Methylation in the Livers of db/db and NC Mice
3.3. Distribution and Biological Function of Different m5C Methylations in db/db and NC Mice
3.3.1. The Analysis of Differentially Methylated m5C Sites (DMMSs) in db/db and NC Mice
3.3.2. Biological Function of Differentially Methylated m5C Genes (DMMGs) in db/db and NC Mice
3.4. Detection of RNA-Seq-Based Gene Expression Variations in db/db Mice
3.5. Integrated Analysis of RNA-BS-Seq and RNA-Seq Data
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
DMMGs | Differentially methylated m5C genes |
DMMSs | Differentially methylated m5C sites |
HCC | Hepatocellular carcinoma |
MASH | Metabolic dysfunction-associated steatohepatitis |
MASL | Metabolic dysfunction-associated steatotic liver |
RNA-BS-Seq | RNA bisulfite sequencing |
RNA-Seq | RNA transcriptome sequencing |
m5C | 5-methylcytosine |
MASLD | Metabolic dysfunction-associated steatotic liver disease |
H&E | Hematoxylin and eosin |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
GO | Gene Ontology |
DEGs | Differentially expressed genes |
References
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Chromosome | RefPos | RefStrand | GeneName | Foldchange |
---|---|---|---|---|
19 | 7516421 | + | Atl3 | 3.577619607 |
10 | 76896699 | − | Col18a1 | 3.101572825 |
19 | 7516425 | + | Atl3 | 3.090842199 |
11 | 118302035 | − | Cant1 | 3.044066762 |
19 | 7516426 | + | Atl3 | 2.946495372 |
10 | 75773545 | + | Chchd10 | 2.677710514 |
11 | 118302029 | − | Cant1 | 2.591881931 |
2 | 144112449 | − | Snx5 | 2.581124981 |
19 | 38111275 | − | Rbp4 | 2.529759085 |
10 | 30076483 | − | Cenpw | 2.507066041 |
Chromosome | RefPos | RefStrand | GeneName | Foldchange |
---|---|---|---|---|
4 | 148543216 | + | Mtor | 3.739900791 |
6 | 94676492 | − | Lrig1 | 3.61000291 |
19 | 47568459 | + | Slk | 3.462946262 |
12 | 51737918 | + | Ap4s1 | 3.441410522 |
3 | 108191651 | + | Sort1 | 3.301221634 |
8 | 123876449 | − | Sult5a1 | 3.264812185 |
7 | 127159861 | + | Gm42715 | 3.23104311 |
1 | 9818350 | − | Vcpip1 | 3.21986455 |
14 | 70526697 | − | Ppp3cc | 3.197623321 |
17 | 31519274 | + | Slc37a1 | 3.164549205 |
Gene Name | Chrome | Strand | Regulation | Fold Change | p-Value |
---|---|---|---|---|---|
Sult3a1 | chr10:33863934–33879475 | + | Up | 980.08 | 0.00185 |
Cyp2b13 | chr7:26061494–26096196 | + | Up | 901.21 | 0.0039 |
Sult1e1 | chr5:87575967–87591611 | − | Up | 875.72 | 0.00005 |
Cyp2b9 | chr7:26173410–26210661 | + | Up | 649.61 | 0.00005 |
Sult2a5 | chr7:13623966–13670801 | + | Up | 647.37 | 0.0499 |
Hao2 | chr3:98874576–98893239 | − | Up | 287.06 | 0.0491 |
Cyp3a41a | chr5:145694059–145720136 | − | Up | 235.47 | 0.0018 |
Sult2a7 | chr7:14465158–14492926 | − | Up | 226.97 | 0.00005 |
A4gnt | chr9:99612501–99622367 | + | Up | 204.94 | 0.01895 |
Ly6d | chr15:74762055–74763567 | − | Up | 179.17 | 0.00005 |
Serpina9 | chr12:103980242–104013755 | − | Down | 252.27 | 0.0255 |
Rpl21 | chr5:146832889–146837032 | + | Down | 207.83 | 0.00005 |
Camk2b | chr11:5969643–6066362 | − | Down | 159.94 | 0.00005 |
Hsd3b5 | chr3:98382480–98763128 | − | Down | 102.79 | 0.02555 |
Serpina1e | chr12:103946930–103958975 | − | Down | 97.10 | 0.00005 |
Adh6-ps1 | chr3:138374120–138388291 | + | Down | 70.99 | 0.00005 |
Enho | chr4:41569774–41641416 | − | Down | 64.92 | 0.00005 |
BC048546 | chr6:128539821–128581606 | − | Down | 62.24 | 0.00005 |
Cib3 | chr8:72204334–72212837 | − | Down | 46.44 | 0.0108 |
Gm3839 | chr14:11280734–11356726 | − | Down | 42.66 | 0.00435 |
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Yang, Y.; Wang, E.; Zhou, B.; Lu, Y.; Ding, X.; Li, Y. Comprehensive Analysis of Differentially Expressed Profiles of mRNA 5-Methylcytosine Modification in Metabolic Dysfunction-Associated Steatotic Liver Disease. Curr. Issues Mol. Biol. 2025, 47, 305. https://doi.org/10.3390/cimb47050305
Yang Y, Wang E, Zhou B, Lu Y, Ding X, Li Y. Comprehensive Analysis of Differentially Expressed Profiles of mRNA 5-Methylcytosine Modification in Metabolic Dysfunction-Associated Steatotic Liver Disease. Current Issues in Molecular Biology. 2025; 47(5):305. https://doi.org/10.3390/cimb47050305
Chicago/Turabian StyleYang, Yueying, E Wang, Bing Zhou, Yan Lu, Xiaoying Ding, and Yao Li. 2025. "Comprehensive Analysis of Differentially Expressed Profiles of mRNA 5-Methylcytosine Modification in Metabolic Dysfunction-Associated Steatotic Liver Disease" Current Issues in Molecular Biology 47, no. 5: 305. https://doi.org/10.3390/cimb47050305
APA StyleYang, Y., Wang, E., Zhou, B., Lu, Y., Ding, X., & Li, Y. (2025). Comprehensive Analysis of Differentially Expressed Profiles of mRNA 5-Methylcytosine Modification in Metabolic Dysfunction-Associated Steatotic Liver Disease. Current Issues in Molecular Biology, 47(5), 305. https://doi.org/10.3390/cimb47050305