Comparative methylation and RNAseq expression analysis on CpG context to identify genes involved in backfat vs liver diversification in Nanchukmacdon pig
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ABSTRACT:
PROVIDER: PRJNA735785 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14752111_1.fastq.gz | Fastqsanger.gz | |||
| SRR14752111_2.fastq.gz | Fastqsanger.gz | |||
| SRR14752112_1.fastq.gz | Fastqsanger.gz | |||
| SRR14752112_2.fastq.gz | Fastqsanger.gz | |||
| SRR14752113_1.fastq.gz | Fastqsanger.gz |
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Project description:We report the significant role methylation in differentially expressed genes in backfat and liver tissue of Nanchukmacdon pig
2021-06-08 | GSE176338 | GEO
Project description:Background DNA methylation and demethylation at CpG islands is one of the main regulatory factors that allow cells to respond to different stimuli. These regulatory mechanisms help in developing tissue without affecting the genomic composition or undergoing selection. Liver and backfat play important roles in regulating lipid metabolism and control various pathways involved in reproductive performance, meat quality, and immunity. Genes inside these tissue store a plethora of information and an understanding of these genes is required to enhance tissue characteristics in the future generation. Results A total of 16 CpG islands were identified, and they were involved in differentially methylation regions (DMRs) as well as differentially expressed genes (DEGs) of liver and backfat tissue samples. The genes C7orf50, ACTB and MLC1 in backfat and TNNT3, SIX2, SDK1, CLSTN3, LTBP4, CFAP74, SLC22A23, FOXC1, GMDS, GSC, GATA4, SEMA5A and HOXA5 in the liver, were categorized as differentially-methylated. Subsequently, Motif analysis for DMRs was performed to understand the role of the methylated motif for tissue-specific differentiation. Gene ontology studies revealed association with collagen fibril organization, the Bone Morphogenetic Proteins (BMP) signaling pathway in backfat and cholesterol biosynthesis, bile acid and bile salt transport, and immunity-related pathways in methylated genes expressed in the liver. Conclusions In this study, to understand the role of genes in the differentiation process, we have performed whole-genome bisulfite sequencing (WGBS) and RNA-seq analysis of Nanchukmacdon pigs. Methylation and motif analysis reveals the critical role of CpG islands and transcriptional factors binding site (TFBS) in guiding the differential patterns. Our findings could help in understanding how methylation of certain genes plays an important role and can be used as biomarkers to study tissue specific characteristics. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08123-x.
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Project description:Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification
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Project description:Purpose: Analysis of the effect of different fats and amonut of cDDGS in the feedstuff on miRNA expression in porcine backfat Methods: miRNA-seq analysis was performed on backfat samples collected from 24 male and female crossbred fatteners originating from sows (Polish Landrace × White Large Polish) mated with a boar (Duroc × Pietrain) divided into four dietary groups: 7-cDDGS+rapeseed oil (group I), n=6 (+cDDGS+rapeseed oil -group II), n= 6 (+cDDGS+beeftallow -group III),n=5 (+cDDGS+coconut oil -group IV). The miRNA libraries were constructed from total RNA using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to the manufacturer protocol. The quantification of the obtained libraries was performed on a Qubit 2.0 spectrophotometer (Invitrogen, Life Technologies), while a quality control on a TapeStation 2200 instrument (D1000 ScreenTape; Agilent). 100 single-end cycle sequencing was performed on the HiScanSQ platform (Illumina) with the use of TruSeq SR Cluster Kit v3- CBOT-HS and TruSeq SBS Kit v 3 - HS (Illumina). MicroRNA differentially expressed between dietary groups were identified with the DESeq2 software. Results: The comparison of miRNA profiles between dietary groups showed The highest number of miRNAs with altered expression was identified in the comparison of animals fed the diet containing cDDGS and coconut oil (group IV) with animals from the –cDDGS + rapeseed oil (group I) (37 miRNA, p adjusted <0.01). Moreover, in comparison between the group IV and groups III and II , 29 (12 upregulated and 17 downregulated in +cDDGS+coconut oil group) and 28 (10 upregulated and 18 downregulated in +cDDGS+coconut oil group) miRNAs were identified, respectively (p adjusted <0.1) Conclusions: Obtained results suggest that coconut oil induces changes in miRNA profile of backfat in pigs.
2021-09-17 | GSE184177 | GEO
Project description:The posttranscriptional gene regulation mediated by microRNA (miRNA) plays an important role in various species. Recently, a large number of miRNAs and their expression patterns have been identified. However, to date, limited miRNAs have been reported to modulate adipogenesis and lipid deposition in beef cattle. Total RNAs from Chinese Qinchuan bovine backfat at fetal and adult stages were used to construct small RNA libraries for Illumina next-generation sequencing. A total of 13,915,411 clean reads were obtained from a fetal library and 14,244,946 clean reads from an adult library. In total, 475 known and 36 novel miRNA candidates from backfat were identified. The nucleotide bias, base editing, and family of the known miRNAs were also analyzed. Based on stem-loop qPCR, 15 specific miRNAs were detected, and the results showed that bta-miRNAn25 and miRNAn26 were highly expressed in backfat tissue, suggesting these small RNAs play a role in the development and maintenance of bovine subcutaneous fat tissue. Putative targets for miRNAn25 and miRNAn26 were predicted, and the 61 most significant target transcripts were related to lipid and fatty acid metabolism. Of interest, the canonical pathway and gene networks analyses revealed that PPARα/RXRα activation and LXR/RXR activation were important components of the gene interaction hierarchy results. In the present study, we explored the backfat miRNAome differences between cattle of different developmental stages, expanding the expression repertoire of bovine miRNAs that could contribute to further studies on the fat development of cattle. The expression analysis of the differential target genes of miRNAn25 and miRNAn26 showed potential gene networks that affect lipid and fatty acid metabolism. These results may help in the design of new intervention strategies to improve beef quality. Examination of Chinese Qinchuan bovine backfat miRNAs by deep sequencing.
2015-12-31 | E-GEOD-48569 | biostudies-arrayexpress
Project description:We report the application of Illumina RNA sequencing for characterization and discovery of genes and transcripts in Italian Large Whtie pig backfat tissue. RNAs sequencing for long RNA quantification, discovery, characterisation and differential expression evaluation.
2016-03-15 | E-GEOD-68007 | biostudies-arrayexpress
Project description:We report the application of Illumina RNA sequencing for characterization and discovery of genes and transcripts in Italian Large Whtie pig backfat tissue.
2016-03-15 | GSE68007 | GEO
Project description:Fat deposition is a prominent economic trait and complex process in pigs. Ningxiang pig, one of the four famous indigenous breeds in China, is characterized by high fat content. The underlying gene expression pattern in different developmental periods of backfat tissue remains unclear, and the purpose of this investigation is to explore the potential molecular regulators of backfat tissue development in Ningxiang pigs. Histological analysis of backfat tissue showed that adipocyte area increased and adipocyte number decreased with the development of backfat tissue in different stages (60d, 120d, 180d, 240d, 300d, and 360d). Meanwhile, a total of 1024 differentially expressed genes were identified in five comparison groups (120d vs 60d, 180d vs 120d, 240d vs 180d, 300d vs 240d, and 360d vs 300d). And then strongly co-expressed genes in modules were clustered by Weighted gene co-expression network analysis (WGCNA). Among these modules, turquoise, red, pink, paleturquoise, darkorange, and darkgreen module had close correlation with 60d, 120d, 180d, 240d, 300d, and 360d developmental stage, respectively, while tan, black and turquoise module had intimate relation with backfat thickness, adipocyte area and adipocyte number, respectively. Furthermore, GO and KEGG enrichment were analyzed in each module, the gene co-expression network was constructed, and the hub genes were described. According to the co-expression network, 13 genes (ACSL1, ACOX1, FN1, DCN, CHST13, COL1A1, COL1A2, COL6A3, COL5A1, COL14A1, OAZ3, DNM1, and SELP) were recognized as hub genes. Further analysis revealed that ACSL1 and ACOX1 might perform considerable function in early developmental stage of backfat tissue before 60d. FN1, DCN, COL1A1, COL1A2, COL5A1, COL6A3, and COL14A1 have unignorable position around 120d developmental stage. Besides, the functional relevance associated with SELP and backfat thickness, DNM1 and adipocyte area needs to be elucidated. In addition, QCR analysis validated the strong consistency of genes expressions with RNA-seq data, manifesting the reliability and accuracy of our study. The present research preliminarily depicted the gene co-expression network for each period of backfat developmental stage in Ningxiang pigs, which not only help to understand the integrated mechanism underlying backfat tissue development and lipid metabolism, but also promotes the progress of genetic improvement in pigs.
2023-08-10 | GSE234796 | GEO