Transcriptome Analysis of Three Sheep Intestinal Regions reveals Key Pathways and Hub Regulatory Genes of Large Intestinal Lipid Metabolism

Chao, Tianle; Wang, Guizhi; Ji, Zhibin; Liu, Zhaohua; Hou, Lei; Wang, Jin

doi:10.1038/s41598-017-05551-2

Cited by 19 publications

(13 citation statements)

References 64 publications

(74 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The rumen and ileum are important organs for the digestion and absorption of nutrients in ruminants. The molecular mechanisms and key drivers underlying developmental changes in rumen and ileum in the early part of life have been revealed in several omics studies such as transcriptome analysis [ 54 , 55 ] and microbiome analysis [ 56 ]. In this study, we observed that 20.8% (33,107 genes) and 27.0% (4217) bovine genes were significantly DE between the pre-weaning (D33) and post-weaning (D96) periods in ileum and rumen tissues, respectively ( Figure 1 and Figure 2 , Supplementary Table S6 ).…”

Section: Discussionmentioning

confidence: 99%

Integration of lncRNA and mRNA Transcriptome Analyses Reveals Genes and Pathways Potentially Involved in Calf Intestinal Growth and Development during the Early Weeks of Life

Ibeagha‐Awemu

Ngoc

Dudemaine

et al. 2018

Genes

View full text Add to dashboard Cite

A better understanding of the factors that regulate growth and immune response of the gastrointestinal tract (GIT) of calves will promote informed management practices in calf rearing. This study aimed to explore genomics (messenger RNA (mRNA)) and epigenomics (long non-coding RNA (lncRNA)) mechanisms regulating the development of the rumen and ileum in calves. Thirty-two calves (≈5-days-old) were reared for 96 days following standard procedures. Sixteen calves were humanely euthanized on experiment day 33 (D33) (pre-weaning) and another 16 on D96 (post-weaning) for collection of ileum and rumen tissues. RNA from tissues was subjected to next generation sequencing and 3310 and 4217 mRNAs were differentially expressed (DE) between D33 and D96 in ileum and rumen tissues, respectively. Gene ontology and pathways enrichment of DE genes confirmed their roles in developmental processes, immunity and lipid metabolism. A total of 1568 (63 known and 1505 novel) and 4243 (88 known and 4155 novel) lncRNAs were detected in ileum and rumen tissues, respectively. Cis target gene analysis identified BMPR1A, an important gene for a GIT disease (juvenile polyposis syndrome) in humans, as a candidate cis target gene for lncRNAs in both tissues. LncRNA cis target gene enrichment suggested that lncRNAs might regulate growth and development in both tissues as well as posttranscriptional gene silencing by RNA or microRNA processing in rumen, or disease resistance mechanisms in ileum. This study provides a catalog of bovine lncRNAs and set a baseline for exploring their functions in calf GIT development.

show abstract

Section: Discussionmentioning

confidence: 99%

Integration of lncRNA and mRNA Transcriptome Analyses Reveals Genes and Pathways Potentially Involved in Calf Intestinal Growth and Development during the Early Weeks of Life

Ibeagha‐Awemu

Ngoc

Dudemaine

et al. 2018

Genes

View full text Add to dashboard Cite

show abstract

“…CPT1A was the most DEG. CPT1A gene can catalyze the transfer of the acyl group of long-chain fatty acid-CoA conjugates to carnitine and plays an important role in triglyceride metabolism [ 2 , 14 ]. Up-regulation of CPT1A gene in intramuscular adipose from Jinhua pigs may play an important role in intramuscular adipose metabolism through the PPAR signaling pathway.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome analysis reveals differential gene expression in intramuscular adipose tissues of Jinhua and Landrace pigs

Miao

Wei

Khan

et al. 2018

The Journal of Veterinary Medical Science

View full text Add to dashboard Cite

Meat is a rich source of protein, fatty acids and carbohydrates for human needs. In addition to necessary nutrients, high fat contents in pork increase the tenderness and juiciness of the meat, featuring diverse application in various dishes. This study investigated the transcriptomic profiles of intramuscular adipose tissues in Jinhua and Landrace pigs by employing advanced RNA sequencing. Results showed significant interesting to note that there were significant differences in the expression of genes. 1,632 genes showed significant differential expression, 837 genes were up-regulated and 195 genes were down-regulated. Variations in genes responsible for cell aggregation, extracellular matrix formation, cellular lipid catabolic process, and fatty acid binding strongly supported that both pig breeds feature variable fat and muscle metabolism. Certain differentially expressed genes are included in the pathway of mitogen-activated protein kinase signaling pathway, Ras signaling pathway and insulin pathway. Results from real-time quantitative polymerase chain reaction also validated the differential expression of 17 mRNAs between meats of the two pig breeds. Overall, these findings reveal significant differences in fat and protein metabolism of intramuscular adipose tissues of two pig breeds at the transcriptomic level and suggest diversification at the genetic level between breeds of the same species.

show abstract

“…In addition, MBOAT1, which was enriched in glycerolipid metabolism pathway, also showed higher expression in the F line. MBOAT1 has been reported to be associated with phosphatidylcholine metabolism [46] and large intestine lipid metabolism [47]. An upregulation of MBOAT1 may, thus, also be associated with differences in IMF deposition between the two lines.…”

Section: Other Pathways Contribute To Increased Imf Deposition In F Linementioning

confidence: 99%

Effect of Divergent Selection for Intramuscular Fat Content on Muscle Lipid Metabolism in Chickens

Liu

Cui

Xing

et al. 2019

Animals

View full text Add to dashboard Cite

Simple Summary: Intramuscular fat is an important factor affecting meat quality and consumer acceptance. Appropriate increases in the intramuscular fat content contribute to the improvement of meat quality, and genetic selection is an effective method to increase the intramuscular fat content in chickens. In this study, chicken lines divergently selected for their intramuscular fat content were used to investigate the mechanisms behind differential intramuscular fat deposition. These results found in this study may contribute to the improvement of meat quality in chickens.Abstract: Intramuscular fat (IMF)-an important factor affecting meat quality-can be appropriately increased by genetic selection. Chicken lines divergently selected for IMF content were used in this study to investigate the mechanisms behind differential IMF deposition. Sixty 15th generation chickens were genotyped using the IASCHICK 55K single nucleotide polymorphism (SNP) chip. After quality control, 59 chickens and 36,893 SNPs were available for subsequent analysis. Population structure assessment indicated that the lines were genetically differentiated. Based on the top 1% paired fixation index values, three pathways were significantly (p < 0.05) enriched, and nine genes were considered candidate genes for differential IMF deposition. Differences between the lines in the expressions of representative genes involved in the above pathways were detected in 16th generation chickens. This study suggests that genetic selection for increased IMF in the pectoralis major muscle may enhance fatty acid synthesis, transport, and esterification, and reduce triglyceride hydrolysis. The peroxisome proliferator-activated receptor (PPAR) signaling pathway, glycerolipid metabolism, and fatty acid degradation pathway may have contributed to the differences in IMF deposition between the lines. These results contribute to the understanding of the genetic mechanisms behind IMF deposition, and the improvement of chicken meat quality.

show abstract

Transcriptome Analysis of Three Sheep Intestinal Regions reveals Key Pathways and Hub Regulatory Genes of Large Intestinal Lipid Metabolism

Cited by 19 publications

References 64 publications

Integration of lncRNA and mRNA Transcriptome Analyses Reveals Genes and Pathways Potentially Involved in Calf Intestinal Growth and Development during the Early Weeks of Life

Integration of lncRNA and mRNA Transcriptome Analyses Reveals Genes and Pathways Potentially Involved in Calf Intestinal Growth and Development during the Early Weeks of Life

Transcriptome analysis reveals differential gene expression in intramuscular adipose tissues of Jinhua and Landrace pigs

Effect of Divergent Selection for Intramuscular Fat Content on Muscle Lipid Metabolism in Chickens

Contact Info

Product

Resources

About