A comparative study of food selectivity of the benthic copepod Tigriopus japonicus and the pelagic copepod Paracyclopina nana: A genome-wide identification of fatty acid conversion genes and nitrogen isotope investigation

We previously reported the findings from a genome-wide association study of the response of maximal oxygen uptake (V̇o2max) to an exercise program. Here we follow up on these results to generate hypotheses on genes, pathways, and systems involved in the ability to respond to exercise training. A systems biology approach can help us better establish a comprehensive physiological description of what underlies V̇o2maxtrainability. The primary material for this exploration was the individual single-nucleotide polymorphism (SNP), SNP-gene mapping, and statistical significance levels. We aimed to generate novel hypotheses through analyses that go beyond statistical association of single-locus markers. This was accomplished through three complementary approaches: 1) building de novo evidence of gene candidacy through informatics-driven literature mining; 2) aggregating evidence from statistical associations to link variant enrichment in biological pathways to V̇o2max trainability; and 3) predicting possible consequences of variants residing in the pathways of interest. We started with candidate gene prioritization followed by pathway analysis focused on overrepresentation analysis and gene set enrichment analysis. Subsequently, leads were followed using in silico analysis of predicted SNP functions. Pathways related to cellular energetics (pantothenate and CoA biosynthesis; PPAR signaling) and immune functions (complement and coagulation cascades) had the highest levels of SNP burden. In particular, long-chain fatty acid transport and fatty acid oxidation genes and sequence variants were found to influence differences in V̇o2max trainability. Together, these methods allow for the hypothesis-driven ranking and prioritization of genes and pathways for future experimental testing and validation.

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Genome-wide identification of nuclear receptor (NR) superfamily genes in the copepod Tigriopus japonicus

BMC Genomics ◽

10.1186/1471-2164-15-993 ◽

2014 ◽

Vol 15 (1) ◽

pp. 993 ◽

Cited By ~ 13

Author(s):

Dae-Sik Hwang ◽

Bo-Young Lee ◽

Hui-Su Kim ◽

Min Lee ◽

Do-Hyun Kyung ◽

...

Keyword(s):

Nuclear Receptor ◽

Tigriopus Japonicus ◽

Genome Wide ◽

Copepod Tigriopus Japonicus

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Integrated analysis of the methylome and transcriptome of chickens with fatty liver hemorrhagic syndrome

BMC Genomics ◽

10.1186/s12864-020-07305-3 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Xiaodong Tan ◽

Ranran Liu ◽

Yonghong Zhang ◽

Xicai Wang ◽

Jie Wang ◽

...

Keyword(s):

Dna Methylation ◽

Fatty Acid ◽

Fatty Liver ◽

Negative Relationship ◽

Integrated Analysis ◽

Pathway Enrichment Analysis ◽

Gene Body ◽

Genome Wide ◽

A Genome ◽

Differentially Methylated Genes

Abstract Background DNA methylation, a biochemical modification of cytosine, has an important role in lipid metabolism. Fatty liver hemorrhagic syndrome (FLHS) is a serious disease and is tightly linked to lipid homeostasis. Herein, we compared the methylome and transcriptome of chickens with and without FLHS. Results We found genome-wide dysregulated DNA methylation pattern in which regions up- and down-stream of gene body were hypo-methylated in chickens with FLHS. A total of 4155 differentially methylated genes and 1389 differentially expressed genes were identified. Genes were focused when a negative relationship between mRNA expression and DNA methylation in promoter and gene body were detected. Based on pathway enrichment analysis, we found expression of genes related to lipogenesis and oxygenolysis (e.g., PPAR signaling pathway, fatty acid biosynthesis, and fatty acid elongation) to be up-regulated with associated down-regulated DNA methylation. In contrast, genes related to cellular junction and communication pathways (e.g., vascular smooth muscle contraction, phosphatidylinositol signaling system, and gap junction) were inhibited and with associated up-regulation of DNA methylation. Conclusions In the current study, we provide a genome-wide scale landscape of DNA methylation and gene expression. The hepatic hypo-methylation feature has been identified with FLHS chickens. By integrated analysis, the results strongly suggest that increased lipid accumulation and hepatocyte rupture are central pathways that are regulated by DNA methylation in chickens with FLHS.

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Use of multivariate factor analysis of detailed milk fatty acid profile to perform a genome-wide association study in Italian Simmental and Italian Holstein

Journal of Applied Genetics ◽

10.1007/s13353-020-00568-2 ◽

2020 ◽

Vol 61 (3) ◽

pp. 451-463 ◽

Cited By ~ 1

Author(s):

Valentino Palombo ◽

Giuseppe Conte ◽

Marcello Mele ◽

Nicolò Pietro Paolo Macciotta ◽

Bruno Stefanon ◽

...

Keyword(s):

Factor Analysis ◽

Fatty Acid ◽

Association Study ◽

Fatty Acid Profile ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Milk Fatty Acid ◽

Genome Wide ◽

A Genome ◽

Multivariate Factor Analysis

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Studies of human twins reveal genetic variation that affects dietary fat perception

10.1101/2020.01.18.910448 ◽

2020 ◽

Author(s):

Cailu Lin ◽

Lauren Colquitt ◽

Paul Wise ◽

Paul A. S. Breslin ◽

Nancy E. Rawson ◽

...

Keyword(s):

Fatty Acid ◽

Dietary Fat ◽

Genome Wide Association Study ◽

Corn Oil ◽

Fatty Acid Content ◽

Potato Chips ◽

Hexadecanoic Acid ◽

Genome Wide ◽

A Genome ◽

Multivariate Gwas

AbstractTo learn more about the mechanisms of human dietary fat perception, 398 human twins rated fattiness and liking for six types of potato chips that differed in triglyceride content (2.5, 5, 10, and 15% corn oil); reliability estimates were obtained from a subset (n = 50) who did the task twice. Some chips also had a saturated long-chain fatty acid (hexadecanoic acid, 16:0) added (0.2%) to evaluate its effect on fattiness and liking. We computed the heritability of these measures and conducted a genome-wide association study (GWAS) to identify regions of the genome that co-segregate with fattiness and liking. Perceived fattiness and liking for the potato chips were reliable (r = 0.31-0.62, p < 0.05) and heritable (up to h2 = 0.29, p < 0.001, for liking). Adding hexadecanoic acid to the potato chips significantly increased ratings of fattiness but decreased liking. Twins with the G allele of rs263429 near GATA3-AS1 or the G allele of rs8103990 within ZNF729 reported more liking for potato chips than did twins with the other allele (multivariate GWAS, p < 1×10-5), with results reaching genome-wide suggestive but not significance criteria. Person-to-person variation in the perception and liking of dietary fat was (a) negatively affected by the addition of a saturated fatty acid and (b) related to inborn genetic variants. These data suggest liking for dietary fat is not due solely to fatty acid content and highlight new candidate genes and proteins within this sensory pathway.

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