Dynamic changes in genes related to glucose uptake and utilization during pig skeletal and cardiac muscle development

Figures & data

Table 1. The biological process enrichment of genes in significant expression pattern.

Tissue	Processes	PErminJ	Gene numbers	Genes
CM	Glycolysis	0	3	PDH1, HK2, LDHB
	Glycogen biosynthetic process	0	4	GYS1,ATK1, PRKAG3, GYG1,
	Generation of precursor metabolites and energy	0.025	5	PRKAG3, AKT1, GYG1, GYS1, PCK1,
	Phosphate metabolic process	0	6	PDK1, PCK1, HK2, InsR, GPD, AKT1
	Transmembrane transport	0	2	MCT-1, GLUT4
	Lipid metabolic process	0	4	PRKAG3, MAPK, GPD, PCK1
	Heart development	0.0083	2	GYS1, InsR
	Protein kinase cascade	0	4	InsR, PRKAG3, AKT1, MAPK
	Carbohydrate homeostasis	0	9	PRKAG3, AKT1, GYG1, GYS1, PCK1, GPD, LDHB, MAPK, HK2
LDM	Phosphate metabolic process	0	5	GPD, AKT1, InsR, G6PC, PI3 K
	Primary metabolic process	0	8	GPD, AKT1, InsR, G6PC, PI3 K, PGM1, PFKM, PRKAG3
	Transmembrane transport	0	2	GLUT4, MCT-1
	Glycogenesis	0.0128	2	GPD, PGM1
	Regulation of gene expression	0.0385	2	AKT1, InsR
	Regulation of protein kinase activity	0.0385	2	AKT1, InsR
	Cofactor metabolic process	0.0128	2	GPD, CS
PMM	Carbohydrate metabolic process	0	6	HK1, GYS1, AKT1, TPI1, PDH1, PFKM
	Small molecule metabolic process	0	7	HK1, GYS1, AKT1, TPI1, PDH1, PFKM, CS
	Generation of precursor metabolites and energy	0	6	HK1, GYS1, AKT1, PDH1, PFKM, CS
	Energy derivation by oxidation of organic compounds	0.0275	3	GYS1, AKT1, CS

Note: Genes in expression pattern 1 of CM and LDM and that in expression pattern 2 and 7 of PMM were performed biological process enrichment by ErminJ based on GO annotations. The FDR adjusted permutation P values were analyzed using gene score resampling (or p values among the five age stages) algorithm to determine which process was significant with Benjamini–Hochberg FDR-corrected p value (P_ErmineJ) < 0.05 or 0.01. Genes in pattern 7 had no significant enriched processes. CM, cardiac muscle; LDM, longissimus doris muscle; PMM, psoas major muscles.

Fig. 1. The trends of 30 mRNA were divided into groups according to their dynamic expression patterns at the age of embryonic day 90 (E90d), postnatal day 0 (0d), day 30 (30d), day 180 (180d), and 7 years (7y) for (A) cardiac muscle, (B) longissimus dorsi Muscle, and (C) psoas major Muscle.

Notes: The dashed line indicates no change in expression at different age stages. The number in the top left corner of each square indicates the expression pattern ID. The blank, bold lines in the squares are trendlines of the expression patterns, and the gray lines represent gene expression from embryonic day 90 to 7 years postnatally. The p value is the corrected p value between the number of genes expected (n_(E)) and the number of genes assigned (n), with p values < 0.05 considered to be statistically significant. Four other expressions were normalized to the highest one in four stages firstly, and then all expressions were log₂-transformed.

Fig. 2. Gene expression related to glycolysis in cardiac and skeletal muscle during development.

Notes: Triose phosphate isomerase 1 (TPI1), muscle phosphofructokinase (PFKM), and monocarboxylate transporter 4 (MCT-4) are important glycolytic enzymes that are mainly expressed in white muscle, and significantly up-regulated in LDM compared with CM and PMM in the study. The data were normalized to the highest expression of the three muscles and presented as mean ± SD. n = 3 for each age stages of tissues. CM, cardiac muscle; LDM, longissimus dorsi muscle; PMM, psoas major muscles.

**p < 0.01, *p < 0.05.

Fig. 3. Gene expression related to oxidation in cardiac and skeletal muscle during development.

Notes: ATPase-ß, citrate synthase (CS), and pyruvate dehydrogenase (PDH1) are related to mitochondrial oxidation, which were up-regulated in PMM compared with CM and LDM in this study. The data were normalized to the highest expression of the three muscles and presented as mean ± SD. n = 3 for each age stages of tissues. CM: cardiac muscle, LDM, longissimus dorsi muscle, PMM: psoas major muscle.

**p < 0.01, *p < 0.05.

Fig. 4. The trends of 10 miRNA were divided into groups according to heir dynamic expression patterns for (A) Cardiac Muscle, (B) longissimus dorsi Muscle, and (C) psoas major muscles at the age of embryonic day 90 (E90d), postnatal day 0 (0d), day 30 (30d), day 180 (180d), and 7 years (7y).

Notes: The dashed line indicates no change in expression among different stages. The number in the top left corner of each square is the expression pattern ID. The blank, bold lines in the squares are trendlines of the expression patterns, and the gray lines represent gene expression from embryonic day 90 to 7 years postnatally. The p-value is the corrected P-value between the number of genes expected (n_(E)) and the number of genes assigned (n), with p values < 0.05 considered to be statistically significant. Four other expressions were normalized to the highest one in four stages firstly, and then all expressions were log₂-transformed.

Fig. 5. Correlation in Gene Expression between PFKM and miR-320, PI3 K and miR-126, MAPK and miR-24 at the Stage of Embryonic day 90 (E90d), Postnatal day 0 (0 d), Day 30 (30d), Day 180 (180d), and 7 years (7y).

Notes: The data were normalized to the highest expression of the three muscles and presented as mean ± SD. n = 3 for each age stages of tissues. CM, cardiac muscle; LDM, longissimus dorsi muscle; PMM, psoas major muscles.

**p < 0.01, *p < 0.05.