Functional analysis of transcriptome dynamics during growth in Angus cattle longissimus muscle
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ABSTRACT:
ORGANISM(S): Bos taurus
PROVIDER: GSE48136 | GEO | 2013/06/21
SECONDARY ACCESSION(S): PRJNA208994
REPOSITORIES: GEO
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Project description:The bovine transcriptome dynamics in logissimus muscle (LM) during the post-natal growth remain unknown. Biopsies of LM from Angus steers were harvested at 0, 60, 120, and 220 d from early-weaning. A 13,153 bovine oligonucleotide array was used for transcript profiling. Functional analysis of microarray data was performed using the Dynamic Impact Approach (DIA) by means of KEGG and DAVID databases. During the growing phase, most of the highly-impacted pathways (e.g. Ascorbate and aldarate metabolism, Drug metabolism - cytochrome P450 and Retinol metabolism) were inhibited. The finishing phase, was characterized with the most striking differences with 3,784 differentially expressed genes (DEG; FDR <0.01). The functional analysis of those DEG revealed that the most-impacted KEGG canonical pathway was M-bM-^@M-^\Glycosylphosphatidylinositol (GPI) - anchor biosynthesisM-bM-^@M-^]. The inhibition of this pathway suggested a unique role of GPI-anchor proteins in intracellular trafficking during the finishing phase. A mechanism regulating muscle growth during the finishing phase was uncovered in which inhibition of calpastatin and activation of tyrosine aminotransferase ubiquitination promote proteasomal degradation, while the concurrent activation of ribosomal proteins promotes protein synthesis, thus, the balance of these processes likely results in a steady state of protein turnover during the finishing phase. Overall, results underscored the importance of transcriptome dynamics in LM to support key biological functions during rapid growth. The study utilized a subset of 14 animals from a larger study encompassing 32 purebred Aberdeen Angus steers from the University of Illinois beef cattle herd. Steer calves were early-weaned (134 M-BM-1 10 d age) and after weaning were placed on a diet of 85% corn silage and 15% wet distillerM-bM-^@M-^Ys grains (as-fed basis) for 3 wk. Subsequently, one half of Angus (n = 16) steers was randomly assigned to a high-byproduct or high-grain diet for a 112 d growing phase. The high-byproduct diet contained (dry matter basis) 35% corn silage, 20% corn gluten feed, 38% soyhulls, 3% cracked corn, and 3% soybean meal (49% crude protein). The high-grain diet contained 20% corn silage, 68% cracked corn, and 11% soybean meal (49% crude protein). Both diets contained 1% limestone/dicalcium phosphate/mineral/vitamin/urea/dry molasses mixture. Calculated NEG for the high-byproduct diet was 1.19 Mcal/kg and 1.43 Mcal/kg for the high-grain diet. At the end of the growing phase, steers on each group were fed M-bM-^@M-^\step-up dietsM-bM-^@M-^] for 10 d. Step-up diet for high-byproduct-fed steers contained 1.37 Mcal NEG/kg. Step-up diet for high-grain-fed steers contained 1.43 Mcal NEG/kg but contained distillerM-bM-^@M-^Ys dried grains (16% of dry matter). After the M-bM-^@M-^\step-upM-bM-^@M-^] period, all steers were finished on a common high-grain finishing diet containing 1.44 Mcal NEG/kg (15% corn silage, 58% cracked corn, 25% dried distillerM-bM-^@M-^Ys grains, 1% limestone, and 1% urea/mineral/vitamin mixture). All diets were offered on an ad libitum basis. Steers had an individual electronic identification ear tag and individual feed intake data were collected using the GrowSafe system (GrowSafe Systems Ltd., Alberta, Canada). Cattle were harvested at approximately 13 mo age. A bovine oligonucleotide (70-mers) microarray with >13,000 annotated sequences developed at the University of Illinois, was used for transcript profiling. Details on the development, annotation, and use of this microarray have been reported previously by Loor et al., 2007 (http://physiolgenomics.physiology.org/content/32/1/105.abstract). Methods for microarray hybridization and scanning were as reported by Loor et al. (2007). Briefly, slides were hydrated, dried, and placed in a UV Stratalinker 1800 (Stratagene, La Joya, CA) for ~5 min. Slides were washed with 0.2% SDS solution, rinsed with MilliQ (Millipore) H2O, and placed in warm prehybridization soln for 45 min at 42 C. The same amount of Cy3- or Cy5-labelled cDNA from muscle and a reference standard RNA pool (made of different bovine tissues) were co-hybridized using a dye-swap design (i.e., two microarrays per sample). Slides were incubated for 48 h at 45 C prior to scanning. Criteria for evaluation of slide quality included: identification of number of spots with a minimum median signal intensity of 3 SD above background; keeping slides with a minimum of 20,000 spots with minimum median signal intensity of 3 SD above background in both Cy3 and Cy5 channels; and keeping slides with a minimum mean intensity of 400 relative fluorescent units in both Cy3 and Cy5 channels across the entire slide. Data from a total of 112 microarrays were normalized for dye and microarray effects (i.e., Lowess normalization and microarray centering) and used for statistical analysis. Data were analyzed using the Proc MIXED procedure of SAS (SAS, SAS Inst. Inc., Cary, NC). Fixed effects were treatment (high-byproduct, high-grain) and time (0, 56, 120, and 220 d), and dye. Random effects included steer and microarray. A covariate adjustment was used to assess treatment and treatment M-CM-^W time interactions, but time effects on gene expression were assessed without covariate adjustment. Raw P values were adjusted using Benjamini and HochbergM-bM-^@M-^Ys false discovery rate (FDR). Differences in relative expression due to treatment M-CM-^W time interactions were considered significant at an FDR-adjusted P < 0.25 or at P < 0.01 for time effects. qPCR data were normalized using the median of 4 suitable internal control genes, and were analyzed using the same statistical model described above. Differences were considered significant at P-value of 0.05.
2013-06-21 | E-GEOD-48136 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE30971: The Histone Methyltransferase Wbp7 Controls Macrophage Function through GPI Glycolipid Anchor Synthesis. [Expression Profile] GSE30972: The Histone Methyltransferase Wbp7 Controls Macrophage Function through GPI Glycolipid Anchor Synthesis. [ChIP_seq] Refer to individual Series
2012-04-08 | E-GEOD-30973 | biostudies-arrayexpress
Project description:We show that the human monocyte model BLaER1 contains GPI-anchor-deficient cells, which lack CD14 surface expression when differentiated to monocytes, resulting in diminished LPS/TLR4 responsiveness. We found that this GPI anchor defect is caused by epigenetic silencing of the PIGH gene, leading to a random distribution of intact and PIGH-deficient clones after single-cell cloning.
2021-07-28 | GSE169623 | GEO
Project description:Histone methyltransferases catalyze site-specific deposition of methyl groups, enabling recruitment of transcriptional regulators. In mammals, trimethylation of lysine 4 in histone H3, a modification localized at the transcription start sites of active genes, is catalyzed by six enzymes (SET1a and SET1b, MLL1M-bM-^@M-^SMLL4) whose specific functions are largely unknown. By using a genomic approach, we found that in macrophages, MLL4 (also known as Wbp7) was required for the expression of Pigp, an essential component of the GPI-GlcNAc transferase, the enzyme catalyzing the first step of glycosylphosphatidylinositol (GPI) anchor synthesis. Impaired Pigp expression in Wbp7-/- macrophages abolished GPI anchor-dependent loading of proteins on the cell membrane. Consistently, loss of GPI-anchored CD14, the coreceptor for lipopolysaccharide (LPS) and other bacterial molecules, markedly attenuated LPS-triggered intracellular signals and gene expression changes. These data link a histone-modifying enzyme to a biosynthetic pathway and indicate a specialized biological role for Wbp7 in macrophage function and antimicrobial response. Gene expression profiles for bone marrow-derived macrophages (BMDM) from either Wbp7+/- (HET) or Wbp7-/- (KO). Cells were left untreated or challenged with lipopolysaccharide (LPS) for 2hrs or 4hrs. Each genotype-treatment combination were performed in triplicate.
2012-04-08 | E-GEOD-30971 | biostudies-arrayexpress
Project description:We performed neuron and glia specific knockdown of PIG-A in Drosophila to understand the molecular defects that occur with loss of GPI anchored proteins. PIG-A encodes an enzyme responsible for the first step in GPI anchor biosynthesis. Loss of PIG-A in neurons and glia results in different neurological defects.
2023-10-31 | GSE241512 | GEO
Project description:Histone methyltransferases catalyze site-specific deposition of methyl groups, enabling recruitment of transcriptional regulators. In mammals, trimethylation of lysine 4 in histone H3, a modification localized at the transcription start sites of active genes, is catalyzed by six enzymes (SET1a and SET1b, MLL1M-bM-^@M-^SMLL4) whose specific functions are largely unknown. By using a genomic approach, we found that in macrophages, MLL4 (also known as Wbp7) was required for the expression of Pigp, an essential component of the GPI-GlcNAc transferase, the enzyme catalyzing the first step of glycosylphosphatidylinositol (GPI) anchor synthesis. Impaired Pigp expression in Wbp7-/- macrophages abolished GPI anchor-dependent loading of proteins on the cell membrane. Consistently, loss of GPI-anchored CD14, the coreceptor for lipopolysaccharide (LPS) and other bacterial molecules, markedly attenuated LPS-triggered intracellular signals and gene expression changes. These data link a histone-modifying enzyme to a biosynthetic pathway and indicate a specialized biological role for Wbp7 in macrophage function and antimicrobial response. Chromatin immuno-precipitations of H3 histone try-methylated on lysine 4 followed by multiparallel sequencing performed in murine bone marrow-derive macrophages (BMDM). Experiments carried out in untreated cells as well as in cells treated for 4hrs with lipopolysaccharide (LPS), for both Wbp7+/- (HET) and Wbp7-/- (KO) mice.
2012-04-09 | E-GEOD-30972 | biostudies-arrayexpress
Project description:Histone methyltransferases catalyze site-specific deposition of methyl groups, enabling recruitment of transcriptional regulators. In mammals, trimethylation of lysine 4 in histone H3, a modification localized at the transcription start sites of active genes, is catalyzed by six enzymes (SET1a and SET1b, MLL1–MLL4) whose specific functions are largely unknown. By using a genomic approach, we found that in macrophages, MLL4 (also known as Wbp7) was required for the expression of Pigp, an essential component of the GPI-GlcNAc transferase, the enzyme catalyzing the first step of glycosylphosphatidylinositol (GPI) anchor synthesis. Impaired Pigp expression in Wbp7-/- macrophages abolished GPI anchor-dependent loading of proteins on the cell membrane. Consistently, loss of GPI-anchored CD14, the coreceptor for lipopolysaccharide (LPS) and other bacterial molecules, markedly attenuated LPS-triggered intracellular signals and gene expression changes. These data link a histone-modifying enzyme to a biosynthetic pathway and indicate a specialized biological role for Wbp7 in macrophage function and antimicrobial response.
2012-04-09 | GSE30972 | GEO
Project description:Histone methyltransferases catalyze site-specific deposition of methyl groups, enabling recruitment of transcriptional regulators. In mammals, trimethylation of lysine 4 in histone H3, a modification localized at the transcription start sites of active genes, is catalyzed by six enzymes (SET1a and SET1b, MLL1–MLL4) whose specific functions are largely unknown. By using a genomic approach, we found that in macrophages, MLL4 (also known as Wbp7) was required for the expression of Pigp, an essential component of the GPI-GlcNAc transferase, the enzyme catalyzing the first step of glycosylphosphatidylinositol (GPI) anchor synthesis. Impaired Pigp expression in Wbp7-/- macrophages abolished GPI anchor-dependent loading of proteins on the cell membrane. Consistently, loss of GPI-anchored CD14, the coreceptor for lipopolysaccharide (LPS) and other bacterial molecules, markedly attenuated LPS-triggered intracellular signals and gene expression changes. These data link a histone-modifying enzyme to a biosynthetic pathway and indicate a specialized biological role for Wbp7 in macrophage function and antimicrobial response.
2012-04-09 | GSE30971 | GEO
Project description:We evaluated if a higher plane of maternal nutrition during late gestation and weaning age alters the offspringM-bM-^@M-^Ys Longissimus muscle (LM) transcriptome. A microarray analysis was performed in LM samples of early (EW) and normal weaned (NW) Angus M-CM-^W Simmental calves born from cows that were grazing endophyte-infected tall fescue/red clover pastures with no supplement (low plane of nutrition (LPN)), or supplemented with 2.3 kg of dried distillerM-bM-^@M-^Ys grains with solubles and soyhulls (70% DDGS/30% soyhulls) (medium plane of nutrition (MPN)) during the last 90 days of gestation. Biopsies were harvested at 78, 187 and 354 days of age. Bioinformatics analysis highlighted that offspring transcriptome did not respond markedly to cow plane of nutrition, resulting in only 13 differentially expressed genes. However, weaning age and a high-starch diet strongly impacted the transcriptome, especially the immediate activation of the lipogenic program in EW steers. In addition, between 78 and 187 days of age, these animals had an activation of the innate immune system due presumably to macrophage infiltration in intramuscular fat. Between 187 and 354 days of age (i.e. the fattening phase), NW steers had an activation of the lipogenic transcriptome machinery, while EW steers had a clear gene transcription inhibition. The latter appears to have occurred through the epigenetic control of histone acetylases, which were down-regulated. Higher cow plane of nutrition alone affected 35 genes in the LM of steers that underscore the presence of a mechanism of macrophage infiltration likely originating from localized oxidative stress as a result of increased levels of hypoplasia and hypertrophy in LM. A subset of 20 Angus x Simmental beef cows from the University of Illinois Dixon Springs Agriculture Center (DSAC) in Simpson, IL, were selected from a group of animals utilized in a parallel study75. Main effects evaluated were maternal plane of nutrition during late gestation and postnatal management of the offspring. Three months prior to the projected parturition date cows were assigned to treatments (low or medium plane of nutrition) in a split-plot design. Low plane of nutrition (LPN) was achieved by grazing endophyte-infected tall fescue/red clover pastures during July, August, and September with no supplement. Medium plane of nutrition cow diet (MPN) was achieved by grazing endophyte-infected tall fescue/red clover pastures supplemented with 2.3 kg of dried distillerM-bM-^@M-^Ys grains with solubles and soyhulls (70% DDGS/30% soyhulls). Angus x Simmental steer calves were randomly assigned to early or normal weaning treatments within each gestational treatment. This allowed for 10 animals for each postnatal treatment and 5 animals of each of the interactions of gestational M-CM-^W postnatal treatments. At 78 M-BM-1 2 days postpartum, early-wean offspring were weaned, transported to Urbana Beef Unit, and adapted to a high-starch diet until they had ad libitum consumption. At 187 M-BM-1 2 days postpartum, normal-wean offspring were weaned and transported to Urbana Beef Unit. All offspring were co-mingled among treatments. LM biopsies were sampled from a subset of 5 animals per gestational M-CM-^W postnatal treatment at time of early weaning (~78 days) and at time of normal weaning (~187 days), and during the last week prior to harvest (~ 354 days). After normal weaning, all offspring were placed on a common, corn grain-based high-starch finishing diet that is typical of industry management (CP% = 18.1, NDF% = 25.3, ADF% = 14.3, crude fat % = 5.1). All the offspring in the study were harvested at a commercial packing plant when they reached the selected end point target back fat thickness of 1.1 cm. Reported final body weight (BW) was calculated from hot carcass weight using a 62% dressing percentage. In the present study, we used a transcriptome-wide bovine microarray (Agilent-015354 Bovine Oligo Microarray-4x44K) that contains 21,475 unique genes and transcripts of Bos Taurus, with two probes per gene. The methods used for hybridization and scanning were according to manufacturerM-bM-^@M-^Ys protocols and Loor et al45. The microarray data were deposited in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/gds) with accession number GSE-XXXX. GeneSpring GX (Agilent Technologies) was used for data visualization and preliminary data mining. Subsequently, the entire microarray data set with associated statistical P-values were imported into Ingenuity Pathways Analysis M-BM-. (IPA, www.ingenuity.com) in order to examine the number of activated and inhibited differentially expressed genes (DEG). Entrez Gene IDs were used to identify individual sequences. Data from the microarray analysis were normalized for dye and microarray effects (i.e., Lowess normalization and array centering) and used for statistical analysis. The MIXED procedure of SAS (SAS Institute, Inc., Cary, NC, USA) was used for statistical analysis. Fixed effects were treatment (early weaning, normal weaning), diet (low and medium cow plane of nutrition), time (78, 187, and 354 days of age), first, second and third order interactions between diet, time and treatment, and dye (Cy3, Cy5) and random effects included steer and microarray. Raw P values were adjusted using Benjamini and HochbergM-bM-^@M-^Ys false discovery rate (FDR). Bioinformatics analysis of microarray data was performed using DIA 10 and information from the freely-available online databases Kyoto Encyclopedia of Genes and Genomes (KEGG) and Database for Annotation, Visualization, and Integrated Discovery (DAVID) v6.7 databases. A list of gene identifiers (Entrez Gene IDs) was uploaded all at once to extract and summarize functional annotations associated with groups of genes or with each individual gene. The significance value associated with biological processes and pathways is a measure of the likelihood that the distribution of DEG in these pathways and biological processes is due to chance. The significance is expressed as a P-value, which is calculated using the right-tailed Fisher's Exact Test and adjusted using FDR. Details of the DIA approach and its validation have been reported previously. The interpretation of the bioinformatics analysis was performed following the same approach as our previous study.
2015-02-03 | E-GEOD-65560 | biostudies-arrayexpress
Project description:Growing and finishing phases are two important animal production stages, which differ fundamentally in compositional growth. However, the physiological mechanisms altered concomitantly with the shift in whole-body compositional gain as cattle fatten (growing vs. finished steers), are poorly understood. Microarray analysis using the Bovine Gene 1.0 ST Array was conducted to determine shifts in hepatic genomic expression profiles of growing vs. finishing beef steers. The specific overall hypothesis tested was that genes involved in amino acid, carbohydrate and lipid metabolism, antioxidant capacity and immune responses were differentially expressed in growing vs. finishing steers.
2017-12-11 | GSE107881 | GEO