Comparison of five different RNA sources to examine the lactating bovine mammary gland transcriptome using RNA-Sequencing

Cánovas, Ángela; Rincón, Gonzalo; Bevilacqua, Claudia; Islas‐Trejo, Alma; Brenaut, Pauline; Hovey, Russell C.; Boutinaud, Marion; Morgenthaler, Caroline; VanKlompenberg, Monica K.; Martin, Patrice; Medrano, Juan F.

doi:10.1038/srep05297

Cited by 135 publications

(140 citation statements)

References 24 publications

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“…MSCs are a representative source of lactating sheep mammary gland19. The top-20 expressed genes in the MSCs in this study were consistent with other studies performed on lactating mammary gland, with genes codifying for caseins, whey proteins and GLYCAM1 at the top of the list202122.…”

Section: Discussionsupporting

confidence: 90%

Elucidating fish oil-induced milk fat depression in dairy sheep: Milk somatic cell transcriptome analysis

Suárez-Vega

Toral

Hervás

et al. 2017

Sci Rep

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In this study, RNA sequencing was used to obtain a comprehensive profile of the transcriptomic changes occurring in the mammary gland of lactating sheep suffering from fish oil-induced milk fat depression (FO-MFD). The milk somatic cell transcriptome analysis of four control and four FO-MFD ewes generated an average of 42 million paired-end reads per sample. In both conditions, less than 220 genes constitute approximately 89% of the total counts. These genes, which are considered as core genes, were mainly involved in cytoplasmic ribosomal proteins and electron transport chain pathways. In total, 117 genes were upregulated, and 96 genes were downregulated in FO-MFD samples. Functional analysis of the latter indicated a downregulation of genes involved in the SREBP signaling pathway (e.g., ACACA, ACSL, and ACSS) and Gene Ontology terms related to lipid metabolism and lipid biosynthetic processes. Integrated interpretation of upregulated genes indicated enrichment in genes encoding plasma membrane proteins and proteins regulating protein kinase activity. Overall, our results indicate that FO-MFD is associated with the downregulation of key genes involved in the mammary lipogenesis process. In addition, the results also suggest that this syndrome may be related to upregulation of other genes implicated in signal transduction and codification of transcription factors.

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Section: Discussionsupporting

confidence: 90%

Elucidating fish oil-induced milk fat depression in dairy sheep: Milk somatic cell transcriptome analysis

Suárez-Vega

Toral

Hervás

et al. 2017

Sci Rep

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“…In all these studies different experimental design, sampling, and sequencing depth were described but from a global point of view a media of 15,000-24,000 expressed genes have been identified [27, 28, 36]. In a previous work a threshold value of 0.2 RPKM was found for detectable gene expression in milk somatic cells [58].…”

Section: Discussionmentioning

confidence: 99%

RNA-Sequencing for profiling goat milk transcriptome in colostrum and mature milk

Crisà

Ferré

Chillemi³

et al. 2016

BMC Vet Res

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BackgroundIn this work we aimed at sequencing and assembling the goat milk transcriptome corresponding at colostrum and 120 days of lactation. To reconstruct transcripts we used both the genome as reference, and a de novo assembly approach. Additionally, we aimed at identifying the differentially expressed genes (DEGs) between the two lactation stages and at analyzing the expression of genes involved in oligosaccharides metabolism.ResultsA total of 44,635 different transcripts, organized in 33,757 tentative genes, were obtained using the goat genome as reference. A significant sequence similarity match was found for 40,353 transcripts (90%) against the NCBI NT and for 35,701 (80%) against the NR databases. 68% and 69% of the de novo assembled transcripts, in colostrum and 120 days of lactation samples respectively, have a significant match with the merged transcriptome obtained using Cufflinks/Cuffmerge. CSN2, PAEP, CSN1S2, CSN3, LALBA, TPT1, FTH1, M-SAA3, SPP1, GLYCAM1, EEF1A1, CTSD, FASN, RPS29, CSN1S1, KRT19 and CHEK1 were found between the top fifteen highly expressed genes. 418 loci were differentially expressed between lactation stages, among which 207 and 122 were significantly up- and down-regulated in colostrum, respectively. Functional annotation and pathway enrichment analysis showed that in goat colostrum somatic cells predominate biological processes involved in glycolysis, carbohydrate metabolism, defense response, cytokine activity, regulation of cell proliferation and cell death, vasculature development, while in mature milk, biological process associated with positive regulation of lymphocyte activation and anatomical structure morphogenesis are enriched. The analysis of 144 different oligosaccharide metabolism-related genes showed that most of these (64%) were more expressed in colostrum than in mature milk, with eight expressed at very high levels (SLCA3, GMSD, NME2, SLC2A1, B4GALT1, B3GNT2, NANS, HEXB).ConclusionsTo our knowledge, this is the first study comparing goat transcriptome of two lactation stages: colostrum and 120 days. Our findings suggest putative differences of expression between stages and can be envisioned as a base for further research in the topic. Moreover because a higher expression of genes involved in immune defense response, carbohydrate metabolism and related to oligosaccharide metabolism was identified in colostrum we here corroborate the potential of goat milk as a natural source of lactose-derived oligosaccharides and for the development of functional foods.Electronic supplementary materialThe online version of this article (doi:10.1186/s12917-016-0881-7) contains supplementary material, which is available to authorized users.

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“…Quality control analysis was performed using the NGS quality control tool, which assesses sequence quality indicators based on the FastQC-project (FastQC-project ). Quality was measured taking into account sequence-read lengths and base-coverage, nucleotide contributions and base ambiguities, quality scores as emitted by the base caller and over-represented sequences [33]. All the samples analyzed passed all the QC parameters having the same length (76 bp), 100% coverage in all bases, 25% of A, T, G and C nucleotide contributions, 50% GC on base content and less than 0.1% over-represented sequences.…”

Section: Methodsmentioning

confidence: 99%

Developmental Stage, Muscle and Genetic Type Modify Muscle Transcriptome in Pigs: Effects on Gene Expression and Regulatory Factors Involved in Growth and Metabolism

Ayuso

Fernández²,

Núñez³

et al. 2016

PLoS ONE

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Iberian pig production includes purebred (IB) and Duroc-crossbred (IBxDU) pigs, which show important differences in growth, fattening and tissue composition. This experiment was conducted to investigate the effects of genetic type and muscle (Longissimus dorsi (LD) vs Biceps femoris (BF)) on gene expression and transcriptional regulation at two developmental stages. Nine IB and 10 IBxDU piglets were slaughtered at birth, and seven IB and 10 IBxDU at four months of age (growing period). Carcass traits and LD intramuscular fat (IMF) content were measured. Muscle transcriptome was analyzed on LD samples with RNA-Seq technology. Carcasses were smaller in IB than in IBxDU neonates (p < 0.001), while growing IB pigs showed greater IMF content (p < 0.05). Gene expression was affected (p < 0.01 and Fold change > 1.5) by the developmental stage (5,812 genes), muscle type (135 genes), and genetic type (261 genes at birth and 113 at growth). Newborns transcriptome reflected a highly proliferative developmental stage, while older pigs showed upregulation of catabolic and muscle functioning processes. Regarding the genetic type effect, IBxDU newborns showed enrichment of gene pathways involved in muscle growth, in agreement with the higher prenatal growth observed in these pigs. However, IB growing pigs showed enrichment of pathways involved in protein deposition and cellular growth, supporting the compensatory gain experienced by IB pigs during this period. Moreover, newborn and growing IB pigs showed more active glucose and lipid metabolism than IBxDU pigs. Moreover, LD muscle seems to have more active muscular and cell growth, while BF points towards lipid metabolism and fat deposition. Several regulators controlling transcriptome changes in both genotypes were identified across muscles and ages (SIM1, PVALB, MEFs, TCF7L2 or FOXO1), being strong candidate genes to drive expression and thus, phenotypic differences between IB and IBxDU pigs. Many of the identified regulators were known to be involved in muscle and adipose tissues development, but others not previously associated with pig muscle growth were also identified, as PVALB, KLF1 or IRF2. The present study discloses potential molecular mechanisms underlying phenotypic differences observed between IB and IBxDU pigs and highlights candidate genes implicated in these molecular mechanisms.

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Comparison of five different RNA sources to examine the lactating bovine mammary gland transcriptome using RNA-Sequencing

Cited by 135 publications

References 24 publications

Elucidating fish oil-induced milk fat depression in dairy sheep: Milk somatic cell transcriptome analysis

Elucidating fish oil-induced milk fat depression in dairy sheep: Milk somatic cell transcriptome analysis

RNA-Sequencing for profiling goat milk transcriptome in colostrum and mature milk

Developmental Stage, Muscle and Genetic Type Modify Muscle Transcriptome in Pigs: Effects on Gene Expression and Regulatory Factors Involved in Growth and Metabolism

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