Genome-wide analysis of mRNAs and lncRNAs in Mycoplasma bovis infected and non-infected bovine mammary gland tissues

Özdemir, Selçuk; Altun, Serdar

doi:10.1016/j.mcp.2020.101512

Cited by 20 publications

(25 citation statements)

References 62 publications

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“…Bowtie2 (v2.2.5) was used to generate the index of the reference genome, and alignment of paired-end clean reads to the reference genome was performed with HISAT2 (v2.1.0). The assembly of mapped transcripts for each sample was performed with Scripture (beta2) and Cu inks (v2.1.1) in a reference-based approach [15].…”

Section: Reference Genome Alignment and Genome-wide Reads Distributiomentioning

confidence: 99%

“…In order to predict the targets of lncRNAs in MAC-T cells and thus understand potential functions of lncRNAs. Method as in previous research [15]. Firstly, we searched the 10 k/100 k coding genes upstream and downstream of lncRNA to nd cis role lncRNA.…”

Section: Prediction Of Lncrna-gene Interactionsmentioning

confidence: 99%

“…The GOseq R package was used to analyze GO enrichment for differentially expressed genes or lncRNA target genes [15]. GO terms with Q values < 0.05 were considered signi cantly enriched by differentially expressed genes.…”

Section: Kyoto Encyclopedia Of Genes and Genomes (Kegg) Biological Pamentioning

confidence: 99%

“…We used the RPKM/COUNT of the differential gene as the expression level. Hierarchical Clustering analysis was performed to cluster genes with the same or similar expression patterns into clusters, and used different colored regions to represent different clustering grouping information to determine clustering mode of different sample control modes [15,19]. In this study, the hierarchical clustering analysis of differentially expressed genes is shown in Fig.…”

Section: Differentially Expressed Genes Analysis In Exosomes Derived mentioning

confidence: 99%

“…GO enrichment analyses were conducted to search for the biological processes, cellular components, and molecular functions of differentially expressed genes in more detail [15,20]. GO analysis was performed on the up-regulated and down-regulated genes.…”

Section: Differentially Expressed Genes Analysis In Exosomes Derived mentioning

confidence: 99%

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LncRNA Profiling of Exosomes Derived From Staphylococcus Aureus-induced Bovine Mammary Epithelial Cell Lines MAC-T

Yu¹,

Jing²,

Chen³

et al. 2020

Preprint

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Background: Exosomes (carrying proteins, miRNA, lncRNA, etc.) play a vital role in participating in the occurrence and development of mastitis. LncRNA can play a variety of regulatory roles by combining with protein, RNA, and DNA. The expression of mRNA and lncRNA in exosomes derived from bovine mammary epithelial cells infected by S. aureus is rarely understood.Methods: We used ultracentrifugation to separate exosomes derived from S. aureus- stimulated MAC-T cells. After extracting exosomal RNA, RNA sequencing was performed. We screened differentially expressed genes, mRNA and lncRNA, and predicted their functions through KEGG and GO analysis. 6 mRNA and lncRNA were randomly selected for RT-qPCR verification.Results: Analysis of the sequencing results showed that there were 186 differentially expressed genes, 431 differentially expressed mRNAs and 19 differentially expressed lncRNAs in the exosomes derived from S. aureus-infected and non-infected MAC-T acells. By predicting lncRNA target genes, it was found that 19 differentially expressed lncRNAs all acted on multiple mRNAs in cis and trans. GO analysis revealed that differentially expressed genes and lncRNA target genes played significant roles in such metabolism, transmembrane transport, cellular response to DNA damage stimulus, response to cytokines. KEGG enrichment indicated that lncRNA target genes gathered in the TNF pathway, Notch pathway, phosphatidylinositol signaling system and p53 pathway. Conclusion: The data suggested that S. aureus induced changes in genes, mRNA, and lncRNA in exosomes secreted by MAC-T cells, which furtherly triggered other cells damage through exosomal delivery. This study would provide valuable resource for understanding the lncRNA information in exosomes derived from dairy cow mammary epithelial cells, and conduced to the study of S. aureus infection in dairy cow mammary glands.

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Section: Reference Genome Alignment and Genome-wide Reads Distributiomentioning

confidence: 99%

Section: Prediction Of Lncrna-gene Interactionsmentioning

confidence: 99%

Section: Kyoto Encyclopedia Of Genes and Genomes (Kegg) Biological Pamentioning

confidence: 99%

Section: Differentially Expressed Genes Analysis In Exosomes Derived mentioning

confidence: 99%

Section: Differentially Expressed Genes Analysis In Exosomes Derived mentioning

confidence: 99%

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LncRNA Profiling of Exosomes Derived From Staphylococcus Aureus-induced Bovine Mammary Epithelial Cell Lines MAC-T

Yu¹,

Jing²,

Chen³

et al. 2020

Preprint

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LncRNAs in domesticated animals: from dog to livestock species

et al. 2021

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Animal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.

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RNA-Seq analysis of long non-coding RNA in human intestinal epithelial cells infected by Shiga toxin-producing Escherichia coli

Zhang,

Ma,

Tong

et al. 2024

Cytokine

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Genome-wide analysis of mRNAs and lncRNAs in Mycoplasma bovis infected and non-infected bovine mammary gland tissues

Cited by 20 publications

References 62 publications

LncRNA Profiling of Exosomes Derived From Staphylococcus Aureus-induced Bovine Mammary Epithelial Cell Lines MAC-T

LncRNA Profiling of Exosomes Derived From Staphylococcus Aureus-induced Bovine Mammary Epithelial Cell Lines MAC-T

LncRNAs in domesticated animals: from dog to livestock species

RNA-Seq analysis of long non-coding RNA in human intestinal epithelial cells infected by Shiga toxin-producing Escherichia coli

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Genome-wide analysis of mRNAs and lncRNAs in Mycoplasma bovis infected and non-infected bovine mammary gland tissues

Cited by 20 publications

References 62 publications

LncRNA&nbsp;Profiling of Exosomes Derived From Staphylococcus Aureus-induced Bovine Mammary Epithelial Cell Lines MAC-T

LncRNA&nbsp;Profiling of Exosomes Derived From Staphylococcus Aureus-induced Bovine Mammary Epithelial Cell Lines MAC-T

LncRNAs in domesticated animals: from dog to livestock species

RNA-Seq analysis of long non-coding RNA in human intestinal epithelial cells infected by Shiga toxin-producing Escherichia coli

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Product

Resources

About

LncRNA Profiling of Exosomes Derived From Staphylococcus Aureus-induced Bovine Mammary Epithelial Cell Lines MAC-T

LncRNA Profiling of Exosomes Derived From Staphylococcus Aureus-induced Bovine Mammary Epithelial Cell Lines MAC-T