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Elucidation of the open chromatin regions in the bronchial lymph nodes of dairy calves experimentally challenged with bovine respiratory syncytial virus, using ATAC-Seq

ABSTRACT: Bovine Respiratory Syncytial Virus (BRSV) is a cause of Bovine Respiratory Disease (BRD). The objective of this study was to elucidate the chromatin regions which were differentially open in the bronchial lymph nodes (BLN) of dairy calves experimentally challenged with BRSV, relative to unchallenged control calves. Holstein-Friesian calves were either challenged with BRSV inoculum (n=12) or mock challenged with PBS (n=6). Calves were euthanised on day 7 post-challenge. ATAC-Seq libraries were prepared from fresh BLN tissues and sequenced (75 bp paired-end). Sequence reads were aligned to the UMD3.1 reference genome and peak calling (q < 0.01) was performed with MACS2, employing the BAMPE model. Using Diffbind, 9,144 and 5,096 differentially accessible peaks were identified between BRSV challenged and control calves (P < 0.05, FDR < 0.05) using DeSeq2 and EdgeR, respectively. There were 169 and 110 genes previously found to be differentially expressed using RNA-Seq located within or up to 2kb upstream of the differentially accessible peaks identified by the DeSeq 2 and EdgeR analyses, respectively. There were 237 differentially accessible peaks positioned within 40 previously identified susceptibility loci for BRD. These open chromatin regions are likely involved in the gene transcriptional and regulatory response to infection by BRSV.

ORGANISM(S): Bos taurus

PROVIDER: GSE148056 | GEO | 2021/01/13

REPOSITORIES: GEO

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Project description:Bovine Respiratory Disease (BRD) is responsible for the majority of calf morbidity and mortality. One of the main causes of BRD is initial infection with Bovine Respiratory Syncytial Virus (BRSV). The objective of this study was to elucidate the changes in the host's bronchial lymph node miRNA transcriptome in response to BRSV in a controlled viral challenge. Holstein-Friesian calves were either inoculated with BRSV (103.5 TCID50/ml x 15 ml) (n=12) or mock challenged with phosphate buffered saline (n=6). Clinical signs were scored daily until euthanasia at day 7 post-challenge. Total RNA was extracted and sequenced (75 bp) from bronchial lymph nodes. Sequences were filtered for contaminant short RNA species, and subsequently read counts for known miRNAS were generated using the miRDeep2 package with the UMD 3.1 version of the genome and the bovine mature miRNA sequences from the miRBase database (release 22). EdgeR was used for differential expression analysis and Targetscan was used to identify target genes for the differentially expressed (DE) miRNAs. Pathway and gene ontology analyses on target genes were carried out using Ingenuity Pathway analysis (Qiagen). There was a clear separation between BRSV challenged and control calves based on miRNA gene expression changes, despite an observed mild clinical manifestation of the disease. There were 119 DE miRNAs (p<0.05, FDR<0.1, fold change>1.5) between the BRSV challenged and control calves. The DE miRNAs were predicted to target 465 genes which were previously found to be DE in bronchial lymph node tissue, between these BRSV challenged and control calves. Out of the DE predicted target genes, 455 genes had inverse fold changes to that of the DE miRNAs. There were 8 enriched pathways among the DE predicted target genes with inverse fold changes to that of the DE miRNA including: granulocyte and agranulocyte adhesion and diapedesis, interferon signaling and role of pathogen recognition receptors in recognition of bacteria and viruses. Functions predicted to be increased included: T cell response, apoptosis of leukocytes, immune response of cells and stimulation of cells. Pathogen recognition and proliferation of cytotoxic T cells are vital for the recognition and subsequent elimination of the virus.

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Elucidation of the open chromatin regions in the bronchial lymph nodes of dairy calves experimentally challenged with bovine respiratory syncytial virus, using ATAC-Seq

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