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

Abstract

Background Bovine Respiratory Syncytial Virus (BRSV) is a cause of Bovine Respiratory Disease (BRD). DNA-based biomarkers contributing to BRD resistance are potentially present in non-protein-coding regulatory regions of the genome, which can be determined using ATAC-Seq. The objectives of this study were to: (i) identify regions of open chromatin in DNA extracted from bronchial lymph nodes (BLN) of healthy dairy calves experimentally challenged with BRSV and compare them with those from non-challenged healthy control calves, (ii) elucidate the chromatin regions that were differentially or uniquely open in the BRSV challenged relative to control calves, and (iii) compare the genes found in regions proximal to the differentially open regions to the genes previously found to be differentially expressed in the BLN in response to BRSV and to previously identified BRD susceptibility loci. This was achieved by challenging clinically healthy Holstein-Friesian calves (mean age 143 ± 14 days) with either BRSV inoculum (n = 12) or with sterile phosphate buffered saline (PBS) (n = 6) and preparing and sequencing ATAC-Seq libraries from fresh BLN tissues. Results Using Diffbind, 9,144 and 5,096 differentially accessible regions (P < 0.05, FDR < 0.05) were identified between BRSV challenged and control calves employing DeSeq2 and EdgeR, respectively. Additionally, 8,791 chromatin regions were found to be uniquely open in BRSV challenged calves. Seventy-six and 150 of the genes that were previously found to be differentially expressed using RNA-Seq, were located within 2 kb downstream of the differentially accessible regions, and of the regions uniquely open in BRSV challenged calves, respectively. Pathway analyses within ClusterProfiler indicated that these genes were involved in immune responses to infection and participated in the Th1 and Th2 pathways, pathogen recognition and the anti-viral response. There were 237 differentially accessible regions positioned within 40 previously identified BRD susceptibility loci. Conclusions The identified open chromatin regions are likely to be involved in the regulatory response of gene transcription induced by infection with BRSV. Consequently, they may contain variants which impact resistance to BRD that could be used in breeding programmes to select healthier, more robust cattle.

The Bacterial and Viral Agents of BRDC: Immune Evasion and Vaccine Developments

“…Multiple predisposing environmental factors have been identified which contribute to BRDC development, but these are not present in every case and cannot be used reliably to predict cases [7,115]. Genetic polymorphisms may act as diagnostic biomarkers of susceptibility to infection with HRSV [116,117] and BRSV [118,119].…”

“…In 2014, 116 genomic loci were identified which were associated with BRDC susceptibility [123]. A recent study identified multiple open chromatin regions in the bronchial lymph nodes of calves infected with BRSV [119]. These regions were found to be involved in Th1 and Th2 pathways, pathogen recognition and the anti-viral response [119].…”

“…A recent study identified multiple open chromatin regions in the bronchial lymph nodes of calves infected with BRSV [119]. These regions were found to be involved in Th1 and Th2 pathways, pathogen recognition and the anti-viral response [119]. Likely to be involved in the regulatory response of gene transcription induced by BRSV infection, these regions may contain genetic variations which may confer resistance to BRDC.…”

“…Likely to be involved in the regulatory response of gene transcription induced by BRSV infection, these regions may contain genetic variations which may confer resistance to BRDC. Further characterization and investigation may provide a useful tool for genomic selection to decrease BRDC prevalence within herds [118,119].…”

Optimisation of rapid untargeted nanopore DNA virus metagenomics using cell cultures and calves experimentally infected with bovine herpes virus-1

“…Bovine respiratory disease (BRD) is the leading cause of morbidity, mortality and economic loss in cattle of all ages both in Ireland, and internationally [1][2][3][4][5] . The extensive use of vaccines against BRD-associated viral and bacterial pathogens has not reduced the incidence or severity of BRD in cattle.…”