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

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dc.contributor.authorJohnston, Dayle
dc.contributor.authorJaeWoo, Kim
dc.contributor.authorTaylor, Jeremy F.
dc.contributor.authorEarley, Bernadette
dc.contributor.authorMcCabe, Matthew S.
dc.contributor.authorLemon, Ken
dc.contributor.authorDuffy, Catherine
dc.contributor.authorMcMenamy, Michael
dc.contributor.authorCosby, S. Louise
dc.contributor.authorWaters, Sinéad M.
dc.date.accessioned2021-04-14T14:44:32Z
dc.date.available2021-04-14T14:44:32Z
dc.date.issued2021-01-06
dc.descriptionPublication history: Accepted - 23 November 2020; Published online - 6 January 2021.en_US
dc.description.abstractBackground: 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 ATACSeq 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.en_US
dc.description.sponsorshipThis project was funded by the Irish Department of Agriculture and the Department of Agriculture, Environment and Rural Affairs, Northern Ireland, as part of the US-Ireland R&D partnership call (RMIS_0033 Project 16/RD/USROI/ 11). JFT and JWK were supported by grant number 2017–67015-26760 from the United States Department for Agriculture National Institute for Food and Agriculture.en_US
dc.identifierhttp://hdl.handle.net/20.500.12518/232
dc.identifier.citationJohnston, D., Kim, J., Taylor, J. F., Earley, B., McCabe, M. S., Lemon, K., Duffy, C., McMenamy, M., Cosby, S. L. and Waters, S. M. (2021) ‘ATAC-Seq identifies regions of open chromatin in the bronchial lymph nodes of dairy calves experimentally challenged with bovine respiratory syncytial virus’, BMC Genomics. Springer Science and Business Media LLC, 22(1). doi: 10.1186/s12864-020-07268-5.en_US
dc.identifier.issn1471-2164
dc.identifier.urihttps://doi.org/10.1186/s12864-020-07268-5
dc.language.isoenen_US
dc.publisherBMC (Springer nature)en_US
dc.rights© The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.en_US
dc.subjectATAC-Seqen_US
dc.subjectBRSVen_US
dc.subjectBovine respiratory diseaseen_US
dc.subjectDairy calvesen_US
dc.subjectOpen chromatinen_US
dc.subjectGene regulationen_US
dc.titleATAC-Seq identifies regions of open chromatin in the bronchial lymph nodes of dairy calves experimentally challenged with bovine respiratory syncytial virusen_US
dc.typeArticleen_US
dcterms.dateAccepted2020-11-23
dcterms.dateSubmitted2020-08-10

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