ATAC-Seq identifies regions of open chromatin in the bronchial lymph nodes of dairy calves experimentally challenged with bovine respiratory syncytial virus.
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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DOI：
10.1186/s12864-020-07268-5
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发表时间：
2021-01-06
期刊：
影响因子：
4.4
通讯作者：
Waters SM
中科院分区：
文献类型：
--
作者：
Johnston D;Kim J;Taylor JF;Earley B;McCabe MS;Lemon K;Duffy C;McMenamy M;Cosby SL;Waters SM
牛呼吸道合胞病毒（BRSV）是引起牛呼吸道疾病（BRD）的一种病毒。有助于BRD抗性的基于DNA的生物标志物可能存在于基因组的非蛋白质编码调控区中，这可以使用ATAC-Seq来确定。本研究的目的是：（i）鉴定从用BRSV实验攻击的健康奶牛的支气管淋巴结（BLN）提取的DNA中开放染色质的区域，并将其与来自未攻击的健康对照小牛的那些进行比较，（ii）阐明相对于对照小牛，在BRSV攻击中差异或独特开放的染色质区域，和（iii）将在差异开放区域附近区域发现的基因与先前发现的在BLN中响应BRSV和先前鉴定的BRD易感性基因座差异表达的基因进行比较。这是通过用BRSV接种物（n = 12）或无菌磷酸盐缓冲盐水（PBS）（n = 6）挑战临床健康的荷斯坦-弗里斯兰小牛（平均年龄143 ± 14天），并从新鲜BLN组织制备ATAC-Seq文库并对其进行测序来实现的。使用Diffbind，分别使用DeSeq 2和EdgeR在BRSV攻击和对照小牛之间鉴定了9，144和5，096个差异可及区域（P < 0.05，FDR < 0.05）。此外，在BRSV攻毒小牛中发现8，791个染色质区域是唯一开放的。先前使用RNA-Seq发现差异表达的76个和150个基因分别位于差异可及区域下游2 kb内，以及BRSV攻毒小牛中独特开放区域的下游2 kb内。Pathway Profiler中的通路分析表明，这些基因参与了对感染的免疫应答，并参与了Th 1和Th 2通路、病原体识别和抗病毒应答。有237个差异访问区域位于40个以前确定的BRD易感基因座。所鉴定的开放染色质区域可能参与BRSV感染诱导的基因转录调控反应。因此，它们可能含有影响BRD抗性的变异体，可用于育种计划，以选择更健康，更健壮的牛。在线版本包含补充材料，可通过10.1186/s12864-020-07268-5获得。
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. 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. 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 online version contains supplementary material available at 10.1186/s12864-020-07268-5.