The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK.
Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK.
G3 (Bethesda). 2022 Feb 4;12(2). doi: 10.1093/g3journal/jkab424.
There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the "Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)" to identify putative regulatory regions in flash-frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest-, average-, and largest-sized male piglets from each litter through five developmental time points. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs.
关于家猪（Sus scrofa）基因组是如何调控的，信息非常有限。这种知识的缺乏阻碍了在猪的育种计划中定义和预测遗传变异影响的努力。为了弥补这一知识空白，我们需要从开放染色质区域开始，鉴定猪基因组中的调控序列。我们使用“改良的转座酶可及染色质分析（Omni-ATAC-Seq）”协议，鉴定了 24 头公仔猪的冷冻半腱肌中的潜在调控区域。我们通过五个发育时间点，从每个窝中最小、平均和最大的公仔猪中收集样本。在代表开放染色质区域的 4661 个 ATAC-Seq 峰中，超过 50%位于已知转录起始位点的 1kb 内。差异读计数分析显示，在发育时间点上，染色质可及性有显著差异的 377 个 ATAC-Seq 定义的基因组区域。我们发现了与肌肉发育相关基因下调相关的开放染色质区域，这些区域存在于小型胎儿仔猪中，但在妊娠 90 天的大型胎儿仔猪中不存在。我们生成的数据集为猪基因组调控研究提供了资源，并为筛选用于猪育种计划基因组选择的遗传变异提供了有价值的功能注释信息。
