Department of Animal Science, University of California Davis, Davis, CA, 95616, USA.
Department of Animal Science, Iowa State University, Ames, 50011, IA, USA.
BMC Genomics. 2020 Oct 7;21(1):698. doi: 10.1186/s12864-020-07078-9.
Although considerable progress has been made towards annotating the noncoding portion of the human and mouse genomes, regulatory elements in other species, such as livestock, remain poorly characterized. This lack of functional annotation poses a substantial roadblock to agricultural research and diminishes the value of these species as model organisms. As active regulatory elements are typically characterized by chromatin accessibility, we implemented the Assay for Transposase Accessible Chromatin (ATAC-seq) to annotate and characterize regulatory elements in pigs and cattle, given a set of eight adult tissues.
Overall, 306,304 and 273,594 active regulatory elements were identified in pig and cattle, respectively. 71,478 porcine and 47,454 bovine regulatory elements were highly tissue-specific and were correspondingly enriched for binding motifs of known tissue-specific transcription factors. However, in every tissue the most prevalent accessible motif corresponded to the insulator CTCF, suggesting pervasive involvement in 3-D chromatin organization. Taking advantage of a similar dataset in mouse, open chromatin in pig, cattle, and mice were compared, revealing that the conservation of regulatory elements, in terms of sequence identity and accessibility, was consistent with evolutionary distance; whereas pig and cattle shared about 20% of accessible sites, mice and ungulates only had about 10% of accessible sites in common. Furthermore, conservation of accessibility was more prevalent at promoters than at intergenic regions.
The lack of conserved accessibility at distal elements is consistent with rapid evolution of enhancers, and further emphasizes the need to annotate regulatory elements in individual species, rather than inferring elements based on homology. This atlas of chromatin accessibility in cattle and pig constitutes a substantial step towards annotating livestock genomes and dissecting the regulatory link between genome and phenome.
尽管在注释人类和小鼠基因组的非编码部分方面已经取得了相当大的进展，但其他物种（如家畜）的调控元件仍然知之甚少。这种缺乏功能注释的情况对农业研究构成了重大障碍，并降低了这些物种作为模式生物的价值。由于活性调控元件通常以染色质可及性为特征，因此我们实施了转座酶可及染色质分析（ATAC-seq），以注释和表征猪和牛的调控元件，使用了一组 8 种成年组织。
总体而言，分别在猪和牛中鉴定出 306304 个和 273594 个活性调控元件。71478 个猪和 47454 个牛调控元件具有高度的组织特异性，并且相应地富含已知组织特异性转录因子的结合基序。然而，在每种组织中，最常见的可及基序对应于绝缘子 CTCF，表明其广泛参与 3-D 染色质组织。利用小鼠中的类似数据集，比较了猪、牛和小鼠中的开放染色质，发现调控元件的保守性（就序列同一性和可及性而言）与进化距离一致；而猪和牛共享约 20%的可及位点，而小鼠和有蹄类动物只有约 10%的可及位点相同。此外，启动子处的可及性保守性比基因间区更为普遍。
在远端元件处缺乏保守的可及性与增强子的快速进化一致，进一步强调了在单个物种中注释调控元件的必要性，而不是基于同源性推断元件。牛和猪的染色质可及性图谱构成了注释家畜基因组和剖析基因组与表型之间调控联系的重要一步。
