Yang Pengxin, Corbett Ryan, Daharsh Lance, Uribe Juber Herrera, Byrne Kristen A, Loving Crystal L, Tuggle Christopher
Department of Animal Science, Iowa State University, Ames, IA, 50011, USA; Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.
Genomics. 2024 Nov;116(6):110944. doi: 10.1016/j.ygeno.2024.110944. Epub 2024 Sep 24.
The transcriptome of porcine peripheral blood mononuclear cells (PBMC) at single cell (sc) resolution is well described, but little is understood about the cis-regulatory mechanism behind scPBMC gene expression. Here, we profiled the open chromatin landscape of porcine PBMC that define cis-regulatory elements and mechanism contributing to the transcription using single nucleus ATAC sequencing (snATAC-seq). Approximately 22 % of the identified peaks overlapped with annotated transcription start sites (TSS). Using clustering based on open chromatin pattern similarity, we demonstrate that cell type annotations using snATAC-seq are highly concordant to that reported for sc RNA sequencing (scRNA-seq). The differentially accessible peaks (DAPs) for each cell type were characterized and the pattern of accessibility of the DAPs near cell type markers across cell types was similar to that of the average gene expression level of corresponding marker genes. Additionally, we found that peaks identified in snATAC-seq have the potential power to predict the cell type specific transcription starting site (TSS). We identified both transcription factors (TFs) whose binding motif were enriched in cell type DAPs of multiple cell types and cell type specific TFs by conducting transcription factor binding motif (TFBM) analysis. Furthermore, we identified the putative enhancer or promoter regions bound by TFs for each differentially expressed gene (DEG) with a DAP that overlapped with its TSS by generating cis-co-accessibility networks (CCAN). To predict the regulators of such DEGs, TFBM analysis was performed for each CCAN. The regulator TF-target DEG pairs predicted in this way were largely consistent with the results reported in the ENCODE Transcription Factor Targets Dataset (TFTD). This snATAC-seq approach provides insights into the regulation of chromatin accessibility landscape of porcine PBMCs and enables discovery of TFs predicted to control DEG through binding regulatory elements whose chromatin accessibility correlates with the DEG promoter region.
猪外周血单个核细胞（PBMC）的单细胞（sc）分辨率转录组已有详尽描述，但对于scPBMC基因表达背后的顺式调控机制却知之甚少。在此，我们利用单核ATAC测序（snATAC-seq）对猪PBMC的开放染色质景观进行了分析，该景观定义了顺式调控元件以及有助于转录的机制。约22%已识别的峰与注释的转录起始位点（TSS）重叠。基于开放染色质模式相似性进行聚类分析，我们证明利用snATAC-seq进行的细胞类型注释与scRNA测序（scRNA-seq）所报道的结果高度一致。对每种细胞类型的差异可及峰（DAP）进行了表征，且跨细胞类型的细胞类型标志物附近DAP的可及性模式与相应标志物基因的平均基因表达水平相似。此外，我们发现snATAC-seq中识别出的峰具有预测细胞类型特异性转录起始位点（TSS）的潜在能力。通过进行转录因子结合基序（TFBM）分析，我们识别出了其结合基序在多种细胞类型的细胞类型DAP中富集的转录因子（TF）以及细胞类型特异性TF。此外，我们通过生成顺式共可及性网络（CCAN），识别出了由TF结合的每个差异表达基因（DEG）的假定增强子或启动子区域，这些DEG的DAP与其TSS重叠。为了预测此类DEG的调控因子，对每个CCAN进行了TFBM分析。以这种方式预测的调控因子TF-靶标DEG对在很大程度上与ENCODE转录因子靶标数据集（TFTD）中报道的结果一致。这种snATAC-seq方法为猪PBMC染色质可及性景观的调控提供了见解，并能够发现预测通过结合调控元件来控制DEG的TF，这些调控元件的染色质可及性与DEG启动子区域相关。
