Fig. 3: Ly49 coding sequence and cis-regulatory evolution across mammalian lineages.
From: Cis-regulatory evolution of the recently expanded Ly49 gene family
a Amino acid sequence alignment of selected Ly49 sequences from mice and the single copy Ly49 sequences from squirrels, humans, cattle, and dogs. Amino acids were translated from DNA sequence alignment of the exons. b–d Ly49 gene expression patterns in humans, cattle, and dogs. Human single cell multiome data was obtained from 10x Genomics public datasets and reprocessed in-house (Methods). CD8B, CD3G, and TCRa are markers for T cells. CD56 marks human NK cells. Cattle RNA-seq data was obtained from GSE15843092, re-analyzed using a custom pipeline (Methods), and normalized using cpm (counts per million). Normalized dog gene expression values were directly obtained from BarkBase93. e WashU Comparative Epigenome Browser94 view of the upstream region of Ly49 genes. Data sources: Mouse NK ATAC: B6_Ly49Dp_ATAC_rep1 (this study, Supplementary Data 1); mouse NK cell T-bet ChIP-seq: GSM431440531; human cluster 5 (b) ATAC-seq: 10x public multiome dataset (10 k PBMC from a healthy individual with granulocytes removed by sorting); human T-bet ChIP-seq: GSM77655795; cattle spleen ATAC-seq: GSM479963492; dog spleen ATAC-seq: SRX581251093. Multiple sequence alignment was generated using “mafft --auto”.
