de Vos Jani, Crooijmans Richard P M A, Derks Martijn F L, Kloet Susan L, Dibbits Bert, Groenen Martien A M, Madsen Ole
Animal Breeding and Genomics, Wageningen University & Research, Wageningen 6708PB, the Netherlands.
Human Genetics, Leids Universitair Medisch Centrum, Leiden 2333ZC, the Netherlands.
iScience. 2023 Feb 20;26(3):106252. doi: 10.1016/j.isci.2023.106252. eCollection 2023 Mar 17.
The pig IPEC-J2 and chicken SL-29 cell lines are of interest because of their untransformed nature and wide use in functional studies. Molecular characterization of these cell lines is important to gain insight into possible molecular aberrations. The aim of this paper is to provide a molecular and epigenetic characterization of the IPEC-J2 and SL-29 cell lines, a cell-line reference for the FAANG community, and future biomedical research. Whole genome sequencing, gene expression, DNA methylation, chromatin accessibility, and ChIP-seq of four histone marks (H3K4me1, H3K4me3, H3K27ac, H3K27me3) and an insulator (CTCF) are used to achieve these aims. Heteroploidy (aneuploidy) of various chromosomes was observed from whole genome sequencing analysis in both cell lines. Furthermore, higher gene expression for genes located on chromosomes with aneuploidy in comparison to diploid chromosomes was observed. Regulatory complexity of gene expression, DNA methylation, and chromatin accessibility was investigated through an integrative approach.
猪的IPEC-J2细胞系和鸡的SL-29细胞系因其未转化的特性以及在功能研究中的广泛应用而备受关注。对这些细胞系进行分子表征对于深入了解可能存在的分子异常情况非常重要。本文的目的是对IPEC-J2和SL-29细胞系进行分子和表观遗传表征，为FAANG群体及未来的生物医学研究提供细胞系参考。通过全基因组测序、基因表达、DNA甲基化、染色质可及性以及四种组蛋白标记（H3K4me1、H3K4me3、H3K27ac、H3K27me3）和一种绝缘子（CTCF）的ChIP-seq来实现这些目标。在两个细胞系的全基因组测序分析中均观察到了各种染色体的异倍性（非整倍性）。此外，与二倍体染色体相比，观察到非整倍性染色体上的基因具有更高的基因表达。通过综合方法研究了基因表达、DNA甲基化和染色质可及性的调控复杂性。
