TY - JOUR
T1 - Detailed molecular and epigenetic characterization of the pig IPEC-J2 and chicken SL-29 cell lines
AU - de Vos, Jani
AU - Crooijmans, Richard P.M.A.
AU - Derks, Martijn F.L.
AU - Kloet, Susan L.
AU - Dibbits, Bert
AU - Groenen, Martien A.M.
AU - Madsen, Ole
N1 - Publisher Copyright:
© 2023 The Authors
PY - 2023/3/17
Y1 - 2023/3/17
N2 - 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.
AB - 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.
KW - Cell biology
U2 - 10.1016/j.isci.2023.106252
DO - 10.1016/j.isci.2023.106252
M3 - Article
AN - SCOPUS:85149663537
SN - 2589-0042
VL - 26
JO - iScience
JF - iScience
IS - 3
M1 - 106252
ER -