Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2

Abstract

HepG2 is one of the most widely used human cell lines in biomedical research and one of the main cell lines of ENCODE. Although the functional genomic and epigenomic characteristics of HepG2 are extensively studied, its genome sequence has never been comprehensively analyzed and higher-order structural features of its genome beyond its karyotype were only cursorily known. The high degree of aneuploidy in HepG2 renders traditional genome variant analysis methods challenging and partially ineffective. Correct and complete interpretation of the extensive functional genomics data fromHepG2 requires an understanding of the cell line's genome sequence and genome structure. We performed deep whole-genome sequencing, mate-pair sequencing and linked-read sequencing to identify a wide spectrum of genome characteristics in HepG2: copy numbers of chromosomal segments, SNVs and Indels (both corrected for copynumber), phased haplotype blocks, structural variants (SVs) including complex genomic rearrangements, and novel mobile element insertions. A large number of SVs were phased, sequence assembled and experimentally validated. Several chromosomes show striking loss of heterozygosity. We re-analyzed HepG2 RNA-Seq and wholegenome bisulfite sequencing data for allele-specific expression and phased DNA methylation. We show examples where deeper insights into genomic regulatory complexity could be gained by taking knowledge of genomic structural contexts into account. Furthermore, we used the haplotype information to produce an allele-specific CRISPR targeting map. This comprehensive whole-genome analysis serves as a resource for future studies that utilize HepG2.

CRISPR/Cas9 deletions induce adverse on-target genomic effects leading to functional DNA in human cells

“…4C ). HepG2 has a hyperploid karyotype with trisomy of chromosome 17 (52). Therefore, we speculate that two of the target-derived fragments were inserted into one of the three alleles in one daughter cell.…”

rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression

“…The ELOVL2 locus has copy number variation (CNV) in HepG2 cells, which has two copies of chromosome bearing the G allele of rs953413 (Lopez-Terrada et al, 2009;Zhou et al, 2018). To verify that the observed allelic imbalance in rs953413 and rs3798713 is not only caused by the CNV and to identify candidate causal TFs, we employed a more stringent strategy that filtered out PCR duplicates and tolerated no mismatch other than the SNP itself to each TF that mapped to these two regions in ChIP-seq experiments in HepG2 cells.…”

Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA

“…A candidate SNV was predicted as a heterozygous SNV in the cell line if the total read coverage was at least 10 and the allelic ratio of the reference allele was between 0.25 and 0.75. In addition, we used whole-genome DNA sequencing data of the two cell lines to identify heterozygous SNVs using the same method as in our previous work 14 .…”