Assay for transposase-accessible chromatin using sequencing combined with RNA sequencing to explore the effect of helicase like transcription factor deletion on hepatocellular carcinoma

Abstract

Abstract: Objective: To investigate the potential regulatory mechanism of helicase like transcription factor (HLTF) in hepatocellular carcinoma (HCC).
Method: HLTF was knockout through clustered regularly interspaced short palindromic repeats (CRISPR)/ CRISPR-associated protein 9 (Cas9) in HCC cell line. RNA sequencing (RNA-seq) was applied to detect and analyze the differentially expressed genes of the wild type and HLTF knockout cells. Assay for transposase-accessible chromatin using sequencing (ATAC-seq) was applied to detect the changes in chromatin accessibility of the wild type and HLTF knockout cells. The multi-omics analysis of RNA-seq and ATAC-seq was used to find the key signaling pathways and downstream genes of HLTF.
Result: The cancer genome atlas (TCGA) database analysis showed that HLTF was highly expressed in HCC and was associated with poor prognosis; RNA-seq sequencing showed that 563 genes were up-regulated and 656 genes were down-regulated in HLTF knockout cells compared to wild-type cells; ATAC-seq analysis showed a total of 27 818 regions had significantly altered in chromatin accessibility with HLTF deletion, including 14 225 regions with enhanced chromatin accessibility and 13 593 regions with weakened chromatin accessibility; motif enrichment analysis showed that Atf3, Fra1 and BATF were enriched in regions with enhanced chromatin accessibility, Fra1, Fra2 and JunB were enriched in regions with weakened chromatin accessibility; the combination of RNA-seq and ATAC-seq analysis showed that the overlapping genes were mainly enriched in the arachidonic acid metabolism pathway, Wnt signaling pathway, calcium signaling pathway and the transforming growth factor β (TGF-β) signaling pathway; the deletion of HLTF increased the expression of nuclear RNA export factor 3 (NXF3) and highly-expressed NXF3 was associated with better prognosis in HCC patients.
Conclusion: Our study pointed out that HLTF may be involved in regulating arachidonic acid metabolism pathway, Wnt signaling pathway, TGF-β signaling pathway, etc. NXF3 may be a potential downstream gene of HLTF, and our study provided directions and ideas to elucidate the mechanism of HLTF in HCC.

Key words: Assay for transposase-accessible chromatin using sequencing, RNA sequencing, Hepatocellular carcinoma, Helicase like transcription factor

Zhang Yixuan, Ma Yarui, Wang Xiaobing, Jiao Yuchen. Assay for transposase-accessible chromatin using sequencing combined with RNA sequencing to explore the effect of helicase like transcription factor deletion on hepatocellular carcinoma[J]. Electronic Journal of Liver Tumor, 2023, 10(2): 7-15.

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