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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...of the PVT1 promoter was significant in HuH-7 cells but not in Hep G2 cells. HBV-Enh I was the core sequence for transcriptional activation of the MYC promoter (Fig. 7D–F). Analysis of the inserted HBV sequences in the gene regions revealed that the integration of HBV-Enh I could occur near the regions...
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Research: Systematic identification and characterization of exon–intron circRNAs
- Yinchun Zhong,
- Yan Yang,
- Xiaolin Wang,
- Bingbing Ren,
- Xueren Wang,
- Ge Shan,
- and Liang Chen
Genome Res. March 2024 34: 376-393; Published in Advance April 12, 2024, doi:10.1101/gr.278590.123
...knockdown (Fig. 6C; Supplemental Table S8), consistent with the findings of previous reports in HepG2 cells (Middleton et al. 2017). The majority (1741/1879, ∼93%) of genes with significant changes in IR showed only regulated LIRs or regulated CIRs (Fig. 6D). Although most of the genes generally possessed...
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Method: Evidence of widespread, independent sequence signature for transcription factor cobinding
- Manqi Zhou,
- Hongyang Li,
- Xueqing Wang,
- and Yuanfang Guan
Genome Res. February 2021 31: 265-278; Published in Advance December 10, 2020, doi:10.1101/gr.267310.120
...not work alone; they cooperate and interact with each other and thus create complex transcription patterns of the (Lemon and Tjian 2000; Perez-Pinera et al. 2013; Li et al. 2014; Ang et al. 2016).Studying the collaborative patterns of TFs is a much more complicated problem than characterizing...
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Research: Alu insertion variants alter gene transcript levels
- Lindsay M. Payer,
- Jared P. Steranka,
- Maria S. Kryatova,
- Giacomo Grillo,
- Mathieu Lupien,
- Pedro P. Rocha,
- and Kathleen H. Burns
Genome Res. December 2021 31: 2236-2248; Published in Advance November 19, 2021, doi:10.1101/gr.261305.120
...through RNA polymerase III transcription factor C (TFIIIC) recruitment with subsequent altered chromatin looping and histone acetylation resulting in gene expression changes in cis (Ferrari et al. 2020). Alu RNA may also play a role in reducing transcription of RNA polymerase II (Pol II) transcripts...
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Research: A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells
- Alexandra E. Charos,
- Brian D. Reed,
- Debasish Raha,
- Anna M. Szekely,
- Sherman M. Weissman,
- and Michael Snyder
Genome Res. September 2012 22: 1668-1679; doi:10.1101/gr.127761.111
...the promoter of the known HSF1 target gene, HSP90AA1 (Hickey et al. 1989), is displayed in Figure 2D. ChIP-seq reveals -wide patterns of TF binding and colocalization of PPARGC1A and its network partners Our initial ChIP-seq studies suggested that PPARGC1A functions with known and novel partners in HepG2 cells...
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Method: MEDEA: analysis of transcription factor binding motifs in accessible chromatin
- Luca Mariani,
- Kathryn Weinand,
- Stephen S. Gisselbrecht,
- and Martha L. Bulyk
Genome Res. May 2020 30: 736-748; Published in Advance May 18, 2020, doi:10.1101/gr.260877.120
...development. Finally, we show that MEDEA performs well on both bulk and single-cell ATAC-seq data. MEDEA is publicly available as part of our Glossary-GENRE suite for motif enrichment analysis.In eukaryotic development, gene transcription happens in precise spatiotemporal patterns that require the specific...
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Resource: A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells
- William K.M. Lai,
- Luca Mariani,
- Gerson Rothschild,
- Edwin R. Smith,
- Bryan J. Venters,
- Thomas R. Blanda,
- Prashant K. Kuntala,
- Kylie Bocklund,
- Joshua Mairose,
- Sarah N. Dweikat,
- Katelyn Mistretta,
- Matthew J. Rossi,
- Daniela James,
- James T. Anderson,
- Sabrina K. Phanor,
- Wanwei Zhang,
- Zibo Zhao,
- Avani P. Shah,
- Katherine Novitzky,
- Eileen McAnarney,
- Michael-C. Keogh,
- Ali Shilatifard,
- Uttiya Basu,
- Martha L. Bulyk,
- and B. Franklin Pugh
Genome Res. September 2021 31: 1663-1679; Published in Advance August 23, 2021, doi:10.1101/gr.275472.121
...shock and non–heat shock HCT116 cells were washed with PBS before fixing with 1% formaldehyde (Sigma-Aldrich 252549) in PBS for 15 min and processing for ChIP-seq.ChIP-exo testing was initially prioritized in K562, MCF-7, and HepG2, using gene expression values (FPKM in RNA-seq) generated from...
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Method: Fast decoding cell type–specific transcription factor binding landscape at single-nucleotide resolution
- Hongyang Li and
- Yuanfang Guan
Genome Res. April 2021 31: 721-731; Published in Advance March 19, 2021, doi:10.1101/gr.269613.120
...covering 10 TFs (CTCF, EGR1, FOXA1, FOXA2, GABPA, HNF4A, JUND, NANOG, REST, and TAF1) in 13 cell types (A549, GM12878, H1-hESC, HCT116, HeLa-S3, HepG2, iPSC, IMR-90, K562, liver, MCF-7, PANC-1, PC-3). The ChIP-seq data were downloaded from the ENCODE data portal (https...
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Research: Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations
- Ryne C. Ramaker,
- Andrew A. Hardigan,
- Say-Tar Goh,
- E. Christopher Partridge,
- Barbara Wold,
- Sara J. Cooper,
- and Richard M. Myers
Genome Res. July 2020 30: 939-950; Published in Advance July 2, 2020, doi:10.1101/gr.260463.119
...are prevalent in the We used two orthogonal methods to infer DAP associations across the . The first involved analysis of ENCODE ChIP-seq peaks (208, 129, 312 DAPs in the HepG2, GM12878, K562 cell lines) (Supplemental Table S1). A subset of DAPs was further classified into sequence-specific transcription...
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Research: Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types
- Arnoud Boot,
- Alvin W.T. Ng,
- Fui Teen Chong,
- Szu-Chi Ho,
- Willie Yu,
- Daniel S.W. Tan,
- N. Gopalakrishna Iyer,
- and Steven G. Rozen
Genome Res. June 2020 30: 803-813; Published in Advance July 6, 2020, doi:10.1101/gr.255620.119
...SA-exposed HepG2 clones are shown in Figure 5C and Supplemental Figure S12. The mutational signature of duoSA is characterized by strong peaks of T > A mutations with always either an adenine directly 3′ or a thymine directly 5′ of the mutation site. DuoSA-associated mutagenesis showed strong transcriptional...

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