ArticleNature communications2021
CRISPRi screens reveal a DNA methylation-mediated 3D genome dependent causal mechanism in prostate cancer.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 62 citations in OpenAlex.
- Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer.Genome biology · 2026Article
- Exploring Genetic Contributions to Prostate Cancer Risk in an Asian Population-Based Study.Cancer medicine · 2026Article
- CRISPRi-Mediated Epigenetic Suppression of TERT Reduces Cell Growth in Non-Small-Cell Lung Cancer Cells.Cells · 2026Article
- nanoASM: Long-Read Allele-Specific DNA Methylation Profiling Enables Functional Annotation of Regulatory Noncoding Variants in Human Prostate Tissues.bioRxiv : the preprint server for biology · 2026Article
- Integrative Whole-Genome and Epigenome Profiling of cfDNA in Familial Prostate Cancer: Insights from a Pilot Study.Biomedicines · 2026Article
- CMC-WDTK: CpG methylation change prediction by a weight-sharing dual-branch Transformer-Kolmogorov-Arnold network model.BMC genomics · 2026Article
- 5mC and 5hmC methylation sequencing: the power of 6-base sequencing in a multiomic era.Epigenomics · 2026Review
- IP-SNPs-seq links noncoding risk alleles to lineage transcription factor programs in prostate cancer.Cellular and molecular life sciences : CMLS · 2025Article
- Characterization of cis-regulatory elements and functional variants in colorectal cancer using epigenomics and CRISPRi screenings.Nature cancer · 2025Article
- Identifying prognostic targets in metastatic prostate cancer beyond AR.FEBS open bio · 2025Article
- Combined SNPs sequencing and allele specific proteomics capture reveal functional causality underpinning the 2p25 prostate cancer susceptibility locus.Nature communications · 2025Article
- Integrated Omics and Multicohort Analyses Identify an Enhancer Variant Linking Ferroptosis to Precision Therapy in Prostate Cancer.Cancer research · 2025Article
- CanASM: a comprehensive database for genome-wide allele-specific DNA methylation identification and annotation in cancer.BMC genomics · 2025Article
- VCAT: an integrated variant function annotation tools.Human genetics · 2024Article
- Human intermediate prostate cancer stem cells contribute to the initiation and development of prostate adenocarcinoma.Stem cell research & therapy · 2024Article
- ARGV: 3D genome structure exploration using augmented reality.BMC bioinformatics · 2024Article
- MethNet: a robust approach to identify regulatory hubs and their distal targets from cancer data.Nature communications · 2024Article
- Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells.Nature genetics · 2024Article
- The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer.Nature structural & molecular biology · 2024Article
- Epiallelic variation of non-coding RNA genes and their phenotypic consequences.Nature communications · 2024Article
Corrections and comments
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Authors and funding
32 authors at 12 institutions in 4 countries.
Funding
Abstract
Prostate cancer (PCa) risk-associated SNPs are enriched in noncoding cis-regulatory elements (rCREs), yet their modi operandi and clinical impact remain elusive. Here, we perform CRISPRi screens of 260 rCREs in PCa cell lines. We find that rCREs harboring high risk SNPs are more essential for cell proliferation and H3K27ac occupancy is a strong indicator of essentiality. We also show that cell-line-specific essential rCREs are enriched in the 8q24.21 region, with the rs11986220-containing rCRE regulating MYC and PVT1 expression, cell proliferation and tumorigenesis in a cell-line-specific manner, depending on DNA methylation-orchestrated occupancy of a CTCF binding site in between this rCRE and the MYC promoter. We demonstrate that CTCF deposition at this site as measured by DNA methylation level is highly variable in prostate specimens, and observe the MYC eQTL in the 8q24.21 locus in individuals with low CTCF binding. Together our findings highlight a causal mechanism synergistically driven by a risk SNP and DNA methylation-mediated 3D genome architecture, advocating for the integration of genetics and epigenetics in assessing risks conferred by genetic predispositions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.