Yifat Edrei, Revital Levy, Daniel Kaye, Anat Marom, Bernhard Radlwimmer et al.
Common diseases manifest differentially between patients, but the genetic origin of this variation remains unclear. To explore possible involvement of gene transcriptional-variation, we produce a DNA methylation-oriented, driver-gene-wide dataset of regulatory elements in human glioblastomas and study their effect on inter-patient gene expression variation. In 175 of 177 analyzed gene regulatory domains, transcriptional enhancers and silencers are intermixed. Under experimental conditions, DNA methylation induces enhancers to alter their enhancing effects or convert into silencers, while silencers are affected inversely. High-resolution mapping of the association between DNA methylation and gene expression in intact genomes reveals methylation-related regulatory units (average size = 915.1 base-pairs). Upon increased methylation of these units, their target-genes either increased or decreased in expression. Gene-enhancing and silencing units constitute cis-regulatory networks of genes. Mathematical modeling of the networks highlights indicative methylation sites, which signified the effect of key regulatory units, and add up to make the overall transcriptional effect of the network. Methylation variation in these sites effectively describe inter-patient expression variation and, compared with DNA sequence-alterations, appears as a major contributor of gene-expression variation among glioblastoma patients. We describe complex cis-regulatory networks, which determine gene expression by summing the effects of positive and negative transcriptional inputs. In these networks, DNA methylation induces both enhancing and silencing effects, depending on the context. The revealed mechanism sheds light on the regulatory role of DNA methylation, explains inter-individual gene-expression variation, and opens the way for monitoring the driving forces behind deferential courses of cancer and other diseases.
Yifat Edrei, Revital Levy, Daniel Kaye, Anat Marom, Bernhard Radlwimmer, Asaf Hellman. Methylation-directed regulatory networks determine enhancing and silencing of mutation disease driver genes and explain inter-patient expression variation. 2023-11-28. https://doi.org/10.1186/s13059-023-03094-6
The AK100 (library #100) target-enriched captured-fragment library was assayed in U87 glioblastoma cells in unmethylated and in-vitro remethylated plasmid states. Public GEO segment-count matrices were mapped to the same 500-bp, 50%-overlapping hg19 windows used for the study summary, and paired windows with observed DNA and reporter RNA in both states were retained.
A representative AK100 (library #100) target-enriched library of captured human glioblastoma regulatory fragments was cloned into a modified episomal self-transcribing reporter and assayed in T98G cells under unmethylated and in-vitro CpG-methylated plasmid conditions. The processed table contains the authors' significant 500-bp, 50%-overlapping reporter windows with paired counts, TAS values, and methylation-response annotations.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
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