Stable DNMT3L overexpression in SH-SY5Y neurons recreates a facet of the genome-wide Down syndrome DNA methylation signature

Abstract

Background Down syndrome (DS) is characterized by a genome-wide profile of differential DNA methylation that is skewed towards hypermethylation in most tissues, including brain, and includes pan-tissue differential methylation. The molecular mechanisms involve the overexpression of genes related to DNA methylation on chromosome 21. Here, we stably overexpressed the chromosome 21 gene DNA methyltransferase 3L (DNMT3L) in the human SH-SY5Y neuroblastoma cell line and assayed DNA methylation at over 26 million CpGs by whole genome bisulfite sequencing (WGBS) at three different developmental phases (undifferentiated, differentiating, and differentiated). Results DNMT3L overexpression resulted in global CpG and CpG island hypermethylation as well as thousands of differentially methylated regions (DMRs). The DNMT3L DMRs were skewed towards hypermethylation and mapped to genes involved in neurodevelopment, cellular signaling, and gene regulation. Consensus DNMT3L DMRs showed that cell lines clustered by genotype and then differentiation phase, demonstrating sets of common genes affected across neuronal differentiation. The hypermethylated DNMT3L DMRs from all pairwise comparisons were enriched for regions of bivalent chromatin marked by H3K4me3 as well as differentially methylated sites from previous DS studies of diverse tissues. In contrast, the hypomethylated DNMT3L DMRs from all pairwise comparisons displayed a tissue-specific profile enriched for regions of heterochromatin marked by H3K9me3 during embryonic development. Conclusions Taken together, these results support a mechanism whereby regions of bivalent chromatin that lose H3K4me3 during neuronal differentiation are targeted by excess DNMT3L and become hypermethylated. Overall, these findings demonstrate that DNMT3L overexpression during neurodevelopment recreates a facet of the genome-wide DS DNA methylation signature by targeting known genes and gene clusters that display pan-tissue differential methylation in DS.

DNA Methylation Alterations in Blood Cells of Toddlers with Down Syndrome

“…A growing body of research on DNA methylation in DS consistently reports trans epigenetic effects, where the presence of an additional chromosome 21 affects methylation on other chromosomes. Chromosome 21 contains epigenetic modifier genes, such as DNA methyltransferase DNMT3L, involved in the de novo methylation process whose extra-activity due to a "dosage effect" may contribute to genome-wide epigenetic dysregulation [2,3]. In addition, an overdosage of transcription factors located on chromosome 21, such as RUNX1 binding to the core element of many enhancers and promoters, may disturb the genome-wide pattern of the chromatin structure and DNA methylation [3,4].…”

Deconvolution of multiplexed transcriptional responses to wood smoke particles defines rapid aryl hydrocarbon receptor signaling dynamics

“…Persistent epigenetic changes such as DNA methylation, which can exert a memory effect on cell phenotype through modifying gene expression, are believed to contribute to long-term health effects of exposure to pollutants ( 56 , 57 ). Through PRO-Seq, we identified rapid and transient induction in response to WSP of the DNA methylase, DNMTL3 ( 58 ). Although PAH-containing pollutants have been previously reported to cause increased DNA methylation ( 59 , 60 ), we are unaware of any reports that have identified specific methylation pathways that might mediate this epigenetic response to WSP or other pollutants containing AHR ligands.…”

Detection of Modified Histones from Oral Mucosa of a Patient with DYT-KMT2B Dystonia

“…cam.ac.uk), encode_tfbs, sheffield_dnase [Sheffield et al, 2013], and ucsc_features. The DMRichR, which utilizes the dmrseq and bsseq algorithms (https://github.com/ben-laufer/ DMRichR), was used [Laufer et al, 2021], and regions containing at least five different CpGs within 1 kb with a minimum methylation difference of 10% were selected to identify differentially methylated regions.…”