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 re...
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| Format: | Article |
| Language: | English |
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BMC
2021-03-01
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| Series: | Epigenetics & Chromatin |
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| Online Access: | https://doi.org/10.1186/s13072-021-00387-7 |
| _version_ | 1818677573968723968 |
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| author | Benjamin I. Laufer J. Antonio Gomez Julia M. Jianu Janine M. LaSalle |
| author_facet | Benjamin I. Laufer J. Antonio Gomez Julia M. Jianu Janine M. LaSalle |
| author_sort | Benjamin I. Laufer |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-17T09:01:32Z |
| format | Article |
| id | doaj.art-e4bb9bad6e9843408caa47e3062cf23a |
| institution | Directory Open Access Journal |
| issn | 1756-8935 |
| language | English |
| last_indexed | 2024-12-17T09:01:32Z |
| publishDate | 2021-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Epigenetics & Chromatin |
| spelling | doaj.art-e4bb9bad6e9843408caa47e3062cf23a2022-12-21T21:55:42ZengBMCEpigenetics & Chromatin1756-89352021-03-0114111510.1186/s13072-021-00387-7Stable DNMT3L overexpression in SH-SY5Y neurons recreates a facet of the genome-wide Down syndrome DNA methylation signatureBenjamin I. Laufer0J. Antonio Gomez1Julia M. Jianu2Janine M. LaSalle3Department of Medical Microbiology and Immunology, School of Medicine, University of CaliforniaDepartment of Medical Microbiology and Immunology, School of Medicine, University of CaliforniaDepartment of Medical Microbiology and Immunology, School of Medicine, University of CaliforniaDepartment of Medical Microbiology and Immunology, School of Medicine, University of CaliforniaAbstract 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.https://doi.org/10.1186/s13072-021-00387-7DNMT3LDown syndromeWhole genome bisulfite sequencingBivalent chromatinEpigenomicsPiggyBac transgenesis |
| spellingShingle | Benjamin I. Laufer J. Antonio Gomez Julia M. Jianu Janine M. LaSalle Stable DNMT3L overexpression in SH-SY5Y neurons recreates a facet of the genome-wide Down syndrome DNA methylation signature Epigenetics & Chromatin DNMT3L Down syndrome Whole genome bisulfite sequencing Bivalent chromatin Epigenomics PiggyBac transgenesis |
| title | Stable DNMT3L overexpression in SH-SY5Y neurons recreates a facet of the genome-wide Down syndrome DNA methylation signature |
| title_full | Stable DNMT3L overexpression in SH-SY5Y neurons recreates a facet of the genome-wide Down syndrome DNA methylation signature |
| title_fullStr | Stable DNMT3L overexpression in SH-SY5Y neurons recreates a facet of the genome-wide Down syndrome DNA methylation signature |
| title_full_unstemmed | Stable DNMT3L overexpression in SH-SY5Y neurons recreates a facet of the genome-wide Down syndrome DNA methylation signature |
| title_short | Stable DNMT3L overexpression in SH-SY5Y neurons recreates a facet of the genome-wide Down syndrome DNA methylation signature |
| title_sort | stable dnmt3l overexpression in sh sy5y neurons recreates a facet of the genome wide down syndrome dna methylation signature |
| topic | DNMT3L Down syndrome Whole genome bisulfite sequencing Bivalent chromatin Epigenomics PiggyBac transgenesis |
| url | https://doi.org/10.1186/s13072-021-00387-7 |
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