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N6-methyladenine in DNA antagonizes SATB1 in early development [ATAC-seq]

ABSTRACT: The recent discovery of N6-methyladenine (N6-mA) in mammalian genomes suggests that it may serve as an epigenetic regulatory mechanism. However, the biological role of N6-mA and the molecular pathways that exert its function remain unclear. Here we show that N6-mA has a key role in changing the epigenetic landscape during cell fate transitions in early development. We found that N6-mA is upregulated during the development of mouse trophoblast stem cells, specifically at regions of stress-induced DNA double helix destabilization (SIDD). Regions of SIDD are conducive to topological stress-induced unpairing of the double helix and have critical roles in organizing large-scale chromatin structures. We show that the presence of N6-mA reduces the in vitro interactions by more than 500-fold between SIDD and SATB1, a crucial chromatin organizer that interacts with SIDD regions. Deposition of N6-mA also antagonizes SATB1 function in vivo by preventing its binding to chromatin. Concordantly, N6-mA functions at the boundaries between euchromatin and heterochromatin to restrict the spread of euchromatin. Repression of SIDD–SATB1 interactions mediated by N6-mA is essential for gene regulation during trophoblast development in cell culture models and in vivo. Overall, our findings demonstrate an unexpected molecular mechanism for N6-mA function via SATB1, and reveal connections between DNA modification, DNA secondary structures and large chromatin domains in early embryonic development.

ORGANISM(S): Mus musculus

PROVIDER: GSE126223 | GEO | 2020/07/15

REPOSITORIES: GEO

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N6-methyladenine in DNA antagonizes SATB1 in early development [RNA-seq]

Project description:The recent discovery of N6-methyladenine (N6-mA) in mammalian genomes suggests that it may serve as an epigenetic regulatory mechanism. However, the biological role of N6-mA and the molecular pathways that exert its function remain unclear. Here we show that N6-mA has a key role in changing the epigenetic landscape during cell fate transitions in early development. We found that N6-mA is upregulated during the development of mouse trophoblast stem cells, specifically at regions of stress-induced DNA double helix destabilization (SIDD). Regions of SIDD are conducive to topological stress-induced unpairing of the double helix and have critical roles in organizing large-scale chromatin structures. We show that the presence of N6-mA reduces the in vitro interactions by more than 500-fold between SIDD and SATB1, a crucial chromatin organizer that interacts with SIDD regions. Deposition of N6-mA also antagonizes SATB1 function in vivo by preventing its binding to chromatin. Concordantly, N6-mA functions at the boundaries between euchromatin and heterochromatin to restrict the spread of euchromatin. Repression of SIDD–SATB1 interactions mediated by N6-mA is essential for gene regulation during trophoblast development in cell culture models and in vivo. Overall, our findings demonstrate an unexpected molecular mechanism for N6-mA function via SATB1, and reveal connections between DNA modification, DNA secondary structures and large chromatin domains in early embryonic development.

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Project description:DNA N6-methyladenine (N6-mA) is an emerging epigenetic mark in the mammalian genome. Levels of N6-mA undergo drastic fluctuation during early embryogenesis, indicative of active regulation. Here we demonstrate that the 2-oxoglurarate oxygenase ALKBH1 functions as a nuclear eraser of N6-mA in unpairing regions (e.g. SIDD, Stress Induced DNA Double Helix Destabilization regions). Enzymatic profiling studies revealed that ALKBH1 displays demethylation activity towards N6-mA on DNA substrates that share a common unpairing feature, e.g. bubbled, bulged or single-stranded DNA oligos. Furthermore, ssDNA-seq and DIP-seq analyses revealed significant genome-wide co-occurrence of base unpairing regions with N6-mA in mouse embryonic stem cells, especially during cell fate transition. Collectively, our biochemical, structural and genomic studies demonstrate that ALKBH1 is an important DNA demethylase that regulates genome N6-mA turnover in unpairing regions associated with dynamic chromatin regulation in early development. This series contains data from ssDNA-seq experiments on mouse ES cells. We used the S1 nuclease and biotin end-labeling to enrich for DNA at ssDNA regions followed by HiSeq4000 sequencing and data analysis.

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