Developmental Accumulation of Gene Body and Transposon Non-CpG Methylation in the Zebrafish Brain

Abstract

DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes; however, non-CG methylation (mCH) is also detectable in vertebrate tissues, most notably in the nervous system. In mammals it is well established that mCH is targeted to CAC trinucleotides by DNMT3A during nervous system development where it is enriched in gene bodies and associated with transcriptional repression. Nevertheless, the conservation of developmental mCH accumulation and its deposition by DNMT3A is largely unexplored and has yet to be functionally demonstrated in other vertebrates. In this study, by analyzing DNA methylomes and transcriptomes of zebrafish brains, we identified enrichment of mCH at CAC trinucleotides (mCAC) at defined transposon motifs as well as in developmentally downregulated genes associated with developmental and neural functions. We further generated and analyzed DNA methylomes and transcriptomes of developing zebrafish larvae and demonstrated that, like in mammals, mCH accumulates during post-embryonic brain development. Finally, by employing CRISPR/Cas9 technology, we unraveled a conserved role for Dnmt3a enzymes in developmental mCAC deposition. Overall, this work demonstrates the evolutionary conservation of developmental mCH dynamics and highlights the potential of zebrafish as a model to study mCH regulation and function during normal and perturbed development.

Taming transposable elements in vertebrates: from epigenetic silencing to domestication

“…Many of these genes show tissue-specific expression, although their functions remain unknown [191]. Such an expanded repertoire may have contributed to novel methylation patterns in fish, such as TGCT methylation in the zebrafish repeat family MOSAT [198][199][200].…”

Experimental and Computational Approaches for Non-CpG Methylation Analysis

“…The study showed that WGBS picked up 250,000 non-CpG loci while RRBS detected 213,000 non-CpG regions with an overlap of only 52,000 loci [ 3 ]. Later, several studies incorporated the RRBS method for the detection of non-CpG methylation over CpG methylation [ 32 , 33 , 34 ]. The MspI-based RRBS method largely enriches CpG methylation compared to non-CpG methylation.…”

Dnmt3aa But Not Dnmt3ab Is Required for Maintenance of Gametogenesis in Nile Tilapia

“…Gonads of the WT, dnmt3aa −/− and dnmt3ab −/− fish were dissected at different developmental stages (5,30,60,90, and 180 dah) for gene expression assay. Total RNA (1.0 μg) was extracted and reverse transcribed using PrimeScript RT Master Mix Perfect Real Time Kit according to the manufacturer's instructions (Takara, Dalian, China).…”

“…These studies suggest that dnmt3aa and dnmt3ab may play important roles in gonadal development of fish, however, their detailed expression profiles during the sex determination and differentiation and gonadal development of teleost are unclear. Recently, some research groups reported the mutation of dnmt3aa and dnmt3ab in zebrafish, demonstrating their critical function on behavior regulation [28], temperature adaptation [29] and brain neural development [30]. Nevertheless, the roles of dnmt3aa and dnmt3ab in gonadal development of fish remain unknown.…”