Ross Samuel E, Hesselson Daniel, Bogdanovic Ozren
Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia.
Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.
Front Cell Dev Biol. 2021 Mar 4;9:643603. doi: 10.3389/fcell.2021.643603. eCollection 2021.
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.
DNA甲基化主要发生在脊椎动物基因组的CG二核苷酸处；然而，非CG甲基化（mCH）在脊椎动物组织中也可检测到，最显著的是在神经系统中。在哺乳动物中，已明确在神经系统发育过程中，DNMT3A将mCH靶向至CAC三核苷酸，mCH在基因体内富集并与转录抑制相关。然而，发育性mCH积累及其由DNMT3A沉积的保守性在很大程度上尚未得到探索，且在其他脊椎动物中尚未得到功能验证。在本研究中，通过分析斑马鱼大脑的DNA甲基化组和转录组，我们在特定转座子基序以及与发育和神经功能相关的发育下调基因中，鉴定出了CAC三核苷酸（mCAC）处mCH的富集。我们进一步生成并分析了发育中的斑马鱼幼虫的DNA甲基化组和转录组，并证明，与哺乳动物一样，mCH在胚胎后脑发育过程中积累。最后，通过应用CRISPR/Cas9技术，我们揭示了Dnmt3a酶在发育性mCAC沉积中的保守作用。总体而言，这项工作证明了发育性mCH动态变化的进化保守性，并突出了斑马鱼作为研究正常和受干扰发育过程中mCH调控及功能的模型的潜力。
