Chen Qiujia, Bates Alison M, Hanquier Jocelyne N, Simpson Edward, Rusch Douglas B, Podicheti Ram, Liu Yunlong, Wek Ronald C, Cornett Evan M, Georgiadis Millie M
Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA.
Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA.
J Biol Chem. 2022 May;298(5):101894. doi: 10.1016/j.jbc.2022.101894. Epub 2022 Apr 1.
Extensive portions of the human genome have unknown function, including those derived from transposable elements. One such element, the DNA transposon Hsmar1, entered the primate lineage approximately 50 million years ago leaving behind terminal inverted repeat (TIR) sequences and a single intact copy of the Hsmar1 transposase, which retains its ancestral TIR-DNA-binding activity, and is fused with a lysine methyltransferase SET domain to constitute the chimeric SETMAR gene. Here, we provide a structural basis for recognition of TIRs by SETMAR and investigate the function of SETMAR through genome-wide approaches. As elucidated in our 2.37 Å crystal structure, SETMAR forms a dimeric complex with each DNA-binding domain bound specifically to TIR-DNA through the formation of 32 hydrogen bonds. We found that SETMAR recognizes primarily TIR sequences (∼5000 sites) within the human genome as assessed by chromatin immunoprecipitation sequencing analysis. In two SETMAR KO cell lines, we identified 163 shared differentially expressed genes and 233 shared alternative splicing events. Among these genes are several pre-mRNA-splicing factors, transcription factors, and genes associated with neuronal function, and one alternatively spliced primate-specific gene, TMEM14B, which has been identified as a marker for neocortex expansion associated with brain evolution. Taken together, our results suggest a model in which SETMAR impacts differential expression and alternative splicing of genes associated with transcription and neuronal function, potentially through both its TIR-specific DNA-binding and lysine methyltransferase activities, consistent with a role for SETMAR in simian primate development.
人类基因组的大部分区域功能未知，包括那些源自转座元件的区域。其中一种元件，DNA转座子Hsmar1，大约在5000万年前进入灵长类谱系，留下了末端反向重复（TIR）序列和Hsmar1转座酶的一个完整拷贝，该转座酶保留了其祖先的TIR-DNA结合活性，并与赖氨酸甲基转移酶SET结构域融合，构成嵌合的SETMAR基因。在这里，我们提供了SETMAR识别TIRs的结构基础，并通过全基因组方法研究了SETMAR的功能。正如我们在2.37 Å晶体结构中所阐明的，SETMAR形成二聚体复合物，每个DNA结合结构域通过形成32个氢键特异性地与TIR-DNA结合。我们发现，通过染色质免疫沉淀测序分析评估，SETMAR主要识别人类基因组中的TIR序列（约5000个位点）。在两个SETMAR基因敲除细胞系中，我们鉴定出163个共享的差异表达基因和233个共享的可变剪接事件。这些基因中包括几个前体mRNA剪接因子、转录因子以及与神经元功能相关的基因，还有一个可变剪接的灵长类特异性基因TMEM14B，它已被确定为与大脑进化相关的新皮层扩张的标志物。综上所述，我们的结果提出了一个模型，其中SETMAR可能通过其TIR特异性DNA结合和赖氨酸甲基转移酶活性影响与转录和神经元功能相关基因的差异表达和可变剪接，这与SETMAR在猿猴灵长类动物发育中的作用一致。
