Transition of allele-specific DNA hydroxymethylation at regulatory loci is associated with phenotypic variation in monozygotic twins discordant for psychiatric disorders.
Transition of allele-specific DNA hydroxymethylation at regulatory loci is associated with phenotypic variation in monozygotic twins discordant for psychiatric disorders.
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DOI：
10.1186/s12916-023-03177-y
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发表时间：
2023-12-12
期刊：
影响因子：
9.3
通讯作者：
Zhao, Cunyou
中科院分区：
文献类型：
--
作者：
Ye, Junping;Huang, Zhanwang;Li, Qiyang;Li, Zhongwei;Lan, Yuting;Wang, Zhongju;Ni, Chaoying;Wu, Xiaohui;Jiang, Tingyun;Li, Yujing;Yang, Qiong;Lim, Junghwa;Ren, Cun-Yan;Jiang, Meijun;Li, Shufen;Jin, Peng;Chen, Jian-Huan;Zhao, Cunyou
精神分裂症（SCZ）和双相情感障碍（BPD）等主要精神疾病是复杂的遗传性精神疾病。他们的非孟德尔特征，如在SCZ或BPD不一致的单卵双胞胎中观察到的特征，可能因遗传效应的环境修饰剂而复杂化。5-羟甲基胞嘧啶（5 hmC）是基因调控中重要的表观遗传标记，它是否与导致非孟德尔特征的遗传变异有关，在很大程度上尚未探索。我们将5 hmC选择性化学标记法（5 hmC-seq）和全基因组测序（WGS）分析从SCZ或BPD不一致的单卵（MZ）双胞胎获得的外周血DNA，以鉴定羟甲基化图谱中的等位基因不平衡，并基于贝叶斯因子（BF）研究了等位基因特异性羟甲基化（AShM）转换与疾病易感性的关联贝叶斯广义加性线性混合模型。然后，我们进行了多组学综合分析，以确定这些AShM位点的分子致病基础。最后，我们采用荧光素酶报告基因、CRISPR/Cas9技术、电泳迁移率变动分析（EMSA）、染色质免疫沉淀（ChIP）、PCR、FM 4 -64成像分析和RNA测序来验证感兴趣的AShM位点在人神经母细胞瘤SK-N-SH细胞和人胚肾293 T（HEK 293 T）细胞中的功能。我们发现了数千种与ASHM失衡相关的遗传变异，这些变异在调控基因座上表现出表型变异相关的ASHM变化。这些AShM标记显示了与SCZ或BPD的合理关联，基于它们对转录因子（TF），DNA甲基化水平或其他表观基因组标记之间相互作用的影响，从而导致基因表达失调，最终增加疾病易感性。然后，我们验证了在PLLP增强的PLLP表达中，POU 3F 2在AShM位点rs 4558409（G/T）处的替代等位基因上的竞争性结合，而减轻POU 3F 2在rs 4558409位点的结合活性的羟甲基化替代等位基因可能与在BPD或SCZ中观察到的PLLP表达下调有关。此外，破坏rs 4558409促进神经发育和囊泡运输。我们的研究提供了一个强有力的策略，优先考虑监管风险的变种，并有助于我们了解遗传和表观遗传因素之间的相互作用，介导SCZ或BPD的易感性。在线版本包含补充材料，可通过10.1186/s12916-023-03177-y获得。
Major psychiatric disorders such as schizophrenia (SCZ) and bipolar disorder (BPD) are complex genetic mental illnesses. Their non-Mendelian features, such as those observed in monozygotic twins discordant for SCZ or BPD, are likely complicated by environmental modifiers of genetic effects. 5-Hydroxymethylcytosine (5hmC) is an important epigenetic mark in gene regulation, and whether it is linked to genetic variants that contribute to non-Mendelian features remains largely unexplored. We combined the 5hmC-selective chemical labeling method (5hmC-seq) and whole-genome sequencing (WGS) analysis of peripheral blood DNA obtained from monozygotic (MZ) twins discordant for SCZ or BPD to identify allelic imbalances in hydroxymethylome maps, and examined association of allele-specific hydroxymethylation (AShM) transition with disease susceptibility based on Bayes factors (BF) derived from the Bayesian generalized additive linear mixed model. We then performed multi-omics integrative analysis to determine the molecular pathogenic basis of those AShM sites. We finally employed luciferase reporter, CRISPR/Cas9 technology, electrophoretic mobility shift assay (EMSA), chromatin immunoprecipitation (ChIP), PCR, FM4-64 imaging analysis, and RNA sequencing to validate the function of interested AShM sites in the human neuroblastoma SK-N-SH cells and human embryonic kidney 293T (HEK293T) cells. We identified thousands of genetic variants associated with AShM imbalances that exhibited phenotypic variation-associated AShM changes at regulatory loci. These AShM marks showed plausible associations with SCZ or BPD based on their effects on interactions among transcription factors (TFs), DNA methylation levels, or other epigenomic marks and thus contributed to dysregulated gene expression, which ultimately increased disease susceptibility. We then validated that competitive binding of POU3F2 on the alternative allele at the AShM site rs4558409 (G/T) in PLLP-enhanced PLLP expression, while the hydroxymethylated alternative allele, which alleviated the POU3F2 binding activity at the rs4558409 site, might be associated with the downregulated PLLP expression observed in BPD or SCZ. Moreover, disruption of rs4558409 promoted neural development and vesicle trafficking. Our study provides a powerful strategy for prioritizing regulatory risk variants and contributes to our understanding of the interplay between genetic and epigenetic factors in mediating SCZ or BPD susceptibility. The online version contains supplementary material available at 10.1186/s12916-023-03177-y.
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