de Sá Machado Araújo Graziela, da Silva Francisco Junior Ronaldo, Dos Santos Ferreira Cristina, Mozer Rodrigues Pedro Thyago, Terra Machado Douglas, Louvain de Souza Thais, Teixeira de Souza Jozimara, Figueiredo Osorio da Silva Cleiton, Alves da Silva Antônio Francisco, Andrade Claudia Caixeta Franco, da Silva Alan Tardin, Ramos Victor, Garcia Ana Beatriz, Machado Filipe Brum, Medina-Acosta Enrique
Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.
Laboratório Nacional de Computação Científica, Petrópolis, Brazil.
Front Genet. 2018 Mar 1;9:36. doi: 10.3389/fgene.2018.00036. eCollection 2018.
A hallmark of imprinted genes in mammals is the occurrence of parent-of-origin-dependent asymmetry of DNA cytosine methylation (5C) of alleles at CpG islands (CGIs) in their promoter regions. This 5CpG asymmetry between the parental alleles creates allele-specific imprinted differentially methylated regions (iDMRs). iDMRs are often coupled to the transcriptional repression of the methylated allele and the activation of the unmethylated allele in a tissue-specific, developmental-stage-specific and/or isoform-specific fashion. iDMRs function as regulatory platforms, built through the recruitment of chemical modifications to histones to achieve differential, parent-of-origin-dependent chromatin segmentation states. Here, we used a comparative computational data mining approach to identify 125 novel constitutive candidate iDMRs that integrate the maximal number of allele-specific methylation region records overlapping CGIs in human methylomes. Twenty-nine candidate iDMRs display gametic 5CpG asymmetry, and another 96 are candidate secondary iDMRs. We established the maternal origin of the 5CpG imprints of one gametic () and one secondary () iDMRs. We also found a constitutively hemimethylated, nonimprinted domain at the promoter CGI with oocyte-derived methylation asymmetry. Given that the 5CpG level at the iDMRs is not a sufficient criterion to predict active or silent locus states and that iDMRs can regulate genes from a distance of more than 1 Mb, we used RNA-Seq experiments from the Genotype-Tissue Expression project and public archives to assess the transcriptional expression profiles of SNPs across 4.6 Mb spans around the novel maternal iDMRs. We showed that and are expressed biallelically in multiple tissues. We found evidence of tissue-specific monoallelic expression of and , located 363 kb upstream and 419 kb downstream, respectively, of the iDMR. We hypothesize that the iDMR regulates the tissue-specific, monoallelic expression of but not of . We annotated the non-coding epigenomic marks in the two maternal iDMRs using data from the Roadmap Epigenomics project and showed that the and iDMRs achieve contrasting activation and repression chromatin segmentations. Lastly, we found that the maternal 5CpG imprints are perturbed in several hematopoietic cancers. We conclude that the maternal 5CpG imprints at and iDMRs are decoupled from parent-of-origin transcriptional expression effects in multiple tissues.
哺乳动物中印记基因的一个标志是其启动子区域CpG岛(CGI)上等位基因的DNA胞嘧啶甲基化(5C)存在亲本来源依赖性不对称性。亲本等位基因之间的这种5CpG不对称性产生了等位基因特异性的印记差异甲基化区域(iDMR)。iDMR通常以组织特异性、发育阶段特异性和/或异构体特异性的方式与甲基化等位基因的转录抑制和未甲基化等位基因的激活相关联。iDMR作为调控平台,通过招募组蛋白化学修饰构建而成,以实现差异的、亲本来源依赖性的染色质分割状态。在这里,我们使用了一种比较计算数据挖掘方法,来识别125个新的组成型候选iDMR,这些iDMR整合了人类甲基化组中与CGI重叠的最大数量的等位基因特异性甲基化区域记录。29个候选iDMR显示出配子5CpG不对称性,另外96个是候选二级iDMR。我们确定了一个配子()和一个二级()iDMR的5CpG印记的母源起源。我们还在启动子CGI处发现了一个组成型半甲基化的非印记区域,具有卵母细胞来源的甲基化不对称性。鉴于iDMR处的5CpG水平不是预测活性或沉默基因座状态的充分标准,并且iDMR可以在超过1 Mb的距离上调控基因,我们使用了基因型-组织表达项目和公共档案中的RNA-Seq实验,来评估新发现的母源iDMR周围4.6 Mb范围内单核苷酸多态性(SNP)的转录表达谱。我们表明,和在多个组织中双等位基因表达。我们发现了和组织特异性单等位基因表达的证据,它们分别位于iDMR上游363 kb和下游419 kb处。我们假设iDMR调节的组织特异性单等位基因表达,但不调节的。我们使用路线图表观基因组学项目的数据注释了两个母源iDMR中的非编码表观基因组标记,并表明和iDMR实现了对比鲜明的激活和抑制染色质分割。最后,我们发现母源5CpG印记在几种血液系统癌症中受到干扰。我们得出结论,和iDMR处的母源5CpG印记在多个组织中与亲本来源的转录表达效应脱钩。