Tissue- and ethnicity-independent hypervariable DNA methylation states show evidence of establishment in the early human embryo.
Tissue- and ethnicity-independent hypervariable DNA methylation states show evidence of establishment in the early human embryo.
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DOI：
10.1093/nar/gkac503
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发表时间：
2022-07-08
影响因子：
14.9
通讯作者：
Silver, Matt J.
中科院分区：
文献类型：
--
作者：
Derakhshan, Maria;Kessler, Noah J.;Ishida, Miho;Demetriou, Charalambos;Brucato, Nicolas;Moore, Gudrun E.;Fall, Caroline H. D.;Chandak, Giriraj R.;Ricaut, Francois-Xavier;Prentice, Andrew M.;Hellenthal, Garrett;Silver, Matt J.
我们分析了来自30个数据集的DNA甲基化数据，这些数据集包括3474个个体、19个组织和8个种族，这些数据集由Illumina450K阵列覆盖。我们确定了4143个高变CpGs（“hvCpGs”），在多个组织和种族中，甲基化程度最高的前5%位点。hvCpG甲基化受遗传变异影响，但不由遗传变异决定，与探针可靠性、表观遗传漂变、年龄、性别或细胞异质性效应无关。hvCpG甲基化倾向于在来自不同胚层的组织中协同变化，并且hvCpG富集于接近ERV1和ERVK逆转录病毒元件。在同卵双胞胎中，hvCpGs还富集了先前与孕产期环境、亲本起源特异性甲基化和独特甲基化特征相关的位点。总之，这些特性使hvCpGs成为研究随机和/或环境影响的DNA甲基化状态的有力候选者，这些甲基化状态在胚胎早期建立并在此后保持稳定，可以影响终身健康和疾病。
We analysed DNA methylation data from 30 datasets comprising 3474 individuals, 19 tissues and 8 ethnicities at CpGs covered by the Illumina450K array. We identified 4143 hypervariable CpGs (‘hvCpGs’) with methylation in the top 5% most variable sites across multiple tissues and ethnicities. hvCpG methylation was influenced but not determined by genetic variation, and was not linked to probe reliability, epigenetic drift, age, sex or cell heterogeneity effects. hvCpG methylation tended to covary across tissues derived from different germ-layers and hvCpGs were enriched for proximity to ERV1 and ERVK retrovirus elements. hvCpGs were also enriched for loci previously associated with periconceptional environment, parent-of-origin-specific methylation, and distinctive methylation signatures in monozygotic twins. Together, these properties position hvCpGs as strong candidates for studying how stochastic and/or environmentally influenced DNA methylation states which are established in the early embryo and maintained stably thereafter can influence life-long health and disease.
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影响因子：
14.9
作者：
Colaprico A;Silva TC;Olsen C;Garofano L;Cava C;Garolini D;Sabedot TS;Malta TM;Pagnotta SM;Castiglioni I;Ceccarelli M;Bontempi G;Noushmehr H
通讯作者：
Noushmehr H
DOI：
10.1073/pnas.2026580118
发表时间：
2021-03-23
影响因子：
11.1
作者：
Carpenter BL;Remba TK;Thomas SL;Madaj Z;Brink L;Tiedemann RL;Odendaal HJ;Jones PA
通讯作者：
Jones PA
影响因子：
4.9
作者：
Elmer JL;Hay AD;Kessler NJ;Bertozzi TM;Ainscough EAC;Ferguson-Smith AC
通讯作者：
Ferguson-Smith AC
影响因子：
4.4
作者：
Bibikova, Marina;Barnes, Bret;Shen, Richard
通讯作者：
Shen, Richard
影响因子：
2.9
作者：
Finer S;Iqbal MS;Lowe R;Ogunkolade BW;Pervin S;Mathews C;Smart M;Alam DS;Hitman GA
通讯作者：
Hitman GA