Kress Clémence, Montillet Guillaume, Jean Christian, Fuet Aurélie, Pain Bertrand
Inserm, U1208, INRA, USC1361, Stem Cell and Brain Research Institute, 18 avenue du Doyen Lépine, 69500 Bron, France ; Université de Lyon, Université Lyon 1, Lyon, France.
Epigenetics Chromatin. 2016 Feb 10;9:5. doi: 10.1186/s13072-016-0056-6. eCollection 2016.
Chromatin epigenetics participate in control of gene expression during metazoan development. DNA methylation and post-translational modifications (PTMs) of histones have been extensively characterised in cell types present in, or derived from, mouse embryos. In embryonic stem cells (ESCs) derived from blastocysts, factors involved in deposition of epigenetic marks regulate properties related to self-renewal and pluripotency. In the germ lineage, changes in histone PTMs and DNA demethylation occur during formation of the primordial germ cells (PGCs) to reset the epigenome of the future gametes. Trimethylation of histone H3 on lysine 27 (H3K27me3) by Polycomb group proteins is involved in several epigenome-remodelling steps, but it remains unclear whether these epigenetic features are conserved in non-mammalian vertebrates. To investigate this question, we compared the abundance and nuclear distribution of the main histone PTMs, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) in chicken ESCs, PGCs and blastodermal cells (BCs) with differentiated chicken ESCs and embryonic fibroblasts. In addition, we analysed the expression of chromatin modifier genes to better understand the establishment and dynamics of chromatin epigenetic profiles.
The nuclear distributions of most PTMs and 5hmC in chicken stem cells were similar to what has been described for mammalian cells. However, unlike mouse pericentric heterochromatin (PCH), chicken ESC PCH contained high levels of trimethylated histone H3 on lysine 27 (H3K27me3). In differentiated chicken cells, PCH was less enriched in H3K27me3 relative to chromatin overall. In PGCs, the H3K27me3 global level was greatly reduced, whereas the H3K9me3 level was elevated. Most chromatin modifier genes known in mammals were expressed in chicken ESCs, PGCs and BCs. Genes presumably involved in de novo DNA methylation were very highly expressed. DNMT3B and HELLS/SMARCA6 were highly expressed in chicken ESCs, PGCs and BCs compared to differentiated chicken ESCs and embryonic fibroblasts, and DNMT3A was strongly expressed in ESCs, differentiated ESCs and BCs.
Chicken ESCs and PGCs differ from their mammalian counterparts with respect to H3K27 methylation. High enrichment of H3K27me3 at PCH is specific to pluripotent cells in chicken. Our results demonstrate that the dynamics in chromatin constitution described during mouse development is not universal to all vertebrate species.
染色质表观遗传学参与后生动物发育过程中的基因表达调控。DNA甲基化和组蛋白的翻译后修饰（PTMs）已在源自小鼠胚胎或存在于小鼠胚胎中的细胞类型中得到广泛表征。在由囊胚衍生的胚胎干细胞（ESC）中，参与表观遗传标记沉积的因子调节与自我更新和多能性相关的特性。在生殖谱系中，原始生殖细胞（PGC）形成过程中发生组蛋白PTMs变化和DNA去甲基化，以重置未来配子的表观基因组。多梳蛋白组对组蛋白H3赖氨酸27位点（H3K27me3）的三甲基化参与了几个表观基因组重塑步骤，但这些表观遗传特征在非哺乳动物脊椎动物中是否保守尚不清楚。为了研究这个问题，我们比较了鸡ESC、PGC和胚盘细胞（BC）与分化的鸡ESC和胚胎成纤维细胞中主要组蛋白PTM、5-甲基胞嘧啶（5mC）和5-羟甲基胞嘧啶（5hmC）的丰度和核分布。此外，我们分析了染色质修饰基因的表达，以更好地了解染色质表观遗传图谱的建立和动态变化。
鸡干细胞中大多数PTM和5hmC的核分布与哺乳动物细胞中描述的相似。然而，与小鼠着丝粒周围异染色质（PCH）不同，鸡ESC的PCH含有高水平的赖氨酸27三甲基化组蛋白H3（H3K27me3）。在分化的鸡细胞中，相对于整体染色质，PCH中H3K27me3的富集程度较低。在PGC中，H3K27me3的整体水平大大降低，而H3K9me3的水平升高。哺乳动物中已知的大多数染色质修饰基因在鸡ESC、PGC和BC中表达。推测参与从头DNA甲基化的基因表达水平非常高。与分化的鸡ESC和胚胎成纤维细胞相比，DNMT3B和HELLS/SMARCA6在鸡ESC、PGC和BC中高表达，DNMT3A在ESC、分化的ESC和BC中强烈表达。
鸡ESC和PGC在H3K27甲基化方面与其哺乳动物对应物不同。PCH处H3K27me3的高富集是鸡多能细胞特有的。我们的结果表明，小鼠发育过程中描述的染色质构成动态变化并非所有脊椎动物物种都具有普遍性。
