Tiling histone H3 lysine 4 and 27 methylation in zebrafish using high-density microarrays.
Tiling histone H3 lysine 4 and 27 methylation in zebrafish using high-density microarrays.
复制标题
使用高密度微阵列在斑马鱼中的瓷砖组蛋白H3赖氨酸4和27甲基化。
DOI：
10.1371/journal.pone.0015651
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发表时间：
2010-12-20
期刊：
影响因子：
3.7
通讯作者：
Collas P
中科院分区：
文献类型：
--
作者：
Lindeman LC;Reiner AH;Mathavan S;Aleström P;Collas P
通过染色质免疫沉淀和微阵列杂交（ChIP-chip）揭示表观遗传状态，有助于在基因组水平上理解基因调控。在老鼠和人类身上进行了许多研究；然而，迄今为止，关于非哺乳动物脊椎动物物种的高分辨率信息有限。我们报道了一个210万特征的高分辨率Nimblegen平铺微阵列，用于斑马鱼（Danio rerio）表观遗传状态的ChIP-chip询问。该阵列以92个碱基对的分辨率覆盖了基因组的251个兆碱基。它包括约15kb的上游调控序列，包括所有RefSeq启动子，以及编码区5 '端超过5kb的调控序列。我们发现，在成纤维细胞系中，启动子富集于H3K4me3、H3K27me3或两种修饰共富集，具有高重复性。ChIP- qpcr和序列ChIP实验验证了ChIP- ChIP数据，并支持三甲基化H3K4和H3K27在一个基因子集上的共富集。H3K4me3-和/或h3k27me3富集基因与不同的转录状态相关，并与不同的功能类别相关。我们为科学界设计并验证了一个全面的高分辨率平铺微阵列，用于研究斑马鱼的表观遗传状态，斑马鱼是一种广泛使用的发育和疾病模式生物。
Uncovering epigenetic states by chromatin immunoprecipitation and microarray hybridization (ChIP-chip) has significantly contributed to the understanding of gene regulation at the genome-scale level. Many studies have been carried out in mice and humans; however limited high-resolution information exists to date for non-mammalian vertebrate species. We report a 2.1-million feature high-resolution Nimblegen tiling microarray for ChIP-chip interrogations of epigenetic states in zebrafish (Danio rerio). The array covers 251 megabases of the genome at 92 base-pair resolution. It includes ∼15 kb of upstream regulatory sequences encompassing all RefSeq promoters, and over 5 kb in the 5′ end of coding regions. We identify with high reproducibility, in a fibroblast cell line, promoters enriched in H3K4me3, H3K27me3 or co-enriched in both modifications. ChIP-qPCR and sequential ChIP experiments validate the ChIP-chip data and support the co-enrichment of trimethylated H3K4 and H3K27 on a subset of genes. H3K4me3- and/or H3K27me3-enriched genes are associated with distinct transcriptional status and are linked to distinct functional categories. We have designed and validated for the scientific community a comprehensive high-resolution tiling microarray for investigations of epigenetic states in zebrafish, a widely used developmental and disease model organism.
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