Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, and Norwegian Center for Stem Cell Research, Oslo, Norway.
PLoS One. 2010 Dec 20;5(12):e15651. doi: 10.1371/journal.pone.0015651.
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.
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，极大地促进了对基因组水平基因调控的理解。许多研究已经在小鼠和人类中进行，但迄今为止，对于非哺乳动物的脊椎动物物种，只有有限的高分辨率信息。
我们报告了一种 210 万个特征的 Nimblegen 平铺微阵列，用于检测斑马鱼（Danio rerio）中表观遗传状态的 ChIP-chip 分析。该阵列以 92 个碱基对的分辨率覆盖了 251 兆碱基对的基因组。它包括约 15 kb 的上游调控序列，涵盖所有 RefSeq 启动子，以及编码区 5'端的 5 kb 以上。我们在成纤维细胞系中以高重复性鉴定了富含 H3K4me3、H3K27me3 或两者共同富集的启动子。ChIP-qPCR 和连续 ChIP 实验验证了 ChIP-chip 数据，并支持在一组基因上三甲基化 H3K4 和 H3K27 的共富集。H3K4me3-和/或 H3K27me3 富集的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种全面的高分辨率平铺微阵列，用于研究斑马鱼中的表观遗传状态，斑马鱼是一种广泛使用的发育和疾病模型生物。
