McCann Jennifer A, Muro Enrique M, Palmer Claire, Palidwor Gareth, Porter Christopher J, Andrade-Navarro Miguel A, Rudnicki Michael A
Ottawa Health Research Institute, Regenerative Medicine Program, 501 Smyth Road, Ottawa, Ontario, K1H 8L6, Canada.
BMC Genomics. 2007 Sep 14;8:322. doi: 10.1186/1471-2164-8-322.
SNP microarrays are designed to genotype Single Nucleotide Polymorphisms (SNPs). These microarrays report hybridization of DNA fragments and therefore can be used for the purpose of detecting genomic fragments.
Here, we demonstrate that a SNP microarray can be effectively used in this way to perform chromatin immunoprecipitation (ChIP) on chip as an alternative to tiling microarrays. We illustrate this novel application by mapping whole genome histone H4 hyperacetylation in human myoblasts and myotubes. We detect clusters of hyperacetylated histone H4, often spanning across up to 300 kilobases of genomic sequence. Using complementary genome-wide analyses of gene expression by DNA microarray we demonstrate that these clusters of hyperacetylated histone H4 tend to be associated with expressed genes.
The use of a SNP array for a ChIP-on-chip application (ChIP on SNP-chip) will be of great value to laboratories whose interest is the determination of general rules regarding the relationship of specific chromatin modifications to transcriptional status throughout the genome and to examine the asymmetric modification of chromatin at heterozygous loci.
单核苷酸多态性（SNP）微阵列旨在对单核苷酸多态性进行基因分型。这些微阵列可报告DNA片段的杂交情况，因此可用于检测基因组片段。
在此，我们证明SNP微阵列可有效地以这种方式用于在芯片上进行染色质免疫沉淀（ChIP），作为平铺微阵列的替代方法。我们通过绘制人类成肌细胞和肌管中的全基因组组蛋白H4高乙酰化图谱来说明这种新应用。我们检测到组蛋白H4高乙酰化簇，其常常跨越长达300千碱基的基因组序列。通过DNA微阵列对基因表达进行全基因组互补分析，我们证明这些组蛋白H4高乙酰化簇往往与表达的基因相关。
将SNP阵列用于芯片上ChIP应用（SNP芯片上的ChIP）对于那些旨在确定关于特定染色质修饰与全基因组转录状态之间关系的一般规则以及检查杂合位点处染色质不对称修饰的实验室具有重要价值。
