DNA immunoprecipitation followed by sequencing (DIP-seq) is a common enrichment method for profiling DNA modifications in mammalian genomes. However, the results of independent DIP-seq studies often show considerable variation between profiles of the same genome and between profiles obtained by alternative methods. Here we show that these differences are primarily due to the intrinsic affinity of IgG for short unmodified DNA repeats. This pervasive experimental error accounts for 50–99% of regions identified as ‘enriched’ for DNA modifications in DIP-seq data. Correction of this error profoundly altered DNA-modification profiles for numerous cell types, including mouse embryonic stem cells, and subsequently revealed novel associations among DNA modifications, chromatin modifications and biological processes. We conclude that both matched input and IgG controls are essential in order for the results of DIP-based assays to be interpreted correctly, and that complementary, non-antibody-based techniques should be used to validate DIP-based findings to avoid further misinterpretation of genome-wide profiling data.

DNA免疫沉淀后再测序（DIP-seq）是在哺乳动物基因组中分析DNA修饰的常用富集方法。但是，独立DIP-seq研究的结果通常表明，同一基因组的谱图之间以及通过其他方法获得的谱图之间存在相当大的差异。在这里，我们显示这些差异主要是由于IgG对短的未修饰DNA重复序列的固有亲和力所致。这种普遍存在的实验错误占DIP-seq数据中被鉴定为DNA修饰“富集”区域的50–99％。对该错误的纠正极大地改变了包括小鼠胚胎干细胞在内的许多细胞类型的DNA修饰谱，随后揭示了DNA修饰，染色质修饰和生物学过程之间的新型关联。