Tracking histone modifications in embryos and low-input samples using ultrasensitive STAR ChIP-seq

Abstract

ChIP-seq is a powerful technique that allows the detection of chromatin localization for proteins and epigenetic modifications. However, conventional ChIP-seq usually requires millions of cells. This becomes a daunting task for applications in which only limited experimental materials are available. For example, during mammalian embryo development, the epigenomes undergo drastic reprogramming which endows a fertilized egg with the potential to develop into the whole body. Low-input ChIP-seq methods would be instrumental to help decipher molecular mechanisms underlying such epigenetic reprogramming. Here we describe an optimized ChIP-seq method—STAR (Small-scale TELP-Assisted Rapid) ChIP-seq—that allows the detection of histone modifications using only a few hundred cells. This method is proven to be robust in epigenomic profiling in both embryos and cultured cells.