Chromatin profiling

Histones allow eukaryotic cells to densely package their genome in the nucleus. A wide spectrum of post-translational histone modifications exists that locally modulate this packing and impact the expression of associated genes by influencing DNA-protein binding. Histone modifications are key players in cell proliferation and differentiation, as well as malignancy processes. Their dysregulation is therefore increasingly being recognized as a hallmark of cancer.

The nuclei are isolated and incubated with a protein A-MNase (pA-MN) fusion protein, which is bound by an antibody against a particular histone modification. The protein A will be able to bind to many different monoclonal antibodies. At the moment we are well familiar with antibodies against:

• H3K4me1
• H3K4me3
• H3K9me3
• H3K27me3
• H3K36me3
• H3K27Ac
• CTCF

Monoclonal antibodies against other histone marks can be used, but would first have to be titrated by us to determine the right concentration for the experiment. Histone modification table 

During the incubation the MNase is kept inactive. After washing away unbound antibody, single cells are sorted into 384-well plates. Next, MNase is activated by adding calcium, resulting in the digestion of the genome that is in close proximity to the antibody. Without the need for purification steps, nucleosomes are stripped off the genome and the genomic fragments are ligated after end processing to barcoded adapters containing a unique molecular identifier (UMI), cell specific barcode, and T7 promoter allowing linear amplification by in vitro transcription (IVT) on the pooled material.

Currently the popular technology to detect histone modifications in single cells is based on chromatin immunoprecipitation (ChIP) (O’Neill and Turner, 1996), which relies on the physical pull-down of histone-DNA complexes. The inefficiency of this separation hinders the efficient detection of histone modification in single cells. Therefore, the Van Oudenaarden lab developed a high-throughput method using chromatin immunocleavage (Schmid et al., 2004; Skene and Henikoff, 2017) that circumvents this pull-down and profiles histone modifications in ten thousands of individual cells (scChIC-seq).