Genome-wide Mapping of Histone Modifications and Transcription Factor Binding Sites in Neuroendocrine Small Cell Lung Cancer Cell Lines Using CUT&RUN

Chromatin remodeling proteins and transcription factors (TFs) play critical roles in the tumor biology of small cell lung cancer (SCLC). Genome-wide characterization of histone post-translational modifications (PTMs) and TF binding sites is essential for identifying regulatory DNA elements and gene pathways that will lead to a deeper mechanistic understanding of SCLC and nominate targets for therapeutic intervention. Cleavage Under Targets and Release Using Nuclease followed by next generation sequencing (CUT&RUN-seq) is a powerful method for mapping specific histone modifications and determining the DNA-binding profiles of a wide range of proteins in situ in the cellular genome. In CUT&RUN, the micrococcal nuclease (MNase) fused to Protein A/G is recruited via antibodies to the genomic locations of chromatin-associated proteins, where the underlying DNA fragments are released from bulk chromatin upon MNase activation and cleavage. This localized digestion generates small, locus-specific DNA fragments suitable for sequencing. Here, we present a detailed protocol for profiling histone modifications H3K4me3 (associated with active or open promoters) and H3K4me1 (associated with active enhancers), as well as the transcription factor E2F7, in SCLC. This protocol has been optimized for neuroendocrine (NE) SCLC cell line models, which are typically characterized by large nuclei, scant cytoplasm, and growth as non-adherent aggregates in suspension.