Chromatin immunoprecipitation paired with next-generation sequencing (ChIP-seq) can be used to determine genome-wide distribution of transcriptions factors, transcriptional machinery, or histone modifications. DNA-protein interactions are covalently cross-linked with the addition of formaldehyde. Chromatin is prepared and sheared, then immunoprecipitated with the appropriate antibody. After reversal of cross-linking and treating with protease, the resulting DNA fragments are sequenced and mapped to the reference genome to determine overall enrichment. Here we describe a method of ChIP-seq for investigating protein-DNA interactions in the filamentous fungus Neurospora crassa.
Keywords: Chromatin immunoprecipitation; Histone modifications; Protein–DNA interactions; Transcription factor binding.