Heterochromatin Profiling in Lymphoma Patient Plasma for the Discovery of Novel Chromatin Variants

摘要: Methods: To address histone modifications linked to heterochromatin domains, we developed a method for comprehensive profiling of H3K27me3 from cf-chromatin. We applied this to conditioned media from SU-DHL-6 (a diffuse large B-cell lymphoma (DLBCL) cell line), and plasma from 78 patients with B-cell lymphomas and 21 non-lymphoma controls. Plasma H3K27me3 profiles were sequenced to a mean of 142.3 million reads, using the Illumina NovaSeq platform. Counts from the sequencing profiles were summarized in 300bp bins, and normalized for library depth. We conducted differential analysis using edgeR. Finally, we assessed the fragment length differences between lymphoma and control plasma H3K27me3 profiles using Picard, and quantified the fraction of fragments 126-135 bp in length (representing the shortened mononucleosome) and 240-330 bp (representing the shortened dinucleosome …