Tsimaratou, K.; Corces, V.

Mammalian sperm chromatin carries epigenetic information with the potential to influence offspring phenotype, making its faithful characterization essential. It has been suggested that cauda sperm preparations are contaminated by somatic chromatin, that this contamination dominates genome-wide profiles, and that valid results require pretreatment with somatic cell lysis buffer, DNase I, and dithiothreitol. Here we show that properly purified cauda sperm contain no detectable somatic cells or cell-free DNA and that this pretreatment disrupts sperm chromatin organization. SCLB permeabilizes the sperm nucleus, allowing DNase I to fragment the sperm genome in situ, while DTT treatment causes chromatin to leak out of the nucleus. Using ATAC-see, we further demonstrate that Tn5 transposase can access intact protamine-condensed sperm chromatin without DTT, refuting the premise that profiles from untreated sperm reflect contamination. Pretreatment therefore damages the chromatin it claims to purify, and published profiles of untreated cauda sperm are valid and require no systematic re-examination.