In living cells, meters of DNA must be significantly compacted to fit inside of the tiny compartment in the cell. In eukaryotic cells, the first level of chromosomal compaction occurs by wrapping the DNA around nucleosomes, which are comprised of histone proteins. The histone proteins are important regulatory proteins, as they are involved in the control of DNA replication, recombination, repair and importantly, gene expression. They contain long, highly basic, unstructured N-terminal tails, which are the sites of various post-translational modifications (PTMs). There are ~20 different PTMs that have been identified and described so far, including lysine acylation, phosphorylation, methylation, and ubiquitination. Interestingly, histones and histone-like proteins (functional homologs) have been identified in all domains of life, including the archaea and eubacteria. Many regulatory functions, and even some PTMs are evolutionarily conserved. Histones were initially discovered and identified in the 1880’s, and now there are many techniques available for histone purification and characterization. With the advances in mass spectrometry technology, mapping of PTMs with site specific resolution and determination of stoichiometry have become possible. In addition, new techniques to study chromosome structure and architecture allows for advanced DNA binding studies of histones. The purpose of this methods collection is to create a comprehensive guide on the most up-to-date protocols for purification and functional characterization of histones and histone-like proteins, and to describe new methodologies for studying DNA-histone interactions.