The N-terminal tail of histone H2A binds to two distinct sites within the nucleosome core

Each of the core histone proteins within the nucleosome has a central “structured” domain that comprises the spool onto which the DNA superhelix is wrapped and an N-terminal “tail” domain in which the structure and molecular interactions have not been rigorously defined. Recent studies have shown that the N-terminal domains of core histones probably contact both DNA and proteins within the nucleus and that these interactions play key roles in the regulation of nuclear processes (such as transcription and replication) and are critical in the formation of the chromatin fiber. An understanding of these complex mechanisms awaits identification of the DNA or protein sites within chromatin contacted by the tail domains. To this end, we have developed a site-specific histone protein–DNA photocross-linking method to identify the DNA binding sites of the N-terminal domains within chromatin complexes. With this approach, we demonstrate that the N-terminal tail of H2A binds DNA at two defined locations within isolated nucleosome cores centered around a position ≈40 bp from the nucleosomal dyad and that this tail probably adopts a defined structure when bound to DNA.