Jumonji, Japanese for cruciform, was originally named for the appearance of the neural plates in jumonji mutant nice, and means cruciform in Japanese. Within the protein, jumonji contains an AT-rich interacting domain, a jmjN domain, and a jmjC domain. Since the discovery of this gene, jmjC domains have been found in over 100 other proteins, and are evolutionarily conserved from human to yeast. JmjC domains play a role in stem cell differentiation and renewal, tumor suppression, obesity resistance, and gene expression.

Recently, some jumonji family members have been identified as histone demethylases. Jumonji member JMJD1A specifically demethylates mono and dimethyl forms of histone 3 Lysine 9. Another member, JMJD2A also works specifically on H3 Lys9, but in the trimethylated form, along with trimethyl H3 Lys36. JMJD2C also works on these sites, but is specific for the trimethyl forms.