This paper describes an approach to annotating noun incorporation in Universal Dependencies. It motivates the need to annotate this particular morphosyntactic phenomenon and justifies it with respect to frequency of the construction. A case study is presented in which the proposed annotation scheme is applied to Chukchi, a language that exhibits noun incorporation. We compare argument encoding in Chukchi, English and Russian and find that while in English and Russian discourse elements are primarily tracked through noun phrases and pronouns, in Chukchi they are tracked through agreement marking and incorporation, with a lesser role for noun phrases.