An initiator RNA (iRNA) is required to prime cellular DNA synthesis. The 
structure of double-stranded DNA allows the synthesis of one strand to be 
continuous but the other must be generated discontinuously. Frequent priming of 
the discontinuous strand results in the formation of many small segments, 
designated Okazaki fragments. These short pieces need to be processed and joined 
to form an intact DNA strand. Our knowledge of the mechanism of iRNA removal is 
still evolving. Early reconstituted systems suggesting that the removal of iRNA 
requires sequential action of RNase H and flap endonuclease 1 (FEN1) led to the 
RNase H/FEN1 model. However, genetic analyses implied that Dna2p, an essential 
helicase/nuclease, is required. Subsequent biochemical studies suggested 
sequential action of RPA, Dna2p, and FEN1 for iRNA removal, leading to the 
second model, the Dna2p/RPA/FEN1 model. Studies of strand-displacement synthesis 
by polymerase delta indicated that in a reconstituted system, FEN1 could act as 
soon as short flaps are created, giving rise to a third model, the FEN1-only 
model. Each of the three pathways is supported by different genetic and 
biochemical results. Properties of the major protein components in this process 
will be discussed, and the validity of each model as a true representation of 
Okazaki fragment processing will be critically evaluated in this review.