biostudies-literaturePike JENIGMS NIH HHS41712-23https://www.ebi.ac.uk/biostudies/studies/S-EPMC3009898biostudies-literatureUnknown285(53)Two pathways have been proposed for eukaryotic Okazaki fragment RNA primer removal. Results presented here provide evidence for an alternative pathway. Primer extension by DNA polymerase δ (pol δ) displaces the downstream fragment into an RNA-initiated flap. Most flaps are cleaved by flap endonuclease 1 (FEN1) while short, and the remaining nicks joined in the first pathway. A small fraction escapes immediate FEN1 cleavage and is further lengthened by Pif1 helicase. Long flaps are bound by replication protein A (RPA), which inhibits FEN1. In the second pathway, Dna2 nuclease cleaves an RPA-bound flap and displaces RPA, leaving a short flap for FEN1. Pif1 flap lengthening creates a requirement for Dna2. This relationship should not have evolved unless Pif1 had an important role in fragment The Journal of biological chemistryAn alternative pathway for Okazaki fragment processing: resolution of fold-back flaps by Pif1 helicase.PMC3009898R01 GM032431GM024441GM078666R01 GM078666GM032431R01 GM024441Pike JEHenry RABambara RACampbell JLBurgers PMfalseAn alternative pathway for Okazaki fragment processing: resolution of fold-back flaps by Pif1 helicase.Two pathways have been proposed for eukaryotic Okazaki fragment RNA primer removal. Results presented here provide evidence for an alternative pathway. Primer extension by DNA polymerase δ (pol δ) displaces the downstream fragment into an RNA-initiated flap. Most flaps are cleaved by flap endonuclease 1 (FEN1) while short, and the remaining nicks joined in the first pathway. A small fraction escapes immediate FEN1 cleavage and is further lengthened by Pif1 helicase. Long flaps are bound by replication protein A (RPA), which inhibits FEN1. In the second pathway, Dna2 nuclease cleaves an RPA-bound flap and displaces RPA, leaving a short flap for FEN1. Pif1 flap lengthening creates a requirement for Dna2. This relationship should not have evolved unless Pif1 had an important role in fragment 2010-01-01T00:00:00Z2010 Dec2025-04-04T20:12:45.035Z2019-03-27T00:37:40ZS-EPMC30098982095945410.1074/jbc.m110.14689410.1074/jbc.M110.146894