Flap Endonuclease 1 Endonucleolytically Processes RNA to Resolve R-Loops through DNA Base Excision Repair
Flap endonuclease 1 (FEN1) is an essential enzyme that removes RNA primers and base lesions during DNA lagging strand maturation and long-patch base excision repair (BER). It plays a crucial role in maintaining genome stability and integrity. FEN1 is also implicated in RNA processing and biogenesis....
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| Format: | Article |
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MDPI AG
2022-12-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/1/98 |
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| author | Eduardo E. Laverde Aris A. Polyzos Pawlos P. Tsegay Mohammad Shaver Joshua D. Hutcheson Lata Balakrishnan Cynthia T. McMurray Yuan Liu |
| author_facet | Eduardo E. Laverde Aris A. Polyzos Pawlos P. Tsegay Mohammad Shaver Joshua D. Hutcheson Lata Balakrishnan Cynthia T. McMurray Yuan Liu |
| author_sort | Eduardo E. Laverde |
| collection | DOAJ |
| description | Flap endonuclease 1 (FEN1) is an essential enzyme that removes RNA primers and base lesions during DNA lagging strand maturation and long-patch base excision repair (BER). It plays a crucial role in maintaining genome stability and integrity. FEN1 is also implicated in RNA processing and biogenesis. A recent study from our group has shown that FEN1 is involved in trinucleotide repeat deletion by processing the RNA strand in R-loops through BER, further suggesting that the enzyme can modulate genome stability by facilitating the resolution of R-loops. However, it remains unknown how FEN1 can process RNA to resolve an R-loop. In this study, we examined the FEN1 cleavage activity on the RNA:DNA hybrid intermediates generated during DNA lagging strand processing and BER in R-loops. We found that both human and yeast FEN1 efficiently cleaved an RNA flap in the intermediates using its endonuclease activity. We further demonstrated that FEN1 was recruited to R-loops in normal human fibroblasts and senataxin-deficient (AOA2) fibroblasts, and its R-loop recruitment was significantly increased by oxidative DNA damage. We showed that FEN1 specifically employed its endonucleolytic cleavage activity to remove the RNA strand in an R-loop during BER. We found that FEN1 coordinated its DNA and RNA endonucleolytic cleavage activity with the 3′-5′ exonuclease of APE1 to resolve the R-loop. Our results further suggest that FEN1 employed its unique tracking mechanism to endonucleolytically cleave the RNA strand in an R-loop by coordinating with other BER enzymes and cofactors during BER. Our study provides the first evidence that FEN1 endonucleolytic cleavage can result in the resolution of R-loops via the BER pathway, thereby maintaining genome integrity. |
| first_indexed | 2024-03-09T12:37:02Z |
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| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T12:37:02Z |
| publishDate | 2022-12-01 |
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| record_format | Article |
| series | Genes |
| spelling | doaj.art-86a35943ac4a4fd8aa36f2fec4d504072023-11-30T22:23:30ZengMDPI AGGenes2073-44252022-12-011419810.3390/genes14010098Flap Endonuclease 1 Endonucleolytically Processes RNA to Resolve R-Loops through DNA Base Excision RepairEduardo E. Laverde0Aris A. Polyzos1Pawlos P. Tsegay2Mohammad Shaver3Joshua D. Hutcheson4Lata Balakrishnan5Cynthia T. McMurray6Yuan Liu7Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USAMolecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USABiochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USADepartment of Biomedical Engineering, Florida International University, Miami, FL 33199, USADepartment of Biomedical Engineering, Florida International University, Miami, FL 33199, USADepartment of Biology, Indiana-Purdue University, Indianapolis, IN 46202, USAMolecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USABiochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USAFlap endonuclease 1 (FEN1) is an essential enzyme that removes RNA primers and base lesions during DNA lagging strand maturation and long-patch base excision repair (BER). It plays a crucial role in maintaining genome stability and integrity. FEN1 is also implicated in RNA processing and biogenesis. A recent study from our group has shown that FEN1 is involved in trinucleotide repeat deletion by processing the RNA strand in R-loops through BER, further suggesting that the enzyme can modulate genome stability by facilitating the resolution of R-loops. However, it remains unknown how FEN1 can process RNA to resolve an R-loop. In this study, we examined the FEN1 cleavage activity on the RNA:DNA hybrid intermediates generated during DNA lagging strand processing and BER in R-loops. We found that both human and yeast FEN1 efficiently cleaved an RNA flap in the intermediates using its endonuclease activity. We further demonstrated that FEN1 was recruited to R-loops in normal human fibroblasts and senataxin-deficient (AOA2) fibroblasts, and its R-loop recruitment was significantly increased by oxidative DNA damage. We showed that FEN1 specifically employed its endonucleolytic cleavage activity to remove the RNA strand in an R-loop during BER. We found that FEN1 coordinated its DNA and RNA endonucleolytic cleavage activity with the 3′-5′ exonuclease of APE1 to resolve the R-loop. Our results further suggest that FEN1 employed its unique tracking mechanism to endonucleolytically cleave the RNA strand in an R-loop by coordinating with other BER enzymes and cofactors during BER. Our study provides the first evidence that FEN1 endonucleolytic cleavage can result in the resolution of R-loops via the BER pathway, thereby maintaining genome integrity.https://www.mdpi.com/2073-4425/14/1/98flap endonuclease 1 (FEN1)R-loopbase excision repair (BER) |
| spellingShingle | Eduardo E. Laverde Aris A. Polyzos Pawlos P. Tsegay Mohammad Shaver Joshua D. Hutcheson Lata Balakrishnan Cynthia T. McMurray Yuan Liu Flap Endonuclease 1 Endonucleolytically Processes RNA to Resolve R-Loops through DNA Base Excision Repair Genes flap endonuclease 1 (FEN1) R-loop base excision repair (BER) |
| title | Flap Endonuclease 1 Endonucleolytically Processes RNA to Resolve R-Loops through DNA Base Excision Repair |
| title_full | Flap Endonuclease 1 Endonucleolytically Processes RNA to Resolve R-Loops through DNA Base Excision Repair |
| title_fullStr | Flap Endonuclease 1 Endonucleolytically Processes RNA to Resolve R-Loops through DNA Base Excision Repair |
| title_full_unstemmed | Flap Endonuclease 1 Endonucleolytically Processes RNA to Resolve R-Loops through DNA Base Excision Repair |
| title_short | Flap Endonuclease 1 Endonucleolytically Processes RNA to Resolve R-Loops through DNA Base Excision Repair |
| title_sort | flap endonuclease 1 endonucleolytically processes rna to resolve r loops through dna base excision repair |
| topic | flap endonuclease 1 (FEN1) R-loop base excision repair (BER) |
| url | https://www.mdpi.com/2073-4425/14/1/98 |
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