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Elango R, Nilavar NM, Li AG, Nguyen D, Rass E, Duffey EE, Jiang Y, Abakir A, Willis NA, Houseley J, Scully R. Two-ended recombination at a Flp-nickase-broken replication fork. Mol Cell 2024:S1097-2765(24)00911-0. [PMID: 39631396 DOI: 10.1016/j.molcel.2024.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 09/23/2024] [Accepted: 11/07/2024] [Indexed: 12/07/2024]
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Abakir A, Ruzov A. A model for a dual function of N6-methyladenosine in R-loop regulation. Nat Genet 2024;56:1995-1998. [PMID: 39289548 DOI: 10.1038/s41588-024-01905-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
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Shah P, Hill R, Dion C, Clark SJ, Abakir A, Willems J, Arends MJ, Garaycoechea JI, Leitch HG, Reik W, Crossan GP. Primordial germ cell DNA demethylation and development require DNA translesion synthesis. Nat Commun 2024;15:3734. [PMID: 38702312 PMCID: PMC11068800 DOI: 10.1038/s41467-024-47219-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 03/25/2024] [Indexed: 05/06/2024]  Open
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Elango R, Nilavar N, Li AG, Duffey EE, Jiang Y, Nguyen D, Abakir A, Willis NA, Houseley J, Scully R. Two-ended recombination at a Flp-nickase-broken replication fork. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588130. [PMID: 38645103 PMCID: PMC11030319 DOI: 10.1101/2024.04.10.588130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
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Shah P, Hill R, Clark S, Dion C, Abakir A, Arends M, Leitch H, Reik W, Crossan G. Primordial germ cell DNA demethylation and development require DNA translesion synthesis.. [DOI: 10.1101/2023.07.05.547775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2024]
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Vijg J, Schumacher B, Abakir A, Antonov M, Bradley C, Cagan A, Church G, Gladyshev VN, Gorbunova V, Maslov AY, Reik W, Sharifi S, Suh Y, Walsh K. Mitigating age-related somatic mutation burden. Trends Mol Med 2023;29:530-540. [PMID: 37121869 DOI: 10.1016/j.molmed.2023.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 05/02/2023]
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Abakir A, Reik W. Direct methylation sequencing. Nat Chem Biol 2023:10.1038/s41589-023-01356-9. [PMID: 37322154 DOI: 10.1038/s41589-023-01356-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
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Starczak M, Abakir A, Ruzov A, Gackowski D. Detection and Quantification of RNA Modifications on RNA-DNA Hybrids Using SID-UPLC-MS/MS. Methods Mol Biol 2022;2528:127-143. [PMID: 35704189 DOI: 10.1007/978-1-0716-2477-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Abakir A, Alenezi F, Ruzov A. Detecting and Mapping N6-Methyladenosine on RNA/DNA Hybrids. Methods Mol Biol 2022;2528:329-344. [PMID: 35704202 DOI: 10.1007/978-1-0716-2477-7_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
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Blythe MJ, Kocer A, Rubio-Roldan A, Giles T, Abakir A, Ialy-Radio C, Wheldon LM, Bereshchenko O, Bruscoli S, Kondrashov A, Drevet JR, Emes RD, Johnson AD, McCarrey JR, Gackowski D, Olinski R, Cocquet J, Garcia-Perez JL, Ruzov A. LINE-1 transcription in round spermatids is associated with accretion of 5-carboxylcytosine in their open reading frames. Commun Biol 2021;4:691. [PMID: 34099857 PMCID: PMC8184969 DOI: 10.1038/s42003-021-02217-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 05/14/2021] [Indexed: 12/12/2022]  Open
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Abakir A, Giles TC, Cristini A, Foster JM, Dai N, Starczak M, Rubio-Roldan A, Li M, Eleftheriou M, Crutchley J, Flatt L, Young L, Gaffney DJ, Denning C, Dalhus B, Emes RD, Gackowski D, Corrêa IR, Garcia-Perez JL, Klungland A, Gromak N, Ruzov A. N6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells. Nat Genet 2019;52:48-55. [PMID: 31844323 PMCID: PMC6974403 DOI: 10.1038/s41588-019-0549-x] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 11/13/2019] [Indexed: 11/21/2022]
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Gackowski D, Gawronski M, Kerr C, Radivoyevitch T, Zarakowska E, Starczak M, Abakir A, Ruzov A, Maciejewski JP, Olinski R. 5-formylcytosine and 5-hydroxymethyluracil as surrogate markers of TET2 and SF3B1 mutations in myelodysplastic syndrome, respectively. Haematologica 2019;105:e213-e215. [PMID: 31488558 DOI: 10.3324/haematol.2019.224030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]  Open
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Ramsawhook AH, Lewis LC, Eleftheriou M, Abakir A, Durczak P, Markus R, Rajani S, Hannan NRF, Coyle B, Ruzov A. Immunostaining for DNA Modifications: Computational Analysis of Confocal Images. J Vis Exp 2017:56318. [PMID: 28930980 PMCID: PMC5752195 DOI: 10.3791/56318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
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Abakir A, Wheldon L, Johnson AD, Laurent P, Ruzov A. Detection of Modified Forms of Cytosine Using Sensitive Immunohistochemistry. J Vis Exp 2016:54416. [PMID: 27585398 PMCID: PMC5091899 DOI: 10.3791/54416] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
15
Eleftheriou M, Pascual AJ, Wheldon LM, Perry C, Abakir A, Arora A, Johnson AD, Auer DT, Ellis IO, Madhusudan S, Ruzov A. 5-Carboxylcytosine levels are elevated in human breast cancers and gliomas. Clin Epigenetics 2015;7:88. [PMID: 26300993 PMCID: PMC4546187 DOI: 10.1186/s13148-015-0117-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/24/2015] [Indexed: 03/05/2023]  Open
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Wheldon LM, Abakir A, Ferjentsik Z, Dudnakova T, Strohbuecker S, Christie D, Dai N, Guan S, Foster JM, Corrêa IR, Loose M, Dixon JE, Sottile V, Johnson AD, Ruzov A. Transient accumulation of 5-carboxylcytosine indicates involvement of active demethylation in lineage specification of neural stem cells. Cell Rep 2014;7:1353-1361. [PMID: 24882006 DOI: 10.1016/j.celrep.2014.05.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 04/04/2014] [Accepted: 05/02/2014] [Indexed: 01/22/2023]  Open
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Alioui A, Wheldon LM, Abakir A, Ferjentsik Z, Johnson AD, Ruzov A. 5-Carboxylcytosine is localized to euchromatic regions in the nuclei of follicular cells in axolotl ovary. Nucleus 2012;3:565-9. [PMID: 23138778 PMCID: PMC3515539 DOI: 10.4161/nucl.22799] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]  Open
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