Daniel F. Bogenhagen - Publications

Affiliations: 
Stony Brook University, Stony Brook, NY, United States 
Area:
Molecular Biology, Biochemistry

80 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Lee KW, Bogenhagen DF. Scalable Isolation of Mammalian Mitochondria for Nucleic Acid and Nucleoid Analysis. Methods in Molecular Biology (Clifton, N.J.). 1351: 67-79. PMID 26530675 DOI: 10.1007/978-1-4939-3040-1_6  1
2014 Lee KW, Bogenhagen DF. Assignment of 2'-O-methyltransferases to modification sites on the mammalian mitochondrial large subunit 16 S ribosomal RNA (rRNA). The Journal of Biological Chemistry. 289: 24936-42. PMID 25074936 DOI: 10.1074/jbc.C114.581868  1
2014 Bogenhagen DF, Martin DW, Koller A. Initial steps in RNA processing and ribosome assembly occur at mitochondrial DNA nucleoids. Cell Metabolism. 19: 618-29. PMID 24703694 DOI: 10.1016/j.cmet.2014.03.013  1
2013 Lee KW, Okot-Kotber C, LaComb JF, Bogenhagen DF. Mitochondrial ribosomal RNA (rRNA) methyltransferase family members are positioned to modify nascent rRNA in foci near the mitochondrial DNA nucleoid. The Journal of Biological Chemistry. 288: 31386-99. PMID 24036117 DOI: 10.1074/jbc.M113.515692  1
2013 Lu B, Lee J, Nie X, Li M, Morozov YI, Venkatesh S, Bogenhagen DF, Temiakov D, Suzuki CK. Phosphorylation of human TFAM in mitochondria impairs DNA binding and promotes degradation by the AAA+ Lon protease. Molecular Cell. 49: 121-32. PMID 23201127 DOI: 10.1016/j.molcel.2012.10.023  1
2012 Bogenhagen DF. Mitochondrial DNA nucleoid structure. Biochimica Et Biophysica Acta. 1819: 914-20. PMID 22142616 DOI: 10.1016/j.bbagrm.2011.11.005  1
2011 Brown TA, Tkachuk AN, Shtengel G, Kopek BG, Bogenhagen DF, Hess HF, Clayton DA. Superresolution fluorescence imaging of mitochondrial nucleoids reveals their spatial range, limits, and membrane interaction. Molecular and Cellular Biology. 31: 4994-5010. PMID 22006021 DOI: 10.1128/MCB.05694-11  1
2010 Bogenhagen DF. Does mtDNA nucleoid organization impact aging? Experimental Gerontology. 45: 473-7. PMID 20004238 DOI: 10.1016/j.exger.2009.12.002  1
2009 Bogenhagen DF. Biochemical isolation of mtDNA nucleoids from animal cells. Methods in Molecular Biology (Clifton, N.J.). 554: 3-14. PMID 19513664 DOI: 10.1007/978-1-59745-521-3_1  1
2008 Zheng L, Zhou M, Guo Z, Lu H, Qian L, Dai H, Qiu J, Yakubovskaya E, Bogenhagen DF, Demple B, Shen B. Human DNA2 is a mitochondrial nuclease/helicase for efficient processing of DNA replication and repair intermediates. Molecular Cell. 32: 325-36. PMID 18995831 DOI: 10.1016/j.molcel.2008.09.024  1
2008 Liu P, Qian L, Sung JS, de Souza-Pinto NC, Zheng L, Bogenhagen DF, Bohr VA, Wilson DM, Shen B, Demple B. Removal of oxidative DNA damage via FEN1-dependent long-patch base excision repair in human cell mitochondria. Molecular and Cellular Biology. 28: 4975-87. PMID 18541666 DOI: 10.1128/MCB.00457-08  1
2008 Bogenhagen DF, Rousseau D, Burke S. The layered structure of human mitochondrial DNA nucleoids. The Journal of Biological Chemistry. 283: 3665-75. PMID 18063578 DOI: 10.1074/jbc.M708444200  1
2008 Watkins J, Basu S, Bogenhagen DF. A quantitative proteomic analysis of mitochondrial participation in p19 cell neuronal differentiation. Journal of Proteome Research. 7: 328-38. PMID 18034457 DOI: 10.1021/pr070300g  1
2007 Yakubovskaya E, Lukin M, Chen Z, Berriman J, Wall JS, Kobayashi R, Kisker C, Bogenhagen DF. The EM structure of human DNA polymerase gamma reveals a localized contact between the catalytic and accessory subunits. The Embo Journal. 26: 4283-91. PMID 17762861 DOI: 10.1038/sj.emboj.7601843  1
2007 Sheehan JJ, Zhou C, Gravanis I, Rogove AD, Wu YP, Bogenhagen DF, Tsirka SE. Proteolytic activation of monocyte chemoattractant protein-1 by plasmin underlies excitotoxic neurodegeneration in mice. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 27: 1738-45. PMID 17301181 DOI: 10.1523/JNEUROSCI.4987-06.2007  1
2006 Wang Y, Bogenhagen DF. Human mitochondrial DNA nucleoids are linked to protein folding machinery and metabolic enzymes at the mitochondrial inner membrane. The Journal of Biological Chemistry. 281: 25791-802. PMID 16825194 DOI: 10.1074/jbc.M604501200  1
2006 Basu S, Bremer E, Zhou C, Bogenhagen DF. MiGenes: a searchable interspecies database of mitochondrial proteins curated using gene ontology annotation. Bioinformatics (Oxford, England). 22: 485-92. PMID 16368773 DOI: 10.1093/bioinformatics/btk009  1
2006 Yakubovskaya E, Chen Z, Carrodeguas JA, Kisker C, Bogenhagen DF. Functional human mitochondrial DNA polymerase gamma forms a heterotrimer. The Journal of Biological Chemistry. 281: 374-82. PMID 16263719 DOI: 10.1074/jbc.M509730200  1
2006 Pinz KG, Bogenhagen DF. The influence of the DNA polymerase gamma accessory subunit on base excision repair by the catalytic subunit. Dna Repair. 5: 121-8. PMID 16202665 DOI: 10.1016/j.dnarep.2005.08.014  1
2003 Bogenhagen DF, Wang Y, Shen EL, Kobayashi R. Protein components of mitochondrial DNA nucleoids in higher eukaryotes. Molecular & Cellular Proteomics : McP. 2: 1205-16. PMID 14514796 DOI: 10.1074/mcp.M300035-MCP200  1
2003 Bogenhagen DF, Clayton DA. Concluding remarks: The mitochondrial DNA replication bubble has not burst. Trends in Biochemical Sciences. 28: 404-5. PMID 12932727 DOI: 10.1016/S0968-0004(03)00165-8  1
2003 Bogenhagen DF, Clayton DA. The mitochondrial DNA replication bubble has not burst. Trends in Biochemical Sciences. 28: 357-60. PMID 12878002 DOI: 10.1016/S0968-0004(03)00132-4  1
2002 Carrodeguas JA, Pinz KG, Bogenhagen DF. DNA binding properties of human pol gammaB. The Journal of Biological Chemistry. 277: 50008-14. PMID 12379656 DOI: 10.1074/jbc.M207030200  1
2002 Bogenhagen DF. Purification of mitochondria for enzymes involved in nucleic acid transactions. Methods in Molecular Biology (Clifton, N.J.). 197: 199-210. PMID 12013797 DOI: 10.1385/1-59259-284-8:199  1
2001 Perez-Jannotti RM, Klein SM, Bogenhagen DF. Two forms of mitochondrial DNA ligase III are produced in Xenopus laevis oocytes. The Journal of Biological Chemistry. 276: 48978-87. PMID 11598119 DOI: 10.1074/jbc.M107177200  1
2001 Bogenhagen DF, Pinz KG, Perez-Jannotti RM. Enzymology of mitochondrial base excision repair. Progress in Nucleic Acid Research and Molecular Biology. 68: 257-71. PMID 11554302  1
2001 Shen EL, Bogenhagen DF. Developmentally-regulated packaging of mitochondrial DNA by the HMG-box protein mtTFA during Xenopus oogenesis. Nucleic Acids Research. 29: 2822-8. PMID 11433028  1
2001 Carrodeguas JA, Theis K, Bogenhagen DF, Kisker C. Crystal structure and deletion analysis show that the accessory subunit of mammalian DNA polymerase γ, PolγB, functions as a homodimer Molecular Cell. 7: 43-54. PMID 11172710 DOI: 10.1016/S1097-2765(01)00153-8  1
2000 Pinz KG, Bogenhagen DF. Characterization of a catalytically slow AP lyase activity in DNA polymerase γ and other family A DNA polymerases Journal of Biological Chemistry. 275: 12509-12514. PMID 10777538 DOI: 10.1074/jbc.275.17.12509  1
2000 Carrodeguas JA, Bogenhagen DF. Protein sequences conserved in prokaryotic aminoacyl-tRNA synthetases are important for the activity of the processivity factor of human mitochondrial DNA polymerase Nucleic Acids Research. 28: 1237-1244. PMID 10666468  1
1999 Carrodeguas JA, Kobayashi R, Lim SE, Copeland WC, Bogenhagen DF. The accessory subunit of Xenopus laevis mitochondrial DNA polymerase γ increases processivity of the catalytic subunit of human DNA polymerase γ and is related to class II aminoacyl-tRNA synthetases Molecular and Cellular Biology. 19: 4039-4046. PMID 10330144  1
1999 Bogenhagen DF. Repair of mtDNA in vertebrates American Journal of Human Genetics. 64: 1276-1251. PMID 10205257 DOI: 10.1086/302392  1
1998 Bogenhagen DF, Pinz KG. The action of DNA ligase at abasic sites in DNA Journal of Biological Chemistry. 273: 7888-7893. PMID 9525883 DOI: 10.1074/jbc.273.14.7888  1
1998 Pinz KG, Bogenhagen DF. Efficient repair of abasic sites in DNA by mitochondrial enzymes Molecular and Cellular Biology. 18: 1257-1265. PMID 9488440  1
1997 Antoshechkin I, Bogenhagen DF, Mastrangelo IA. The HMG-box mitochondrial transcription factor xl-mtTFA binds DNA as a tetramer to activate bidirectional transcription Embo Journal. 16: 3198-3206. PMID 9214636 DOI: 10.1093/emboj/16.11.3198  1
1996 Carrodeguas JA, Yun S, Shadel GS, Clayton DA, Bogenhagen DF. Functional conservation of yeast mtTFB despite extensive sequence divergence. Gene Expression. 6: 219-30. PMID 9196077  1
1996 Mikhailovi VS, Bogenhagen DF. Termination within oligo(dT) tracts in template DNA by DNA polymerase γ occurs with formation of a DNA triplex structure and is relieved by mitochondrial single-stranded DNA-binding protein Journal of Biological Chemistry. 271: 30774-30780. PMID 8940057 DOI: 10.1074/jbc.271.48.30774  1
1996 Pandit SD, Richard RE, Sternglanz R, Bogenhagen DF. Cloning and characterization of the gene for the somatic form of DNA topoisomerase I from Xenopus laevis Nucleic Acids Research. 24: 3593-3600. PMID 8836188  1
1996 Mikhailov VS, Bogenhagen DF. Effects of Xenopus laevis mitochondrial single-stranded DNA-binding protein on primer-template binding and 3'→5' exonuclease activity of DNA polymerase γ Journal of Biological Chemistry. 271: 18939-18946. PMID 8702557 DOI: 10.1074/jbc.271.31.18939  1
1996 Bogenhagen DF. Interaction of mtTFB and mtRNA polymerase at core promoters for transcription of Xenopus laevis mtDNA Journal of Biological Chemistry. 271: 12036-12041. PMID 8662670  1
1996 Ye F, Carrodeguas JA, Bogenhagen DF. The γ subfamily of DNA polymerases: Cloning of a developmentally regulated cDNA encoding Xenopus laevis mitochondrial DNA polymerase γ Nucleic Acids Research. 24: 1481-1488. PMID 8628681 DOI: 10.1093/nar/24.8.1481  1
1995 Antoshechkin I, Bogenhagen DF. Distinct roles for two purified factors in transcription of Xenopus mitochondrial DNA Molecular and Cellular Biology. 15: 7032-7042. PMID 8524270  1
1995 Pinz KG, Shibutani S, Bogenhagen DF. Action of mitochondrial DNA polymerase γ at sites of base loss or oxidative damage Journal of Biological Chemistry. 270: 9202-9206. PMID 7721837 DOI: 10.1074/jbc.270.16.9202  1
1994 Matsumoto Y, Kim K, Bogenhagen DF. Proliferating cell nuclear antigen-dependent abasic site repair in Xenopus laevis oocytes: An alternative pathway of base excision DNA repair Molecular and Cellular Biology. 14: 6187-6197. PMID 7915006  1
1993 Chen YH, Bogenhagen DF. Effects of DNA lesions on transcription elongation by T7 RNA polymerase Journal of Biological Chemistry. 268: 5849-5855. PMID 8449951  1
1993 Bogenhagen DF. Proteolytic footprinting of transcription factor TFIIIA reveals different tightly binding sites for 5S RNA and 5S DNA Molecular and Cellular Biology. 13: 5149-5158. PMID 7689146  1
1992 Bogenhagen DF, Sands MS. Binding of TFIIIA to derivatives of 5S RNA containing sequence substitutions or deletions defines a minimal TFIIIA binding site. Nucleic Acids Research. 20: 2639-45. PMID 1614850 DOI: 10.1093/nar/20.11.2639  1
1991 Chen YH, Matsumoto Y, Shibutani S, Bogenhagen DF. Acetylaminofluorene and aminofluorene adducts inhibit in vitro transcription of a Xenopus 5S RNA gene only when located on the coding strand Proceedings of the National Academy of Sciences of the United States of America. 88: 9583-9587. PMID 1946373  1
1991 Matsumoto Y, Bogenhagen DF. Repair of a synthetic abasic site involves concerted reactions of DNA synthesis followed by excision and ligation Molecular and Cellular Biology. 11: 4441-4447. PMID 1875931  1
1991 Sands MS, Bogenhagen DF. Two zinc finger proteins from Xenopus laevis bind the same region of 5S RNA but with different nuclease protection patterns. Nucleic Acids Research. 19: 1797-803. PMID 1827670 DOI: 10.1093/nar/19.8.1797  1
1991 Sands MS, Bogenhagen DF. The carboxyterminal zinc fingers of TFIIIA interact with the tip of helix V of 5S RNA in the 7S ribonucleoprotein particle. Nucleic Acids Research. 19: 1791-6. PMID 1827669 DOI: 10.1093/nar/19.8.1791  1
1991 Richard RE, Bogenhagen DF. The 165-kDa DNA topoisomerase I from Xenopus laevis oocytes is a tissue-specific variant Developmental Biology. 146: 4-11. PMID 1647991 DOI: 10.1016/0012-1606(91)90441-5  1
1990 Bogenhagen DF, Morvillo MV. Mapping light strand transcripts near the origin of replication of Xenopus laevis; mitochondrial DNA Nucleic Acids Research. 18: 6377-6383. PMID 1700855 DOI: 10.1093/nar/18.21.6377  1
1989 Matsumoto Y, Bogenhagen DF. Repair of a synthetic abasic site in DNA in a Xenopus laevis oocyte extract Molecular and Cellular Biology. 9: 3750-3757. PMID 2779565  1
1989 Insdorf NF, Bogenhagen DF. DNA polymerase γ from Xenopus laevis. II. A 3' → 5' exonuclease is tightly associated with the DNA polymerase activity Journal of Biological Chemistry. 264: 21498-21503. PMID 2600078  1
1989 Insdorf NF, Bogenhagen DF. DNA polymerase γ from Xenopus laevis. I. The identification of a high molecular weight catalytic subunit by a novel DNA polymerase photolabeling procedure Journal of Biological Chemistry. 264: 21491-21497. PMID 2600077  1
1989 Luke M, Bogenhagen DF. Quantitation of type II topoisomerase in oocytes and eggs of Xenopus laevis Developmental Biology. 136: 459-468. PMID 2555235 DOI: 10.1016/0012-1606(89)90271-6  1
1989 Richard RE, Bogenhagen DF. A high molecular weight topoisomerase I from Xenopus laevis ovaries Journal of Biological Chemistry. 264: 4704-4709. PMID 2538454  1
1988 Bogenhagen DF, Romanelli MF. Template sequences required for transcription of Xenopus laevis mitochondrial DNA from two bidirectional promoters Molecular and Cellular Biology. 8: 2917-2924. PMID 3405223  1
1988 McConkey GA, Bogenhagen DF. TFIIIA binds with equal affinity to somatic and major oocyte 5S RNA genes Genes & Development. 2: 205-214. PMID 3360323  1
1988 Bogenhagen DF, Insdorf NF. Purification of Xenopus laevis mitochondrial RNA polymerase and identification of a dissociable factor required for specific transcription Molecular and Cellular Biology. 8: 2910-2916. PMID 2457154  1
1987 McConkey GA, Bogenhagen DF. Transition mutations within the Xenopus borealis somatic 5S RNA gene can have independent effects on transcription and TFIIIA binding Molecular and Cellular Biology. 7: 486-494. PMID 3561399  1
1987 Sands MS, Bogenhagen DF. TFIIIA binds to different domains of 5S RNA and the Xenopus borealis 5S RNA gene. Molecular and Cellular Biology. 7: 3985-93. PMID 3431548  1
1986 Bogenhagen DF, Yoza BK. Accurate in vitro transcription of Xenopus laevis mitochondrial DNA from two bidirectional promoters Molecular and Cellular Biology. 6: 2543-2550. PMID 3023938  1
1986 Bogenhagen DF, Yoza BK, Cairns SS. Identification of initiation sites for transcription of Xenopus laevis mitochondrial DNA Journal of Biological Chemistry. 261: 8488-8494. PMID 3013854  1
1986 Cairns SS, Bogenhagen DF. Mapping of the displacement loop within the nucleotide sequence of Xenopus laevis mitochondrial DNA Journal of Biological Chemistry. 261: 8481-8487. PMID 2424898  1
1985 Bogenhagen DF. The intragenic control region of the Xenopus 5 S RNA gene contains two factor A binding domains that must be aligned properly for efficient transcription initiation Journal of Biological Chemistry. 260: 6466-6471. PMID 2581955  1
1984 Hanas JS, Bogenhagen DF, Wu CW. Binding of Xenopus transcription factor a to 5S RNA and to single stranded DNA Nucleic Acids Research. 12: 2745-2758. PMID 6369252 DOI: 10.1093/nar/12.6.2745  1
1984 Yoza BK, Bogenhagen DF. Identification and in vitro capping of a primary transcript of human mitochondrial DNA Journal of Biological Chemistry. 259: 3909-3915. PMID 6323446  1
1984 Bogenhagen DF, Applegate EF, Yoza BK. Identification of a promoter for transcription of the heavy strand of human mtDNA: In vitro transcription and deletion mutagenesis Cell. 36: 1105-1113. PMID 6323020 DOI: 10.1016/0092-8674(84)90061-8  1
1984 Hanas JS, Bogenhagen DF, Wu CW. DNA unwinding ability of Xenopus transcription factor A Nucleic Acids Research. 12: 1265-1276. PMID 6320121 DOI: 10.1093/nar/12.2.1265  1
1983 Hanas JS, Bogenhagen DF, Wu CW. Cooperative model for the binding of Xenopus transcription factor A to the 5S RNA gene Proceedings of the National Academy of Sciences of the United States of America. 80: 2142-2145. PMID 6572967  1
1983 Gearhart PJ, Bogenhagen DF. Clusters of point mutations are found exclusively around rearranged antibody variable genes Proceedings of the National Academy of Sciences of the United States of America. 80: 3439-3443. PMID 6222379  1
1983 Hanas JS, Hazuda DJ, Bogenhagen DF, Wu FY, Wu CW. Xenopus transcription factor A requires zinc for binding to the 5 S RNA gene Journal of Biological Chemistry. 258: 14120-14125. PMID 6196359  1
1983 Cozzarelli NR, Gerrard SP, Schlissel M, Brown DD, Bogenhagen DF. Purified RNA polymerase III accurately and efficiently terminates transcription of 5S RNA genes. Cell. 34: 829-35. PMID 6194892 DOI: 10.1016/0092-8674(83)90540-8  1
1982 Bogenhagen DF, Wormington WM, Brown DD. Stable transcription complexes of Xenopus 5S RNA genes: a means to maintain the differentiated state. Cell. 28: 413-21. PMID 7060135 DOI: 10.1016/0092-8674(82)90359-2  1
1981 Bogenhagen DF, Brown DD. Nucleotide sequences in Xenopus 5S DNA required for transcription termination. Cell. 24: 261-70. PMID 6263489 DOI: 10.1016/0092-8674(81)90522-5  1
1981 Wormington WM, Bogenhagen DF, Jordan E, Brown DD. A quantitative assay for Xenopus 5S RNA gene transcription in vitro. Cell. 24: 809-17. PMID 6166388 DOI: 10.1016/0092-8674(81)90106-9  1
1980 Bogenhagen DF, Sakonju S, Brown DD. A control region in the center of the 5S RNA gene directs specific initiation of transcription: II. The 3' border of the region. Cell. 19: 27-35. PMID 7357604 DOI: 10.1016/0092-8674(80)90385-2  1
1980 Sakonju S, Bogenhagen DF, Brown DD. A control region in the center of the 5S RNA gene directs specific initiation of transcription: I. The 5' border of the region. Cell. 19: 13-25. PMID 7357599 DOI: 10.1016/0092-8674(80)90384-0  1
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