2023
69. Lee, S.-Y., Miller K.M. & Kim, J.-J. (2023). Clinical and Mechanistic Implications of R-Loops in Human Leukemias. Int. J. Mol. Sci. 24, 5966. DOI: org/10.3390/ijms24065966 ,
2022
68. Kaminski, N., Wondisform, A.R., Kwon, Y., Lynskey, M., Bhargava, R., Barroso-González, J., García-Expósito, L., He, B., Xu, M., Mellacheruvu, D., Watkins, S.C., Modesti, M., Miller, K.M., Nesvizhskii, A.I., Zhang, H., Sung, P., & O'Sullivan, R.J. (2022) RAD51AP1 regulates ALT-HDR through chromatin-directed homeostasis of TERRA. Molecular Cell. DOI: 10.1016/j.molcel.2022.09.025
67. Lee, S.Y., Kim, J.J.* & Miller, K.M.* (2022) Single-Cell Analysis of Histone Acetylation Dynamics at Replication Forks Using PLA and SIRF. Methods in Molecular Biology. DOI: 10.1007/978-1-0716-2788-4_23
66. Bokahari, R.S., Beheshti, A., Blutt, S.E., Bowles, D.E., Brenner, D., Britton, R., Bronk, L., Cao, X., Chatterjee, A., Clay D.E., Courtney, C., Fox, D.T., Gaber, M.W,. Gerecht, S., Grabham, P., Grosshans, D, Guan, F., Jezuit, E.A., Kirsch D.G., Zhandong L., Maletic-Savatic, M., Miller K.M., Montague R.A., Nagpal, P., Osenberg, S., Parkitny, L., Pierce, N.A., Porada, C., Rosenberg, S.M., Sargunas, P., Sharma, S., Spangler, J., Tavakol, D.N., Thomas, D., Vunjak-Novakovic. G., Wang, C., Whitcomb, L., Young, D.W., Donoviel, D. (2022) Looking on the Horizon; Potential and Unique Approaches to Developing Radiation Countermeasures for Deep Space Travel, Life Sciences in Space Research. DOI: https://doi.org/10.1016/j.lssr.2022.08.003
65. Sanchez, A., Buck-Koehntop, B.*, Miller K.M.* (2022) Joining the PARty: PARP Regulation of KDM5A during DNA Repair (and Transcription?). BioEssays. (*co-corresponding authors) DOI: 10.1002/bies.202200015
64. Oberdoerffer, P.*, Miller K.M.* (2022) Histone H2A variants: Diversifying chromatin to ensure genome integrity. Seminars in Cell & Developmental Biology (In Press; *co-corresponding authors) DOI: 10.1016/j.semcdb.2022.03.011
63. Lee D., Apelt K., Lee S., Chan, H., Luijsterburg M.S., Leung J.W.C.*, Miller K.M.* ZMYM2 restricts 53BP1 at DNA double-
strand breaks to favor BRCA1 loading and homologous recombination. Nucleic Acids Research,(2022);, gkac160. (*co-corresponding authors) DOI: 10.1093/nar/gkac160 ,
67. Lee, S.Y., Kim, J.J.* & Miller, K.M.* (2022) Single-Cell Analysis of Histone Acetylation Dynamics at Replication Forks Using PLA and SIRF. Methods in Molecular Biology. DOI: 10.1007/978-1-0716-2788-4_23
66. Bokahari, R.S., Beheshti, A., Blutt, S.E., Bowles, D.E., Brenner, D., Britton, R., Bronk, L., Cao, X., Chatterjee, A., Clay D.E., Courtney, C., Fox, D.T., Gaber, M.W,. Gerecht, S., Grabham, P., Grosshans, D, Guan, F., Jezuit, E.A., Kirsch D.G., Zhandong L., Maletic-Savatic, M., Miller K.M., Montague R.A., Nagpal, P., Osenberg, S., Parkitny, L., Pierce, N.A., Porada, C., Rosenberg, S.M., Sargunas, P., Sharma, S., Spangler, J., Tavakol, D.N., Thomas, D., Vunjak-Novakovic. G., Wang, C., Whitcomb, L., Young, D.W., Donoviel, D. (2022) Looking on the Horizon; Potential and Unique Approaches to Developing Radiation Countermeasures for Deep Space Travel, Life Sciences in Space Research. DOI: https://doi.org/10.1016/j.lssr.2022.08.003
65. Sanchez, A., Buck-Koehntop, B.*, Miller K.M.* (2022) Joining the PARty: PARP Regulation of KDM5A during DNA Repair (and Transcription?). BioEssays. (*co-corresponding authors) DOI: 10.1002/bies.202200015
64. Oberdoerffer, P.*, Miller K.M.* (2022) Histone H2A variants: Diversifying chromatin to ensure genome integrity. Seminars in Cell & Developmental Biology (In Press; *co-corresponding authors) DOI: 10.1016/j.semcdb.2022.03.011
63. Lee D., Apelt K., Lee S., Chan, H., Luijsterburg M.S., Leung J.W.C.*, Miller K.M.* ZMYM2 restricts 53BP1 at DNA double-
strand breaks to favor BRCA1 loading and homologous recombination. Nucleic Acids Research,(2022);, gkac160. (*co-corresponding authors) DOI: 10.1093/nar/gkac160 ,
2021
62. Sanchez, A., Lee, D., Kim, D. and Miller, K.M. (2021) Making Connections: Integrative Signaling Mechanisms Coordinate DNA Break Repair in Chromatin. Front. Genet. 12:747734. DOI: 10.3389/fgene.2021.747734
61. Lee, S.Y., Kim, J.J. & Miller, K.M. (2021) Bromodomain proteins: protectors against endogenous DNA damage and facilitators of genome integrity. Exp Mol Med. DOI: 10.1038/s12276-021-00673-0
60. Kumbhar, R., Sanchez, A. Perren, J., Gong, F., Corujo, D., Medina, F., Devanathan S.K., Xhemalce, B., Matouschek, A., Buschbeck, M., Buck-Koehntop, B, Miller, K.M. (2021) Poly(ADP-ribose)-binding and macroH2A mediate recruitment and functions of KDM5A at DNA lesions, Journal of Cell Biology. 220(7): e202006149. PMCID: PMC8135068 DOI: 10.1083/jcb.202006149
59. Ren, W.*, Fan, H.*, Grimm, S.A., Kim, J.J., Li, L., Guo, Y., Petell, C.J., Tan, X.F., Zhang, Z.M., Coan, J.P., Yin, J., Kim, D., Gao, L., Cai, L., Khudaverdyan, N., Çetin, B., Patel, D.J., Wang, Y., Cui, Q., Strahl, B.D., Gozani, O., Miller, K.M., O'Leary, S.E., Wade, P.A. , Wang, G.G., Song, J. (2021) DNMT1 reads heterochromatic H4K20me3 to reinforce DNA methylation of transposons. Nature Communications. 12(1), 2490. (*Co-first author) DOI: 10.1038/s41467-021-22665-4
61. Lee, S.Y., Kim, J.J. & Miller, K.M. (2021) Bromodomain proteins: protectors against endogenous DNA damage and facilitators of genome integrity. Exp Mol Med. DOI: 10.1038/s12276-021-00673-0
60. Kumbhar, R., Sanchez, A. Perren, J., Gong, F., Corujo, D., Medina, F., Devanathan S.K., Xhemalce, B., Matouschek, A., Buschbeck, M., Buck-Koehntop, B, Miller, K.M. (2021) Poly(ADP-ribose)-binding and macroH2A mediate recruitment and functions of KDM5A at DNA lesions, Journal of Cell Biology. 220(7): e202006149. PMCID: PMC8135068 DOI: 10.1083/jcb.202006149
59. Ren, W.*, Fan, H.*, Grimm, S.A., Kim, J.J., Li, L., Guo, Y., Petell, C.J., Tan, X.F., Zhang, Z.M., Coan, J.P., Yin, J., Kim, D., Gao, L., Cai, L., Khudaverdyan, N., Çetin, B., Patel, D.J., Wang, Y., Cui, Q., Strahl, B.D., Gozani, O., Miller, K.M., O'Leary, S.E., Wade, P.A. , Wang, G.G., Song, J. (2021) DNMT1 reads heterochromatic H4K20me3 to reinforce DNA methylation of transposons. Nature Communications. 12(1), 2490. (*Co-first author) DOI: 10.1038/s41467-021-22665-4
2020
58. Lee, S.Y.*, Kim, J.J.*, Miller, K.M. (2020) Emerging roles of RNA modifications in genome integrity, Briefings in Functional Genomics. (*Co-first author) (published advanced online on December 7, 2020) DOI: 10.1093/bfgp/elaa022
57. Kim, J.J.*, Lee, S.Y.*, Choi, J., Woo H.G., Xhemalce, B., Miller, K.M. (2020) PCAF-mediated histone acetylation promotes replication fork degradation by MRE11 and EXO1 in BRCA-deficient cells, Mol Cell. (*Co-first author) (published online September 22, 2020) DOI: 10.1016/j.molcel.2020.08.018
Highlighted in: Leuzzi G, Taglialatela A and Ciccia A. HATtracting Nucleases to Stalled Forks. Molecular Cell 80, Oct 15
56. Sriraman, A., Debnath, T.K., Xhemalce, B., Miller, K.M. (2020) Making it or Breaking it: DNA methylation and Genome Integrity, Essays Biochem. EBC20200009. PMID: 32808652 DOI: doi.org/10.1042/EBC20200009
55. Ren, W., Fan, H., Grimm, S.A., Guo, Y., Kim, J.J., Li, L., Petell, C.J., Tan, X.F., Zhang, Z.M., Coan, J.P., Yin, J., Gao, L., Cai, L., Detrick, B., Cetin, B., Wang, Y., Cui, Q., Strahl, B.D., Gozani, O., Miller, K.M., O’Leary, S.E., Wade, P.A., Patel, D.J., Wang, G.G., Song, J. (2020) Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation, PNAS. (published online July 16, 2020) PMCID: PMC7414182 DOI: 10.1073/pnas.2009316117
57. Kim, J.J.*, Lee, S.Y.*, Choi, J., Woo H.G., Xhemalce, B., Miller, K.M. (2020) PCAF-mediated histone acetylation promotes replication fork degradation by MRE11 and EXO1 in BRCA-deficient cells, Mol Cell. (*Co-first author) (published online September 22, 2020) DOI: 10.1016/j.molcel.2020.08.018
Highlighted in: Leuzzi G, Taglialatela A and Ciccia A. HATtracting Nucleases to Stalled Forks. Molecular Cell 80, Oct 15
56. Sriraman, A., Debnath, T.K., Xhemalce, B., Miller, K.M. (2020) Making it or Breaking it: DNA methylation and Genome Integrity, Essays Biochem. EBC20200009. PMID: 32808652 DOI: doi.org/10.1042/EBC20200009
55. Ren, W., Fan, H., Grimm, S.A., Guo, Y., Kim, J.J., Li, L., Petell, C.J., Tan, X.F., Zhang, Z.M., Coan, J.P., Yin, J., Gao, L., Cai, L., Detrick, B., Cetin, B., Wang, Y., Cui, Q., Strahl, B.D., Gozani, O., Miller, K.M., O’Leary, S.E., Wade, P.A., Patel, D.J., Wang, G.G., Song, J. (2020) Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation, PNAS. (published online July 16, 2020) PMCID: PMC7414182 DOI: 10.1073/pnas.2009316117
2019
54. Kim, J.J.*, Lee, S.Y.*, Gong, F., Battenhouse, A.M., Boutz, D.R., Bashyal, A., Refvik, S.T., Chiang, C-M., Xhemalce, B., Paull, T.T., Brodbelt, J.S., Marcotte, E.M., & Miller, K.M. (2019) Systematic Bromodomain Protein Screens Identify Homologous Recombination and R-Loop Suppression Pathways Involved in Genome Integrity, Genes & Development. Nov 21;33(23-34):1751-74. (*Co-first author). PMCID: PMC6942044 DOI: 10.1101/gad.331231.119
53. Pudget, N., Miller, K.M.^ and Legube G.^ (2019) Non-canonical DNA/RNA structures during Transcription-Coupled Double-Strand Break Repair: Roadblocks or Bona fide repair intermediates, DNA Repair. Sep;81:102661. (^co-corresponding authors).
PMCID: PMC6764918 DOI: 10.1016/j.dnarep.2019.102661
52. Kim, J.J., Lee, S.Y., and Miller, K.M. (2019) Preserving genome integrity and function: the DNA damage response and histone modifications, Critical Reviews in Biochemistry and Molecular Biology. Jun 4;54(3):208-241. PMCID: PMC6715524
DOI: 10.1080/10409238.2019.1620676
51. Kim J.J., Kumbhar R., Gong F., Miller, K.M. (2019) In Time and Space: Laser Microirradiation and the DNA Damage Response. In: Balakrishnan L., Stewart J. (eds) DNA Repair, Methods in Molecular Biology, vol 1999. Humana, New York, NY. 2019;1999:61-74.
PMCID: PMC7479964 DOI: 10.1007/978-1-4939-9500-4_3
50. Xia, J.*, Chiu, L-Y.*, Nehring, R.B., Bravo Núñez, M.A., Mei, Q., Perez, M., Zhai, Y., Fitzgerald, D.M., Pribis, J.P., Wang, Y., Wang, Y., Hu, C.W., Powell, R.T., LaBonte, S.A., Jalali, A., Matadamas Guzmán, M.L., Lentzsch, A.M., Szafran, A.T., Joshi, M.C., Richters, M., Gibson, J.L., Frisch, R.L., Hastings, P.J., Bates, D., Queitsch, C., Hilsenbeck, S., Coarfa, C., Hu, J.C., Siegele, D.A., Scott, K.L., Liang, H., Mancini, M.A., Herman, C.^, Miller, K.M.^ and Rosenberg, S.M.^ (2019) Bacteria-to-human protein networks reveal origins of endogenous DNA damage, Cell. Jan 10;176(1-2):127-143. (*Co-first author, ^co-corresponding authors). PMCID: PMC6344048
DOI: 10.1016/j.cell.2018.12.008
Research Highlights: Burgess, D.J. (2019) Human protein mutagens found via bacteria, Nature Reviews Genetics.
49. Dilworth, D., Gong, F., Miller, K.M., and Nelson, CJ. (2019) FKBP25 participates in DNA double-strand break repair, Biochemistry and Cell Biology. Feb;98(1):42-49. PMCID: PMC7457334 DOI: 10.1139/bcb-2018-0328
48. Klein, H.L.*, Bačinskaja, G., Che, J., Cheblal, A., Elango, R., Epshtein, A., Fitzgerald, D.M., Gómez-González, B., Khan, S.R., Kumar, S., Leland, B.A., Marie, L., Mei, Q., Miné-Hattab, J., Piotrowska, A., Polleys, E.J., Putnam, C.D., Radchenko, E.A., Saada, A.A., Sakofsky, C.J., Shim, E.Y., Stracy, M., Xia, J., Yan, Z., Yin, Y., Aguilera, A., Argueso, J.L., Freudenreich, C.H., Gasser, S.M., Gordenin, D.A., Haber, J.E., Ira, G., Jinks-Robertson, S., King, M.C., Kolodner, R.D., Kuzminov, A., Lambert, S.A.E., Lee, S.E., Miller, K.M., Mirkin, S.M., Petes, T.D., Rosenberg S.M., Rothstein, R., Symington, L.S., Zawadzki, P., Kim, N.*, Lisby, M.* and Malkova, A*. (2019) Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways, Microbial Cell. Jan 7;6(1):1-64.
PMCID: PMC6334234 DOI: 10.15698/mic2019.01.664
53. Pudget, N., Miller, K.M.^ and Legube G.^ (2019) Non-canonical DNA/RNA structures during Transcription-Coupled Double-Strand Break Repair: Roadblocks or Bona fide repair intermediates, DNA Repair. Sep;81:102661. (^co-corresponding authors).
PMCID: PMC6764918 DOI: 10.1016/j.dnarep.2019.102661
52. Kim, J.J., Lee, S.Y., and Miller, K.M. (2019) Preserving genome integrity and function: the DNA damage response and histone modifications, Critical Reviews in Biochemistry and Molecular Biology. Jun 4;54(3):208-241. PMCID: PMC6715524
DOI: 10.1080/10409238.2019.1620676
51. Kim J.J., Kumbhar R., Gong F., Miller, K.M. (2019) In Time and Space: Laser Microirradiation and the DNA Damage Response. In: Balakrishnan L., Stewart J. (eds) DNA Repair, Methods in Molecular Biology, vol 1999. Humana, New York, NY. 2019;1999:61-74.
PMCID: PMC7479964 DOI: 10.1007/978-1-4939-9500-4_3
50. Xia, J.*, Chiu, L-Y.*, Nehring, R.B., Bravo Núñez, M.A., Mei, Q., Perez, M., Zhai, Y., Fitzgerald, D.M., Pribis, J.P., Wang, Y., Wang, Y., Hu, C.W., Powell, R.T., LaBonte, S.A., Jalali, A., Matadamas Guzmán, M.L., Lentzsch, A.M., Szafran, A.T., Joshi, M.C., Richters, M., Gibson, J.L., Frisch, R.L., Hastings, P.J., Bates, D., Queitsch, C., Hilsenbeck, S., Coarfa, C., Hu, J.C., Siegele, D.A., Scott, K.L., Liang, H., Mancini, M.A., Herman, C.^, Miller, K.M.^ and Rosenberg, S.M.^ (2019) Bacteria-to-human protein networks reveal origins of endogenous DNA damage, Cell. Jan 10;176(1-2):127-143. (*Co-first author, ^co-corresponding authors). PMCID: PMC6344048
DOI: 10.1016/j.cell.2018.12.008
Research Highlights: Burgess, D.J. (2019) Human protein mutagens found via bacteria, Nature Reviews Genetics.
49. Dilworth, D., Gong, F., Miller, K.M., and Nelson, CJ. (2019) FKBP25 participates in DNA double-strand break repair, Biochemistry and Cell Biology. Feb;98(1):42-49. PMCID: PMC7457334 DOI: 10.1139/bcb-2018-0328
48. Klein, H.L.*, Bačinskaja, G., Che, J., Cheblal, A., Elango, R., Epshtein, A., Fitzgerald, D.M., Gómez-González, B., Khan, S.R., Kumar, S., Leland, B.A., Marie, L., Mei, Q., Miné-Hattab, J., Piotrowska, A., Polleys, E.J., Putnam, C.D., Radchenko, E.A., Saada, A.A., Sakofsky, C.J., Shim, E.Y., Stracy, M., Xia, J., Yan, Z., Yin, Y., Aguilera, A., Argueso, J.L., Freudenreich, C.H., Gasser, S.M., Gordenin, D.A., Haber, J.E., Ira, G., Jinks-Robertson, S., King, M.C., Kolodner, R.D., Kuzminov, A., Lambert, S.A.E., Lee, S.E., Miller, K.M., Mirkin, S.M., Petes, T.D., Rosenberg S.M., Rothstein, R., Symington, L.S., Zawadzki, P., Kim, N.*, Lisby, M.* and Malkova, A*. (2019) Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways, Microbial Cell. Jan 7;6(1):1-64.
PMCID: PMC6334234 DOI: 10.15698/mic2019.01.664
2018
47. Makharashvili, N., Arora, S., Yin, Y., Fu, Q., Wen, X., Lee, J-H., Kao, C-H., Leung, J.W.C., Miller, K.M., and Paull T.T. (2018) Sae2/CtIP prevents R-loop accumulation in eukaryotic cells, eLife. 2018;7:e42733. PMCID: PMC6296784 DOI: 10.7554/eLife.42733
46. Cheng, C., Qi, Y., Wang, Y., Chi, K.K., Chung, Y., Ouyang, C., Chen, Y., Oh, M.E., Sheng, X., Tang, Y., Liu, Y., Lin, H.H., Kuo, C., Schones, D., Vidal, C.M., Chu, J.C.Y., Wang, H., Chen, Y., Miller, K.M., Chu, P., Yen, Y., Jiang, L., Kung, H. and Ann, D.K. (2018) Arginine starvation kills tumor cells through aspartate exhaustion and mitochondrial dysfunction, Communications Biology. Oct 26;1:178. PMCID: PMC6203837 DOI: 10.1038/s42003-018-0178-4
45. Hu, D., Jablonowski, C., Cheng, P.-H., AlTahan, A., Li, C., Wang, Y., Palmer, L., Lan, C., Sun, B., Abu-Zaid, A., Fan, Y., Brimble, M., Gamboa, N., Kumbhar, R.C., Yanishevski, D., Miller, K.M., Kang, G., Zambetti, G.P., Chen, T., Yan, Q., Davidoff, A.M., Yang, J. (2018) KDM5A regulates a translational program that controls p53 protein expression, iScience. Nov 20;9:84-100.PMCID:PMC6214872 DOI: 10.1016/j.isci.2018.10.012.
44. Kotlajich, M.V., Xia, J., Zhai, Y., Lin, H.Y., Bradley, C.C., Shen, X., Mei, Q., Wang, A.Z., Lynn, E.J., Shee, C., Chen, L.T., Li, L., Miller, K.M., Herman, C., Hastings, P.J. and Rosenberg, S.M. (2018) Fluorescent fusions of the N protein of phage Mu label DNA Damage in living cells, DNA Repair. Dec;72:86-92. PMCID: PMC6287932 DOI: 10.1016/j.dnarep.2018.09.005
43. Leung J.W.C., Emery L.E., and Miller K.M. (2018) CRISPR/Cas9 Gene Editing of Human Histone H2A Variant H2AX and MacroH2A. In: Orsi G., Almouzni G. (eds) Histone Variants, Methods in Molecular Biology. 1832:255-269. PMID: 30073532 DOI: 10.1007/978-1-4939-8663-7
42. Vilas C.K., Emery L.E., Denchi E.L.^ and Miller K.M.^ (2018) Caught with One's Zinc Fingers in the Genome Integrity Cookie Jar, Trends in Genetics. 34(4):313-325. (^co-corresponding authors). PMCID: PMC5878116 DOI: 10.1016/j.tig.2017.12.011
41. Gong, F. and Miller, K.M. (2018) Double duty: ZMYND8 in the DNA damage response and cancer, Cell Cycle. 17(4):414-420 PMCID: PMC5927707 DOI: 10.1080/15384101.2017.1376150
46. Cheng, C., Qi, Y., Wang, Y., Chi, K.K., Chung, Y., Ouyang, C., Chen, Y., Oh, M.E., Sheng, X., Tang, Y., Liu, Y., Lin, H.H., Kuo, C., Schones, D., Vidal, C.M., Chu, J.C.Y., Wang, H., Chen, Y., Miller, K.M., Chu, P., Yen, Y., Jiang, L., Kung, H. and Ann, D.K. (2018) Arginine starvation kills tumor cells through aspartate exhaustion and mitochondrial dysfunction, Communications Biology. Oct 26;1:178. PMCID: PMC6203837 DOI: 10.1038/s42003-018-0178-4
45. Hu, D., Jablonowski, C., Cheng, P.-H., AlTahan, A., Li, C., Wang, Y., Palmer, L., Lan, C., Sun, B., Abu-Zaid, A., Fan, Y., Brimble, M., Gamboa, N., Kumbhar, R.C., Yanishevski, D., Miller, K.M., Kang, G., Zambetti, G.P., Chen, T., Yan, Q., Davidoff, A.M., Yang, J. (2018) KDM5A regulates a translational program that controls p53 protein expression, iScience. Nov 20;9:84-100.PMCID:PMC6214872 DOI: 10.1016/j.isci.2018.10.012.
44. Kotlajich, M.V., Xia, J., Zhai, Y., Lin, H.Y., Bradley, C.C., Shen, X., Mei, Q., Wang, A.Z., Lynn, E.J., Shee, C., Chen, L.T., Li, L., Miller, K.M., Herman, C., Hastings, P.J. and Rosenberg, S.M. (2018) Fluorescent fusions of the N protein of phage Mu label DNA Damage in living cells, DNA Repair. Dec;72:86-92. PMCID: PMC6287932 DOI: 10.1016/j.dnarep.2018.09.005
43. Leung J.W.C., Emery L.E., and Miller K.M. (2018) CRISPR/Cas9 Gene Editing of Human Histone H2A Variant H2AX and MacroH2A. In: Orsi G., Almouzni G. (eds) Histone Variants, Methods in Molecular Biology. 1832:255-269. PMID: 30073532 DOI: 10.1007/978-1-4939-8663-7
42. Vilas C.K., Emery L.E., Denchi E.L.^ and Miller K.M.^ (2018) Caught with One's Zinc Fingers in the Genome Integrity Cookie Jar, Trends in Genetics. 34(4):313-325. (^co-corresponding authors). PMCID: PMC5878116 DOI: 10.1016/j.tig.2017.12.011
41. Gong, F. and Miller, K.M. (2018) Double duty: ZMYND8 in the DNA damage response and cancer, Cell Cycle. 17(4):414-420 PMCID: PMC5927707 DOI: 10.1080/15384101.2017.1376150
2017
40. Gong F. and Miller K.M. (2019) Histone methylation and the DNA damage response, Mutation Research-Reviews in Mutation Research. Apr - Jun;780:37-47. Epub 2017 Sep 23. DOI: 10.1016/j.mrrev.2017.09.003
39. Chiu L.Y.*, Gong F.*, and Miller K.M. (2017) Bromodomain proteins: Repairing DNA damage within Chromatin, Phil. Trans. R. Soc. B. 372: 20160286. (*Co-first author, Invited review). PMCID: PMC5577464 DOI: 10.1098/rstb.2016.0286
38. Gong, F., Couaire, T., Aguirrebengoa, M., Legube, G. and Miller, K.M. (2017) Histone demethylase KDM5A regulates ZMYND8-NuRD chromatin remodeler to promote DNA repair, Journal of Cell Biology. 216(7):1959-1974. PMCID: PMC5496618
DOI: 10.1083/jcb.201611135
Spotlight: Price, B. (2017) KDM5A demethylase: Erasing histone modifications to promote repair of DNA breaks, Journal of Cell Biology.
37. Zacharioudakis, E.*, Agarwal, P.*, Bartoli, A., Abell, N., Kunalingam, L., Bergoglio, V., Xhemalce, B., Miller, K.M.^ and Rodriguez,R.^ (2017) Chromatin Regulates Genome Targeting with Cisplatin. (*authors contributed equally, ^co-corresponding authors). Angewandte Chemie. 56(23):6483-6487. (*Co-first author, ^co-corresponding authors). PMCID: PMC5488169
DOI: 10.1002/anie.201701144
36. Leung, J.W.C., Makharashvili, N., Agarwal, P., Chiu, L-Y., Pourpre, R., Cammarata, M.B., Cannon, J.R., Sherker, A., Durocher, D., Brodbelt, J.S., Paull, T.T. and Miller, K.M. (2017) ZMYM3 regulates BRCA1 localization at damaged chromatin to promote DNA repair, Genes & Development. Feb 1;31(3):260-274. PMCID: PMC5358723 DOI: 10.1101/gad.292516.116
39. Chiu L.Y.*, Gong F.*, and Miller K.M. (2017) Bromodomain proteins: Repairing DNA damage within Chromatin, Phil. Trans. R. Soc. B. 372: 20160286. (*Co-first author, Invited review). PMCID: PMC5577464 DOI: 10.1098/rstb.2016.0286
38. Gong, F., Couaire, T., Aguirrebengoa, M., Legube, G. and Miller, K.M. (2017) Histone demethylase KDM5A regulates ZMYND8-NuRD chromatin remodeler to promote DNA repair, Journal of Cell Biology. 216(7):1959-1974. PMCID: PMC5496618
DOI: 10.1083/jcb.201611135
Spotlight: Price, B. (2017) KDM5A demethylase: Erasing histone modifications to promote repair of DNA breaks, Journal of Cell Biology.
37. Zacharioudakis, E.*, Agarwal, P.*, Bartoli, A., Abell, N., Kunalingam, L., Bergoglio, V., Xhemalce, B., Miller, K.M.^ and Rodriguez,R.^ (2017) Chromatin Regulates Genome Targeting with Cisplatin. (*authors contributed equally, ^co-corresponding authors). Angewandte Chemie. 56(23):6483-6487. (*Co-first author, ^co-corresponding authors). PMCID: PMC5488169
DOI: 10.1002/anie.201701144
36. Leung, J.W.C., Makharashvili, N., Agarwal, P., Chiu, L-Y., Pourpre, R., Cammarata, M.B., Cannon, J.R., Sherker, A., Durocher, D., Brodbelt, J.S., Paull, T.T. and Miller, K.M. (2017) ZMYM3 regulates BRCA1 localization at damaged chromatin to promote DNA repair, Genes & Development. Feb 1;31(3):260-274. PMCID: PMC5358723 DOI: 10.1101/gad.292516.116
2016
35. Agarwal, P. and Miller, K.M. (2016) Book Chapter: Chromatin Dynamics and DNA Repair. In: Chromatin Regulation and Dynamics Book, Elsevier.
34. Gong, F., Chiu, L-Y. and Miller, K.M. (2016) Acetylation reader proteins: linking acetylation signaling to genome maintenance and cancer, PLoS Genetics. Sep 15;12(9):e1006272. (Invited review). PMCID: PMC5025232 DOI: 10.1371/journal.pgen.1006272
33. Agarwal, P. and Miller, K.M. (2016) The Nucleosome: Orchestrating DNA Damage Signaling and Repair within Chromatin, Biochemistry and Cell Biology. 13:1-15 [Epub ahead of print]. PMID: 27240007 DOI: 10.1139/bcb-2016-0017
32. Gruosso, T., Mieulet, V., Cardon, M., Bourachot, B., Kieffer, Y., Devun, F., Dubois, T., Dutreix, M., Vincent-Salomon, A., Miller, K.M. and Mechta-Grigoriou, F. (2016) Chronic oxidative stress promotes H2AX protein degradation and enhances chemosensitivity in breast cancer patients, EMBO Molecular Medicine. 8(5):527-49. PMCID: PMC5123617 DOI: 10.15252/emmm.201505891
31. Meyer, L.R., Gallardo, I.F., Zhou, Y., Gong, F., Yang, S.H., Wold, M.S., Miller, K.M., Paull, T.T. and Finkelstein, I.J. (2016) Single-molecule imaging reveals the mechanism of Exo1 regulation by single-stranded DNA binding proteins, PNAS. 113(9):e1170-9. PMCID: PMC4780606 DOI:10.1073/pnas.1516674113
34. Gong, F., Chiu, L-Y. and Miller, K.M. (2016) Acetylation reader proteins: linking acetylation signaling to genome maintenance and cancer, PLoS Genetics. Sep 15;12(9):e1006272. (Invited review). PMCID: PMC5025232 DOI: 10.1371/journal.pgen.1006272
33. Agarwal, P. and Miller, K.M. (2016) The Nucleosome: Orchestrating DNA Damage Signaling and Repair within Chromatin, Biochemistry and Cell Biology. 13:1-15 [Epub ahead of print]. PMID: 27240007 DOI: 10.1139/bcb-2016-0017
32. Gruosso, T., Mieulet, V., Cardon, M., Bourachot, B., Kieffer, Y., Devun, F., Dubois, T., Dutreix, M., Vincent-Salomon, A., Miller, K.M. and Mechta-Grigoriou, F. (2016) Chronic oxidative stress promotes H2AX protein degradation and enhances chemosensitivity in breast cancer patients, EMBO Molecular Medicine. 8(5):527-49. PMCID: PMC5123617 DOI: 10.15252/emmm.201505891
31. Meyer, L.R., Gallardo, I.F., Zhou, Y., Gong, F., Yang, S.H., Wold, M.S., Miller, K.M., Paull, T.T. and Finkelstein, I.J. (2016) Single-molecule imaging reveals the mechanism of Exo1 regulation by single-stranded DNA binding proteins, PNAS. 113(9):e1170-9. PMCID: PMC4780606 DOI:10.1073/pnas.1516674113
2015
30. O'Connor, H.F., Lyon, N., Leung, J.W.C., Agarwal, P., Swaim, C.D., Miller, K.M. and Huibregtse, J.M. (2015) Ubiquitin‐Activated Interaction Traps (UBAITs) identify E3 ligase binding partners, EMBO reports, 16(12):1699-712. PMCID: PMC4693525 DOI:10.15252/embr.201540620
29. Chen, W., Ebelt, N.D., Stracker, T.H., Xhemalce, B., Van Den Berg, C.L. and Miller, K.M. (2015) ATM regulation of IL-8 links oxidative stress to cancer cell migration and invasion, eLife. Jun 1;4. PMCID: PMC4463759 DOI: 10.7554/eLife.07270
28. Gong, F.*, Chiu, L.*, Cox, B., Aymard, F., Clouaire, T., Leung, J.W.C., Cammarata, M., Perez, M., Agarwal, P., Brodbelt, J.S., Legube, G. and Miller, K.M. (2015) Screen identifies bromodomain protein ZMYND8 in chromatin recognition of transcription-associated DNA damage that promotes homologous recombination, Genes & Development. 29:1297-211. (*authors contributed equally). PMCID: PMC4298138 DOI: 10.1101/gad.252189.114
27. Mateos-Gomez, P.A., Gong, F., Nair N, Miller, K.M., Lazzerini-Denchi, E. and Sfeir, A. (2015) Mammalian polymerase Theta promotes alternative-NHEJ and suppresses recombination, Nature. 12;518(7538):254-7. PMCID: PMC4718306 DOI: 10.1038/nature14157
Highlighted in News and Views: "DNA repair: Familiar ends with alternative endings" by Cho and Greenberg
29. Chen, W., Ebelt, N.D., Stracker, T.H., Xhemalce, B., Van Den Berg, C.L. and Miller, K.M. (2015) ATM regulation of IL-8 links oxidative stress to cancer cell migration and invasion, eLife. Jun 1;4. PMCID: PMC4463759 DOI: 10.7554/eLife.07270
28. Gong, F.*, Chiu, L.*, Cox, B., Aymard, F., Clouaire, T., Leung, J.W.C., Cammarata, M., Perez, M., Agarwal, P., Brodbelt, J.S., Legube, G. and Miller, K.M. (2015) Screen identifies bromodomain protein ZMYND8 in chromatin recognition of transcription-associated DNA damage that promotes homologous recombination, Genes & Development. 29:1297-211. (*authors contributed equally). PMCID: PMC4298138 DOI: 10.1101/gad.252189.114
27. Mateos-Gomez, P.A., Gong, F., Nair N, Miller, K.M., Lazzerini-Denchi, E. and Sfeir, A. (2015) Mammalian polymerase Theta promotes alternative-NHEJ and suppresses recombination, Nature. 12;518(7538):254-7. PMCID: PMC4718306 DOI: 10.1038/nature14157
Highlighted in News and Views: "DNA repair: Familiar ends with alternative endings" by Cho and Greenberg
2014
26. Rodriguez, R.R and Miller, K.M. (2014) Unravelling the genomic targets of small molecules using high-throughput sequencing, Nature Reviews Genetics. 15(12):783-796 (Invited review article). PMID: 25311424 DOI: 10.1038/nrg3796
25. Aymard, F., Bugler, B., Schmidt, C.K., Guillou, E., Caron, P., Briois, S., Iacovoni, J.S., Daburon, V., Miller, K.M., Jackson, S.P., Legube, G. (2014) Transcriptionally active chromatin recruits homologous recombination at DNA double-strand breaks, Nature Structural & Molecular Biology. 21:366-74. PMCID: PMC4300393 DOI: 10.1038/nsmb.2796
24. Leung, J.W.C.*, Agarwal, P.*, Canny, M.D., Gong, F., Robison, A.D., Finkelstein, I.J., Durocher, D. and Miller, K.M. (2014) Nucleosome Acidic Patch Promotes RNF168- and RING1B/BMI1-Dependent H2AX and H2A Ubiquitination and DNA Damage Signaling, Plos Genetics. 10(3): e1004178. (*authors contributed equally). PMCID: PMC3945288 DOI: 10.1371/journal.pgen.1004178
25. Aymard, F., Bugler, B., Schmidt, C.K., Guillou, E., Caron, P., Briois, S., Iacovoni, J.S., Daburon, V., Miller, K.M., Jackson, S.P., Legube, G. (2014) Transcriptionally active chromatin recruits homologous recombination at DNA double-strand breaks, Nature Structural & Molecular Biology. 21:366-74. PMCID: PMC4300393 DOI: 10.1038/nsmb.2796
24. Leung, J.W.C.*, Agarwal, P.*, Canny, M.D., Gong, F., Robison, A.D., Finkelstein, I.J., Durocher, D. and Miller, K.M. (2014) Nucleosome Acidic Patch Promotes RNF168- and RING1B/BMI1-Dependent H2AX and H2A Ubiquitination and DNA Damage Signaling, Plos Genetics. 10(3): e1004178. (*authors contributed equally). PMCID: PMC3945288 DOI: 10.1371/journal.pgen.1004178
2013
23. Shee, C., Cox, B., Gu, F., Luengas, E., Joshi, M., Chiu, L., Magnan, D., Halliday, J., Frisch, R., Gibson, J., Nehring, R., Do, H., Hernandez, M., Li, L., Herman, C., Hanstings, P.J., Bates, D., Harris, R.1^, Miller, K.M.^ and Rosenberg, S.M.^ (2013) Engineered proteins detect spontaneous DNA breakage in human and bacterial cells, eLife. 2:e01222. (^co-corresponding authors).
PMCID: PMC3809393 DOI: 10.7554/eLife.01222.
Highlighted in Insight: Proteins pinpoint double strand breaks by Michael M Cox (2013) eLife
22. Gong, F. and Miller, K.M. (2013) Mammalian DNA repair: HATs and HDACs make their mark through histone acetylation, Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis. 750:23-30. (Invited review). PMID: 23927873
DOI: 10.1016/j.mrfmmm.2013.07.002
21. Chen, W.*, Alpert, A.*, Leiter, C., Gong, F., Jackson, S.P.^ and Miller, K.M.^ (2013) Systematic identification of functional residues in mammalian histone H2AX, Molecular and Cellular Biology. 33(1):111-126. (*authors contributed equally, ^co-corresponding authors). PMCID: PMC3536310 DOI: 10.1016/j.mrfmmm.2013.07.002
PMCID: PMC3809393 DOI: 10.7554/eLife.01222.
Highlighted in Insight: Proteins pinpoint double strand breaks by Michael M Cox (2013) eLife
22. Gong, F. and Miller, K.M. (2013) Mammalian DNA repair: HATs and HDACs make their mark through histone acetylation, Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis. 750:23-30. (Invited review). PMID: 23927873
DOI: 10.1016/j.mrfmmm.2013.07.002
21. Chen, W.*, Alpert, A.*, Leiter, C., Gong, F., Jackson, S.P.^ and Miller, K.M.^ (2013) Systematic identification of functional residues in mammalian histone H2AX, Molecular and Cellular Biology. 33(1):111-126. (*authors contributed equally, ^co-corresponding authors). PMCID: PMC3536310 DOI: 10.1016/j.mrfmmm.2013.07.002
2012
20. Rodriguez, R.*, Miller, K.M.*, Forment, J.V., Bradshaw, C.R., Nikan, M., Britton, S., Oelschlaegel, T., Xhemalce, B., Balasubramanian, S.^ and Jackson, S.P.^ (2012) Small molecule-induced DNA damage identifies druggable alternative DNA structures in human genes, Nature Chemical Biology. 8, 301–310. (*authors contributed equally, ^co-corresponding authors). PMCID: PMC3433707 DOI: 10.1038/nchembio.780
19. Miller, K.M.^ and Jackson, S.P.^ (2012) Histone marks: repairing DNA breaks within the context of chromatin, Biochemical Society Review. 40(2):370-6. (^co-corresponding authors). PMID: 22435814 DOI: 10.1042/BST20110747
19. Miller, K.M.^ and Jackson, S.P.^ (2012) Histone marks: repairing DNA breaks within the context of chromatin, Biochemical Society Review. 40(2):370-6. (^co-corresponding authors). PMID: 22435814 DOI: 10.1042/BST20110747
2011
18. Miller, K.M. and Rodriguez, R. (2011) G-quadruplexes: selective DNA targeting for cancer therapeutics?, Expt. Rev. Clin. Pharmacol. 4 (2), 139-142. PMID: 22115396 DOI: 10.1586/ECP.11.4.
2010
17. Miller, K.M., Tjeertes, J.V., Coates, J., Legube, G., Polo, S.E., Britton, S. and Jackson, S.P. (2010) Human HDAC1 and HDAC2 function in the DNA-damage response to promote DNA non-homologous end-joining, Nature Structural & Molecular Biology. 17:1144. PMCID: PMC3018776 DOI: 10.1038/nsmb.1899
16. Jain, D., Hebden, A.K., Nakamura, T.M., Miller, K.M. and Cooper, J.P. (2010). HAATI survivors replace canonical telomeres with blocks of generic heterochromatin, Nature. 467(7312), 223-7. PMID: 20829796 DOI: 10.1038/nature09374
15. Miller, K.M. (2010) Advancements in understanding genome maintenance. Genome Biology. 11:301. DOI: 10.1186/gb-2010-11-4-301
16. Jain, D., Hebden, A.K., Nakamura, T.M., Miller, K.M. and Cooper, J.P. (2010). HAATI survivors replace canonical telomeres with blocks of generic heterochromatin, Nature. 467(7312), 223-7. PMID: 20829796 DOI: 10.1038/nature09374
15. Miller, K.M. (2010) Advancements in understanding genome maintenance. Genome Biology. 11:301. DOI: 10.1186/gb-2010-11-4-301
2009
14. Galanty, Y., Belotserkovskaya, R., Coates, J., Polo, SE., Miller, K.M. and Jackson, S.P. (2009) SUMO E3-ligases PIAS1 and PIAS4 promote responses to DNA double-strand breaks in mammalian cells, Nature. 462 (7275):857-8. PMCID: PMC2904806 DOI: 10.1038/nature08657
13. Germe, T., Miller, K.M. and Cooper, J.P. (2009) A non-canonical function of topoisomerase II in disentangling dysfunctional telomeres, EMBO J. 28(18):2803-11. PMCID: PMC2750024 DOI: 10.1038/emboj.2009.223
12. Tjeertes, J.V.*, Miller, K.M.*^ and Jackson, S.P.^ (2009) Screen for DNA-damage-responsive histone modifications identifies H3K9Ac and H3K56Ac in human cells, EMBO J. 28 (13):1878-89. (*authors contributed equally, ^co-corresponding authors).
PMCID: PMC2684025 DOI: 10.1038/emboj.2009.119
11. Rog, O., Miller, K.M., Ferreira, M.G. and Cooper, J.P. (2009) Sumoylation of RecQ helicase controls the fate of dysfunctional telomeres, Mol Cell. 33(5):559-69. PMID: 19285940 DOI: 10.1016/j.molcel.2009.01.027
13. Germe, T., Miller, K.M. and Cooper, J.P. (2009) A non-canonical function of topoisomerase II in disentangling dysfunctional telomeres, EMBO J. 28(18):2803-11. PMCID: PMC2750024 DOI: 10.1038/emboj.2009.223
12. Tjeertes, J.V.*, Miller, K.M.*^ and Jackson, S.P.^ (2009) Screen for DNA-damage-responsive histone modifications identifies H3K9Ac and H3K56Ac in human cells, EMBO J. 28 (13):1878-89. (*authors contributed equally, ^co-corresponding authors).
PMCID: PMC2684025 DOI: 10.1038/emboj.2009.119
11. Rog, O., Miller, K.M., Ferreira, M.G. and Cooper, J.P. (2009) Sumoylation of RecQ helicase controls the fate of dysfunctional telomeres, Mol Cell. 33(5):559-69. PMID: 19285940 DOI: 10.1016/j.molcel.2009.01.027
2007
10. Xhemalce, B., Miller, K.M., Driscoll, R., Masumoto, H., Jackson, S.P., Kouzarides, T., Verreault, A. and Arcangioli, B. (2007) Regulation of Histone H3 lysine 56 acetylation in Schizosaccharomyces pombe, J Biol Chem. 282(20):15040-7. PMID: 17369611
DOI: 10.1074/jbc.M70119720
9. Collins, S.R., Miller, K.M., Maas, N.L., Roguev, A., Fillingham, J., Chu, C.S., Schuldiner, M., Gebbia, M., Recht, J., Shales, M., Ding, H., Xu, H., Han, J., Ingvarsdottir, K., Cheng, B., Andrews, B., Boone, C., Berger, S.L., Hieter, P., Zhang, Z., Brown, G.W., Ingles, C.J., Emili, A., Allis, C.D., Toczyski, D.P., Weissman, J.S., Greenblatt, J.F. and Krogan, N.J. (2007) Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map, Nature. 446 (7137):806-10. PMID: 17314980
DOI: 10.1038/nature05649
DOI: 10.1074/jbc.M70119720
9. Collins, S.R., Miller, K.M., Maas, N.L., Roguev, A., Fillingham, J., Chu, C.S., Schuldiner, M., Gebbia, M., Recht, J., Shales, M., Ding, H., Xu, H., Han, J., Ingvarsdottir, K., Cheng, B., Andrews, B., Boone, C., Berger, S.L., Hieter, P., Zhang, Z., Brown, G.W., Ingles, C.J., Emili, A., Allis, C.D., Toczyski, D.P., Weissman, J.S., Greenblatt, J.F. and Krogan, N.J. (2007) Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map, Nature. 446 (7137):806-10. PMID: 17314980
DOI: 10.1038/nature05649
2006
8. Miller, K.M., Maas, N.L. and Tocyzski, D.P. (2006) Taking It Off: Regulation of H3K56 Acetylation by Hst3 and Hst4, Cell Cycle. 5(22). PMID: 17106263 DOI: 10.4161/cc.5.22.3501
7. Maas, N.L.*, Miller, K.M.*, DeFazio, L.G. and Toczyski, D.P. (2006 ) Cell cycle and checkpoint regulation of histone H3 K56 acetylation by Hst3/4, Mol Cell. 23 (1):109-19. (*authors contributed equally). PMID: 16598261 DOI: 10.1016/j.molcel.2006.06.006
6. Miller, K.M.*, Rog, O.* and Cooper, J.P. (2006) Semi-conservative DNA replication through telomeres requires Taz1, Nature. 440 (7085):824-8. (*authors contributed equally). DOI: 10.1038/nature04638
7. Maas, N.L.*, Miller, K.M.*, DeFazio, L.G. and Toczyski, D.P. (2006 ) Cell cycle and checkpoint regulation of histone H3 K56 acetylation by Hst3/4, Mol Cell. 23 (1):109-19. (*authors contributed equally). PMID: 16598261 DOI: 10.1016/j.molcel.2006.06.006
6. Miller, K.M.*, Rog, O.* and Cooper, J.P. (2006) Semi-conservative DNA replication through telomeres requires Taz1, Nature. 440 (7085):824-8. (*authors contributed equally). DOI: 10.1038/nature04638
2005
5. Miller, K.M., Ferreira, M.G. and Cooper, J.P. (2005) Taz1, Rap1 and Rif1 act both inter-dependently and independently to maintain telomeres, EMBO J. 24(17):3128-35. PMCID: PMC1201358 DOI: 10.1038/sj.emboj.7600779
2004
4. Ferreira, M.G.*, Miller, K.M.* and Cooper, J.P. (2004) Indecent exposure. When telomeres become uncapped, Mol Cell. (2004), Vol. 13 (1), 7-18, (*authors contributed equally). PMID: 14731390 DOI: 10.1016/S1097-2765(03)00531-8
2003
3. Beernink, H.T.H, Miller, K.M., Desphande, A., Bucher, P. and Cooper, J.P. (2003) Telomere Maintenance in Fission Yeast Requires an Est1 Ortholog, Current Biology. 13:575-580. PMID: 12676088 DOI: 10.1016/S0960-9822(03)00169-6
2002
2. Miller, K.M. and Cooper, J.P. (2002) The Telomere Protein Taz1 is Required to Prevent and Repair Genomic DNA Breaks, Mol Cell. 11:303-313. PMID: 12620220 DOI: 10.1016/S1097-2765(03)00041-8
2001
1. Hamilton, E., Miller, K.M., Helm, K.M., Langdon, W.Y. and Anderson, S.M. (2001) Suppression of Apoptosis Induced by Growth Factor Withdrawal by an Oncogenic Form of c-Cbl, J Biol Chem. 276(12):9028-9037. PMID: 11113140 DOI: 10.1074/jbc.M009386200