Publications

1. Feng AC, Thomas BJ, Purbey PK, de Melo FM, Liu X, Daly AE, Sun F, Lo JH, Cheng L, Carey MF, Scumpia PO, Smale ST. The transcription factor NF-κB orchestrates nucleosome remodeling during the primary response to Toll-like receptor 4 signaling.. Immunity, 2024.
2. Li M, Guo H, Carey M, Huang C. Transcriptional and epigenetic dysregulation impairs generation of proliferative neural stem and progenitor cells during brain aging.. Nature aging, 2024.
3. Kronenberg M, Carey MF. Temporal regulation of head-on transcription at replication initiation sites.. iScience, 2022.
4. Sun F, Sun T, Kronenberg M, Tan X, Huang C, Carey MF. The Pol II preinitiation complex (PIC) influences Mediator binding but not promoter-enhancer looping.. Genes & development, 2021.
5. Topal S, Van C, Xue Y, Carey MF, Peterson CL. INO80C Remodeler Maintains Genomic Stability by Preventing Promiscuous Transcription at Replication Origins.. Cell reports, 2020.
6. Attar N, Campos OA, Vogelauer M, Cheng C, Xue Y, Schmollinger S, Salwinski L, Mallipeddi NV, Boone BA, Yen L, Yang S, Zikovich S, Dardine J, Carey MF, Merchant SS, Kurdistani SK. The histone H3-H4 tetramer is a copper reductase enzyme.. Science (New York, N.Y.), 2020.
7. Liu Q, Bischof S, Harris CJ, Zhong Z, Zhan L, Nguyen C, Rashoff A, Barshop WD, Sun F, Feng S, Potok M, Gallego-Bartolome J, Zhai J, Wohlschlegel JA, Carey MF, Long JA, Jacobsen SE. The characterization of Mediator 12 and 13 as conditional positive gene regulators in Arabidopsis.. Nature communications, 2020.
8. Sun F, Chronis C, Kronenberg M, Chen XF, Su T, Lay FD, Plath K, Kurdistani SK, Carey MF. Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods.. Molecular cell, 2018.
9. Gottesfeld JM, Carey MF. Introduction to the Thematic Minireview Series: Chromatin and transcription.. The Journal of biological chemistry, 2018.
10. Xue Y, Pradhan SK, Sun F, Chronis C, Tran N, Su T, Van C, Vashisht A, Wohlschlegel J, Peterson CL, Timmers HTM, Kurdistani SK, Carey MF. Mot1, Ino80C, and NC2 Function Coordinately to Regulate Pervasive Transcription in Yeast and Mammals.. Molecular cell, 2017.
11. Xue Y, Schmollinger S, Attar N, Campos OA, Vogelauer M, Carey MF, Merchant SS, Kurdistani SK. Endoplasmic reticulum-mitochondria junction is required for iron homeostasis.. The Journal of biological chemistry, 2017.
12. Pradhan SK, Su T, Yen L, Jacquet K, Huang C, Côté J, Kurdistani SK, Carey MF. EP400 Deposits H3.3 into Promoters and Enhancers during Gene Activation.. Molecular cell, 2015.
13. Pradhan SK, Xue Y, Carey MF. Fragile Nucleosomes Influence Pol II Promoter Function.. Molecular cell, 2015.
14. Xue Y, Van C, Pradhan SK, Su T, Gehrke J, Kuryan BG, Kitada T, Vashisht A, Tran N, Wohlschlegel J, Peterson CL, Kurdistani SK, Carey MF. The Ino80 complex prevents invasion of euchromatin into silent chromatin.. Genes & development, 2015.
15. Macadangdang BR, Oberai A, Spektor T, Campos OA, Sheng F, Carey MF, Vogelauer M, Kurdistani SK. Evolution of histone 2A for chromatin compaction in eukaryotes.. eLife, 2014.
16. Carey MF, Peterson CL, Smale ST. PCR-mediated site-directed mutagenesis.. Cold Spring Harbor protocols, 2013.
17. Carey MF, Peterson CL, Smale ST. Electrophoretic mobility-shift assays.. Cold Spring Harbor protocols, 2013.
18. Sridharan R, Gonzales-Cope M, Chronis C, Bonora G, McKee R, Huang C, Patel S, Lopez D, Mishra N, Pellegrini M, Carey M, Garcia BA, Plath K. Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency.. Nature cell biology, 2013.
19. Carey MF, Peterson CL, Smale ST. DNase I footprinting.. Cold Spring Harbor protocols, 2013.
20. Carey MF, Peterson CL, Smale ST. Preparation of (32)P-end-labeled DNA fragments for performing DNA-binding experiments.. Cold Spring Harbor protocols, 2013.
21. Carey MF, Peterson CL, Smale ST. The RNase protection assay.. Cold Spring Harbor protocols, 2013.
22. Carey MF, Peterson CL, Smale ST. The primer extension assay.. Cold Spring Harbor protocols, 2013.
23. Chen XF, Lehmann L, Lin JJ, Vashisht A, Schmidt R, Ferrari R, Huang C, McKee R, Mosley A, Plath K, Kurdistani SK, Wohlschlegel J, Carey M. Mediator and SAGA have distinct roles in Pol II preinitiation complex assembly and function.. Cell reports, 2012.
24. Kitada T, Kuryan BG, Tran NN, Song C, Xue Y, Carey M, Grunstein M. Mechanism for epigenetic variegation of gene expression at yeast telomeric heterochromatin.. Genes & development, 2012.
25. Lehmann L, Ferrari R, Vashisht AA, Wohlschlegel JA, Kurdistani SK, Carey M. Polycomb repressive complex 1 (PRC1) disassembles RNA polymerase II preinitiation complexes.. The Journal of biological chemistry, 2012.
26. Carey M. PICking apart Pol II initiation.. Nature structural & molecular biology, 2012.
27. Carey MF, Peterson CL, Smale ST. Confirming the functional importance of a protein-DNA interaction.. Cold Spring Harbor protocols, 2012.
28. Yu Y, Song C, Zhang Q, DiMaggio PA, Garcia BA, York A, Carey MF, Grunstein M. Histone H3 lysine 56 methylation regulates DNA replication through its interaction with PCNA.. Molecular cell, 2012.
29. Carey MF, Peterson CL, Smale ST. Identifying cis-acting DNA elements within a control region.. Cold Spring Harbor protocols, 2012.
30. Carey MF, Peterson CL, Smale ST. Experimental strategies for cloning or identifying genes encoding DNA-binding proteins.. Cold Spring Harbor protocols, 2012.
31. Kuryan BG, Kim J, Tran NN, Lombardo SR, Venkatesh S, Workman JL, Carey M. Histone density is maintained during transcription mediated by the chromatin remodeler RSC and histone chaperone NAP1 in vitro.. Proceedings of the National Academy of Sciences of the United States of America, 2012.
32. Carey MF, Peterson CL, Smale ST. Experimental strategies for the identification of DNA-binding proteins.. Cold Spring Harbor protocols, 2012.
33. Lin JJ, Carey M. In vitro transcription and immobilized template analysis of preinitiation complexes.. Current protocols in molecular biology, 2012.
34. Chen XF, Kuryan B, Kitada T, Tran N, Li JY, Kurdistani S, Grunstein M, Li B, Carey M. The Rpd3 core complex is a chromatin stabilization module.. Current biology : CB, 2011.
35. Lin JJ, Lehmann LW, Bonora G, Sridharan R, Vashisht AA, Tran N, Plath K, Wohlschlegel JA, Carey M. Mediator coordinates PIC assembly with recruitment of CHD1.. Genes & development, 2011.
36. Gordon V, Bhadel S, Wunderlich W, Zhang J, Ficarro SB, Mollah SA, Shabanowitz J, Hunt DF, Xenarios I, Hahn WC, Conaway M, Carey MF, Gioeli D. CDK9 regulates AR promoter selectivity and cell growth through serine 81 phosphorylation.. Molecular endocrinology (Baltimore, Md.), 2010.
37. Carey MF, Peterson CL, Smale ST. Potassium permanganate probing of Pol II open complexes.. Cold Spring Harbor protocols, 2010.
38. Carey MF, Peterson CL, Smale ST. Protein complex binding to promoter DNA: immobilized template assay.. Cold Spring Harbor protocols, 2010.
39. Carey MF, Peterson CL, Smale ST. Purification of epitope-tagged transcription factor IID.. Cold Spring Harbor protocols, 2010.
40. Carey MF, Peterson CL, Smale ST. Purification of mediator from HeLa cell lines expressing a flag-tagged mediator subunit.. Cold Spring Harbor protocols, 2010.
41. Carey MF, Peterson CL, Smale ST. G-less cassette in vitro transcription using HeLa cell nuclear extracts.. Cold Spring Harbor protocols, 2010.
42. Carey MF, Peterson CL, Smale ST. Dignam and Roeder nuclear extract preparation.. Cold Spring Harbor protocols, 2009.
43. Carey MF, Peterson CL, Smale ST. In vitro transcription using HeLa cell extracts and primer extension.. Cold Spring Harbor protocols, 2009.
44. Carey MF, Peterson CL, Smale ST. Chromatin immunoprecipitation (ChIP).. Cold Spring Harbor protocols, 2009.
45. Carey MF, Peterson CL, Smale ST. In vivo DNase I, MNase, and restriction enzyme footprinting via ligation-mediated polymerase chain reaction (LM-PCR).. Cold Spring Harbor protocols, 2009.
46. Carey MF, Peterson CL, Smale ST. In vivo dimethyl sulfate (DMS) footprinting via ligation-mediated polymerase chain reaction (LM-PCR).. Cold Spring Harbor protocols, 2009.
47. Ramirez-Carrozzi VR, Braas D, Bhatt DM, Cheng CS, Hong C, Doty KR, Black JC, Hoffmann A, Carey M, Smale ST. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling.. Cell, 2009.
48. Mosley AL, Pattenden SG, Carey M, Venkatesh S, Gilmore JM, Florens L, Workman JL, Washburn MP. Rtr1 is a CTD phosphatase that regulates RNA polymerase II during the transition from serine 5 to serine 2 phosphorylation.. Molecular cell, 2009.
49. Huyn ST, Burton JB, Sato M, Carey M, Gambhir SS, Wu L. A potent, imaging adenoviral vector driven by the cancer-selective mucin-1 promoter that targets breast cancer metastasis.. Clinical cancer research : an official journal of the American Association for Cancer Research, 2009.
50. Black JC, Mosley A, Kitada T, Washburn M, Carey M. The SIRT2 deacetylase regulates autoacetylation of p300.. Molecular cell, 2008.
51. Ray S, Paulmurugan R, Patel MR, Ahn BC, Wu L, Carey M, Gambhir SS. Noninvasive imaging of therapeutic gene expression using a bidirectional transcriptional amplification strategy.. Molecular therapy : the journal of the American Society of Gene Therapy, 2008.
52. Smallwood A, Black JC, Tanese N, Pradhan S, Carey M. HP1-mediated silencing targets Pol II coactivator complexes.. Nature structural & molecular biology, 2008.
53. Carey M, Smale ST. Hydroxyl-radical footprinting.. CSH protocols, 2007.
54. Carey M, Smale ST. Methylation interference assay.. CSH protocols, 2007.
55. Carey M, Smale ST. Phosphate ethylation interference assay.. CSH protocols, 2007.
56. Carey M, Smale ST. Micrococcal Nuclease-Southern Blot Assay: I. MNase and Restriction Digestions.. CSH protocols, 2007.
57. Carey M, Smale ST. Micrococcal Nuclease-Southern Blot Assay: II. Capillary Transfer and Hybridization.. CSH protocols, 2007.
58. Chin HG, Estève PO, Pradhan M, Benner J, Patnaik D, Carey MF, Pradhan S. Automethylation of G9a and its implication in wider substrate specificity and HP1 binding.. Nucleic acids research, 2007.
59. Smallwood A, Estève PO, Pradhan S, Carey M. Functional cooperation between HP1 and DNMT1 mediates gene silencing.. Genes & development, 2007.
60. Li B, Carey M, Workman JL. The role of chromatin during transcription.. Cell, 2007.
61. Ilagan R, Pottratz J, Le K, Zhang L, Wong SG, Ayala R, Iyer M, Wu L, Gambhir SS, Carey M. Imaging mitogen-activated protein kinase function in xenograft models of prostate cancer.. Cancer research, 2006.
62. Estève PO, Chin HG, Smallwood A, Feehery GR, Gangisetty O, Karpf AR, Carey MF, Pradhan S. Direct interaction between DNMT1 and G9a coordinates DNA and histone methylation during replication.. Genes & development, 2006.
63. Carey M, Li B, Workman JL. RSC exploits histone acetylation to abrogate the nucleosomal block to RNA polymerase II elongation.. Molecular cell, 2006.
64. Black JC, Choi JE, Lombardo SR, Carey M. A mechanism for coordinating chromatin modification and preinitiation complex assembly.. Molecular cell, 2006.
65. Wang Y, Iyer M, Annala A, Wu L, Carey M, Gambhir SS. Noninvasive indirect imaging of vascular endothelial growth factor gene expression using bioluminescence imaging in living transgenic mice.. Physiological genomics, 2006.
66. Kozeracki CA, Carey MF, Colicelli J, Levis-Fitzgerald M, Grossel M. An intensive primary-literature-based teaching program directly benefits undergraduate science majors and facilitates their transition to doctoral programs.. CBE life sciences education, 2006.
67. Iyer M, Salazar FB, Wu L, Carey M, Gambhir SS. Bioluminescence imaging of systemic tumor targeting using a prostate-specific lentiviral vector.. Human gene therapy, 2006.
68. Ilagan R, Zhang LJ, Pottratz J, Le K, Salas S, Iyer M, Wu L, Gambhir SS, Carey M. Imaging androgen receptor function during flutamide treatment in the LAPC9 xenograft model.. Molecular cancer therapeutics, 2005.
69. Johnson M, Sato M, Burton J, Gambhir SS, Carey M, Wu L. Micro-PET/CT monitoring of herpes thymidine kinase suicide gene therapy in a prostate cancer xenograft: the advantage of a cell-specific transcriptional targeting approach.. Molecular imaging, 2005.
70. Sato M, Johnson M, Zhang L, Gambhir SS, Carey M, Wu L. Functionality of androgen receptor-based gene expression imaging in hormone refractory prostate cancer.. Clinical cancer research : an official journal of the American Association for Cancer Research, 2005.
71. Carey M. Chromatin marks and machines, the missing nucleosome is a theme: gene regulation up and downstream.. Molecular cell, 2005.
72. Song MJ, Hwang S, Wong W, Round J, Martinez-Guzman D, Turpaz Y, Liang J, Wong B, Johnson RC, Carey M, Sun R. The DNA architectural protein HMGB1 facilitates RTA-mediated viral gene expression in gamma-2 herpesviruses.. Journal of virology, 2004.
73. Iyer M, Salazar FB, Lewis X, Zhang L, Carey M, Wu L, Gambhir SS. Noninvasive imaging of enhanced prostate-specific gene expression using a two-step transcriptional amplification-based lentivirus vector.. Molecular therapy : the journal of the American Society of Gene Therapy, 2004.
74. Ray S, Paulmurugan R, Hildebrandt I, Iyer M, Wu L, Carey M, Gambhir SS. Novel bidirectional vector strategy for amplification of therapeutic and reporter gene expression.. Human gene therapy, 2004.
75. Bourbon HM, Aguilera A, Ansari AZ, Asturias FJ, Berk AJ, Bjorklund S, Blackwell TK, Borggrefe T, Carey M, Carlson M, Conaway JW, Conaway RC, Emmons SW, Fondell JD, Freedman LP, Fukasawa T, Gustafsson CM, Han M, He X, Herman PK, Hinnebusch AG, Holmberg S, Holstege FC, Jaehning JA, Kim YJ, Kuras L, Leutz A, Lis JT, Meisterernest M, Naar AM, Nasmyth K, Parvin JD, Ptashne M, Reinberg D, Ronne H, Sadowski I, Sakurai H, Sipiczki M, Sternberg PW, Stillman DJ, Strich R, Struhl K, Svejstrup JQ, Tuck S, Winston F, Roeder RG, Kornberg RD. A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II.. Molecular cell, 2004.
76. Johnson KM, Wang J, Smallwood A, Carey M. The immobilized template assay for measuring cooperativity in eukaryotic transcription complex assembly.. Methods in enzymology, 2004.
77. Sato M, Johnson M, Zhang L, Zhang B, Le K, Gambhir SS, Carey M, Wu L. Optimization of adenoviral vectors to direct highly amplified prostate-specific expression for imaging and gene therapy.. Molecular therapy : the journal of the American Society of Gene Therapy, 2003.
78. Zhang L, Johnson M, Le KH, Sato M, Ilagan R, Iyer M, Gambhir SS, Wu L, Carey M. Interrogating androgen receptor function in recurrent prostate cancer.. Cancer research, 2003.
79. Johnson KM, Carey M. Assembly of a mediator/TFIID/TFIIA complex bypasses the need for an activator.. Current biology : CB, 2003.
80. Jain A, Lam A, Vivanco I, Carey MF, Reiter RE. Identification of an androgen-dependent enhancer within the prostate stem cell antigen gene.. Molecular endocrinology (Baltimore, Md.), 2002.
81. Adams JY, Johnson M, Sato M, Berger F, Gambhir SS, Carey M, Iruela-Arispe ML, Wu L. Visualization of advanced human prostate cancer lesions in living mice by a targeted gene transfer vector and optical imaging.. Nature medicine, 2002.
82. Johnson KM, Wang J, Smallwood A, Arayata C, Carey M. TFIID and human mediator coactivator complexes assemble cooperatively on promoter DNA.. Genes & development, 2002.
83. Selig SE, Carey MF, Menzies DG, Patterson J, Geerling RH, Williams AD, Bamroongsuk V, Toia D, Krum H, Hare DL. Reliability of isokinetic strength and aerobic power testing for patients with chronic heart failure.. Journal of cardiopulmonary rehabilitation, 2002.
84. Mitsouras K, Wong B, Arayata C, Johnson RC, Carey M. The DNA architectural protein HMGB1 displays two distinct modes of action that promote enhanceosome assembly.. Molecular and cellular biology, 2002.
85. Zhang L, Adams JY, Billick E, Ilagan R, Iyer M, Le K, Smallwood A, Gambhir SS, Carey M, Wu L. Molecular engineering of a two-step transcription amplification (TSTA) system for transgene delivery in prostate cancer.. Molecular therapy : the journal of the American Society of Gene Therapy, 2002.
86. Wu L, Matherly J, Smallwood A, Adams JY, Billick E, Belldegrun A, Carey M. Chimeric PSA enhancers exhibit augmented activity in prostate cancer gene therapy vectors.. Gene therapy, 2001.
87. Johnson KM, Mitsouras K, Carey M. Eukaryotic transcription: the core of eukaryotic gene activation.. Current biology : CB, 2001.
88. Huang W, Shostak Y, Tarr P, Sawyers C, Carey M. Cooperative assembly of androgen receptor into a nucleoprotein complex that regulates the prostate-specific antigen enhancer.. The Journal of biological chemistry, 1999.
89. Ellwood K, Huang W, Johnson R, Carey M. Multiple layers of cooperativity regulate enhanceosome-responsive RNA polymerase II transcription complex assembly.. Molecular and cellular biology, 1999.
90. Hori R, Carey M. Transcription: TRF walks the walk but can it talk the talk?. Current biology : CB, 1998.
91. Tantin D, Kansal A, Carey M. Recruitment of the putative transcription-repair coupling factor CSB/ERCC6 to RNA polymerase II elongation complexes.. Molecular and cellular biology, 1997.
92. Carey MF. Transcriptional activation. A holistic view of the complex.. Current biology : CB, 1995.
93. Tantin D, Carey M. A heteroduplex template circumvents the energetic requirement for ATP during activated transcription by RNA polymerase II.. The Journal of biological chemistry, 1994.
94. Hori R, Carey M. The role of activators in assembly of RNA polymerase II transcription complexes.. Current opinion in genetics & development, 1994.
95. Chi T, Carey M. The ZEBRA activation domain: modular organization and mechanism of action.. Molecular and cellular biology, 1993.
96. Carey M, Kolman J, Katz DA, Gradoville L, Barberis L, Miller G. Transcriptional synergy by the Epstein-Barr virus transactivator ZEBRA.. Journal of virology, 1992.
97. Carey M. Mechanistic advances in eukaryotic gene activation.. Current opinion in cell biology, 1991.