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Our Science – McNally Website

James G. McNally, Ph.D.

Selected Publications
1)  Mazza D, Abernathy A, Golob N, Morisaki T, McNally JG.
A benchmark for chromatin binding measurements in live cells.
Nucleic Acids Res. 40: e119, 2012. [Journal]
2)  Lickwar CR, Mueller F, Hanlon SE, McNally JG, Lieb JD.
Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function.
Nature. 484: 251-5, 2012. [Journal]
3)  Mueller F, Morisaki T, Mazza D, McNally JG.
Minimizing the impact of photoswitching of fluorescent proteins on FRAP analysis.
Biophys. J. 102: 1656-65, 2012. [Journal]
4)  Mazza D, Stasevich TJ, Karpova TS, McNally JG.
Monitoring dynamic binding of chromatin proteins in vivo by fluorescence correlation spectroscopy and temporal image correlation spectroscopy.
Methods Mol. Biol. 833: 177-200, 2012. [Journal]
5)  Mueller F, Karpova TS, Mazza D, McNally JG.
Monitoring dynamic binding of chromatin proteins in vivo by fluorescence recovery after photobleaching.
Methods Mol. Biol. 833: 153-76, 2012. [Journal]
6)  Quénet D, McNally JG, Dalal Y.
Through thick and thin: the conundrum of chromatin fibre folding in vivo.
EMBO Rep. 13: 943-4, 2012. [Journal]
7)  Müller WG, Heymann JB, Nagashima K, Guttmann P, Werner S, Rehbein S, Schneider G, McNally JG.
Towards an atlas of mammalian cell ultrastructure by cryo soft X-ray tomography.
J. Struct. Biol. 177: 179-92, 2012. [Journal]
8)  Rieder D, Trajanoski Z, McNally JG.
Transcription factories.
Front Genet. 3: 221, 2012. [Journal]
9)  Stasevich TJ, McNally JG.
Assembly of the transcription machinery: ordered and stable, random and dynamic, or both?.
Chromosoma. 120: 533-45, 2011. [Journal]
10)  Maiuri P, Knezevich A, De Marco A, Mazza D, Kula A, McNally JG, Marcello A.
Fast transcription rates of RNA polymerase II in human cells.
EMBO Rep. 12: 1280-5, 2011. [Journal]
11)  McNally JG.
Foreword. Biophysics in chromatin structure and nuclear dynamics.
Chromosome Res. 19: 1-3, 2011. [Journal]
12)  Kuipers MA, Stasevich TJ, Sasaki T, Wilson KA, Hazelwood KL, McNally JG, Davidson MW, Gilbert DM.
Highly stable loading of Mcm proteins onto chromatin in living cells requires replication to unload.
J. Cell Biol. 192: 29-41, 2011. [Journal]
13)  Chernova TA, Romanyuk AV, Karpova TS, Shanks JR, Ali M, Moffatt N, Howie RL, O'Dell A, McNally JG, Liebman SW, Chernoff YO, Wilkinson KD.
Prion induction by the short-lived, stress-induced protein Lsb2 is regulated by ubiquitination and association with the actin cytoskeleton.
Mol. Cell. 43: 242-52, 2011. [Journal]
14)  Gordon SN, Cecchinato V, Andresen V, Heraud JM, Hryniewicz A, Parks RW, Venzon D, Chung HK, Karpova T, McNally J, Silvera P, Reimann KA, Matsui H, Kanehara T, Shinmura Y, Yokote H, Franchini G.
Smallpox vaccine safety is dependent on T cells and not B cells.
J. Infect. Dis. 203: 1043-53, 2011. [Journal]
15)  Raghuram N, Carrero G, Stasevich TJ, McNally JG, Th'ng J, Hendzel MJ.
Core histone hyperacetylation impacts cooperative behavior and high-affinity binding of histone H1 to chromatin.
Biochemistry. 49: 4420-31, 2010. [Journal]
16)  Stasevich TJ, Mueller F, Michelman-Ribeiro A, Rosales T, Knutson JR, McNally JG.
Cross-validating FRAP and FCS to quantify the impact of photobleaching on in vivo binding estimates.
Biophys. J. 99: 3093-101, 2010. [Journal]
17)  Stasevich TJ, Mueller F, Brown DT, McNally JG.
Dissecting the binding mechanism of the linker histone in live cells: an integrated FRAP analysis.
EMBO J. 29: 1225-34, 2010. [Journal]
18)  McNally JG, Mazza D.
Fractal geometry in the nucleus.
EMBO J. 29: 2-3, 2010. [Journal]
19)  Mueller F, Mazza D, Stasevich TJ, McNally JG.
FRAP and kinetic modeling in the analysis of nuclear protein dynamics: what do we really know?.
Curr Opin Cell Biol. 22: 403-11, 2010. [Journal]
20)  Sung MH, McNally JG.
Live cell imaging and systems biology.
Wiley Interdiscip Rev Syst Biol Med. 3: 167-82, 2010. [Journal]
21)  Heyerdahl SL, Rozenberg J, Jamtgaard L, Rishi V, Varticovski L, Akah K, Scudiero D, Shoemaker RH, Karpova TS, Day RN, McNally JG, Vinson C.
The arylstibonic acid compound NSC13746 disrupts B-ZIP binding to DNA in living cells.
Eur. J. Cell Biol. 89: 564-73, 2010. [Journal]
22)  Schneider G, Guttmann P, Heim S, Rehbein S, Mueller F, Nagashima K, Heymann JB, Müller WG, McNally JG.
Three-dimensional cellular ultrastructure resolved by X-ray microscopy.
Nat. Methods. 7: 985-7, 2010. [Journal]
23)  Michelman-Ribeiro A, Mazza D, Rosales T, Stasevich TJ, Boukari H, Rishi V, Vinson C, Knutson JR, McNally JG.
Direct measurement of association and dissociation rates of DNA binding in live cells by fluorescence correlation spectroscopy.
Biophys. J. 97: 337-46, 2009. [Journal]
24)  Stocker G, Fischer M, Rieder D, Bindea G, Kainz S, Oberstolz M, McNally JG, Trajanoski Z.
iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis.
BMC Bioinformatics. 10: 390, 2009. [Journal]
25)  Rochman M, Postnikov Y, Correll S, Malicet C, Wincovitch S, Karpova TS, McNally JG, Wu X, Bubunenko NA, Grigoryev S, Bustin M.
The interaction of NSBP1/HMGN5 with nucleosomes in euchromatin counteracts linker histone-mediated chromatin compaction and modulates transcription.
Mol. Cell. 35: 642-56, 2009. [Journal]
26)  Hager GL, McNally JG, Misteli T.
Transcription dynamics.
Mol. Cell. 35: 741-53, 2009. [Journal]
27)  McNally JG.
Transcription, chromatin condensation, and gene migration.
J. Cell Biol. 185: 7-9, 2009. [Journal]
28)  Karpova TS, Kim MJ, Spriet C, Nalley K, Stasevich TJ, Kherrouche Z, Heliot L, McNally JG.
Concurrent fast and slow cycling of a transcriptional activator at an endogenous promoter.
Science. 319: 466-9, 2008. [Journal]
29)  Sung M, Bagain L, Chen Z, Karpova T, Yang X, Silvin C, Voss T, McNally J, Van Waes C, Hager GL.
Dynamic Effect of Bortezomib on NF-{kappa}B Activity and Gene Expression in Tumor Cells.
Mol Pharmacol. 74: 1215-22, 2008. [Journal]
30)  Mueller F, Wach P, McNally JG.
Evidence for a common mode of transcription factor interaction with chromatin as revealed by improved quantitative fluorescence recovery after photobleaching.
Biophys. J. 94: 3323-39, 2008. [Journal]
31)  Nishiyama A, Mochizuki K, Mueller F, Karpova T, McNally JG, Ozato K.
Intracellular delivery of acetyl-histone peptides inhibits native bromodomain-chromatin interactions and impairs mitotic progression.
FEBS Lett. 582: 1501-7, 2008. [Journal]
32)  McNally JG.
Quantitative FRAP in analysis of molecular binding dynamics in vivo.
Methods Cell Biol. 85: 329-51, 2008. [Journal]
33)  Sprouse RO, Karpova TS, Mueller F, Dasgupta A, McNally JG, Auble DT.
Regulation of TATA-binding protein dynamics in living yeast cells.
Proc. Natl. Acad. Sci. U.S.A. 105: 13304-8, 2008. [Journal]
34)  Park CJ, Park JE, Karpova TS, Soung NK, Yu LR, Song S, Lee KH, Xia X, Kang E, Dabanoglu I, Oh DY, Zhang JY, Kang YH, Wincovitch S, Huffaker TC, Veenstra TD, McNally JG, Lee KS.
Requirement for the budding yeast polo kinase Cdc5 in proper microtubule growth and dynamics.
Eukaryotic Cell. 7: 444-53, 2008. [Journal]
35)  Catalfamo M, Tai X, Karpova T, McNally J, Henkart PA.
TcR-induced regulated secretion leads to surface expression of CTLA-4 in CD4(+)CD25(+) T cells.
Immunology. 125: 70-9, 2008. [Journal]
36)  Braga J, McNally JG, Carmo-Fonseca M.
A reaction-diffusion model to study RNA motion by quantitative fluorescence recovery after photobleaching.
Biophys. J. 92: 2694-703, 2007. [Journal]
37)  Srivastava P, Demarre G, Karpova TS, McNally J, Chattoraj DK.
Changes in nucleoid morphology and origin localization upon inhibition or alteration of the actin homolog, MreB, of Vibrio cholerae.
J. Bacteriol. 189: 7450-63, 2007. [Journal]
38)  Müller WG, Rieder D, Karpova TS, John S, Trajanoski Z, McNally JG.
Organization of chromatin and histone modifications at a transcription site.
J. Cell Biol. 177: 957-67, 2007. [Journal]
39)  Sprague BL, Müller F, Pego RL, Bungay PM, Stavreva DA, McNally JG.
Analysis of binding at a single spatially localized cluster of binding sites by fluorescence recovery after photobleaching.
Biophys. J. 91: 1169-91, 2006. [Journal]
40)  Kruhlak MJ, Celeste A, Dellaire G, Fernandez-Capetillo O, Müller WG, McNally JG, Bazett-Jones DP, Nussenzweig A.
Changes in chromatin structure and mobility in living cells at sites of DNA double-strand breaks.
J. Cell Biol. 172: 823-34, 2006. [Journal]
41)  Karpova T, McNally JG.
Detecting protein-protein interactions with CFP-YFP FRET by acceptor photobleaching.
Curr Protoc Cytom. Chapter 12: Unit12.7, 2006. [Journal]
42)  Koga F, Xu W, Karpova TS, McNally JG, Baron R, Neckers L.
Hsp90 inhibition transiently activates Src kinase and promotes Src-dependent Akt and Erk activation.
Proc. Natl. Acad. Sci. U.S.A. 103: 11318-22, 2006. [Journal]
43)  Stavreva DA, Kawasaki M, Dundr M, Koberna K, Müller WG, Tsujimura-Takahashi T, Komatsu W, Hayano T, Isobe T, Raska I, Misteli T, Takahashi N, McNally JG.
Potential Roles for Ubiquitin and the Proteasome during Ribosome Biogenesis.
Mol. Cell. Biol. 26: 5131-45, 2006. [Journal]
44)  Stavreva DA, McNally JG.
Role of H1 phosphorylation in rapid GR exchange and function at the MMTV promoter.
Histochem. Cell Biol. 125: 83-9, 2006. [Journal]
45)  Arnaoutov A, Azuma Y, Ribbeck K, Joseph J, Boyarchuk Y, Karpova T, McNally J, Dasso M.
Crm1 is a mitotic effector of Ran-GTP in somatic cells.
Nat Cell Biol. 7: 626-32, 2005. [Journal]
46)  Sprague BL, McNally JG.
FRAP analysis of binding: proper and fitting.
Trends Cell Biol. 15: 84-91, 2005. [Journal]
47)  Laricchia-Robbio L, Tamura T, Karpova T, Sprague BL, McNally JG, Ozato K.
Partner-regulated interaction of IFN regulatory factor 8 with chromatin visualized in live macrophages.
Proc. Natl. Acad. Sci. U.S.A. 102: 14368-73, 2005. [Journal]
48)  Sprague BL, Pego RL, Stavreva DA, McNally JG.
Analysis of binding reactions by fluorescence recovery after photobleaching.
Biophys J. 86: 3473-95, 2004. [Journal]
49)  Karpova TS, Chen TY, Sprague BL, McNally JG.
Dynamic interactions of a transcription factor with DNA are accelerated by a chromatin remodeller.
EMBO Rep. 5: 1064-70, 2004. [Journal]
50)  Qian X, Karpova T, Sheppard AM, McNally J, Lowy DR.
E-cadherin-mediated adhesion inhibits ligand-dependent activation of diverse receptor tyrosine kinases.
EMBO J. 23: 1739-84, 2004. [Journal]
51)  Müller WG, Rieder D, Kreth G, Cremer C, Trajanoski Z, McNally JG.
Generic features of tertiary chromatin structure as detected in natural chromosomes.
Mol Cell Biol. 24: 9359-70, 2004. [Journal]
52)  Catalfamo M, Karpova T, McNally J, Costes SV, Lockett SJ, Bos E, Peters PJ, Henkart PA.
Human CD8+ T cells store RANTES in a unique secretory compartment and release it rapidly after TcR stimulation.
Immunity. 20: 219-30, 2004. [Journal]
53)  Kim BC, Lee HJ, Park SH, Lee SR, Karpova TS, McNally JG, Felici A, Lee DK, Kim SJ.
Jab1/CSN5, a component of the COP9 signalosome, regulates transforming growth factor beta signaling by binding to Smad7 and promoting its degradation.
Mol Cell Biol. 24: 2251-62, 2004. [Journal]
54)  Ling Y, Sankpal UT, Robertson AK, McNally JG, Karpova T, Robertson KD.
Modification of de novo DNA methyltransferase 3a (Dnmt3a) by SUMO-1 modulates its interaction with histone deacetylases (HDACs) and its capacity to repress transcription.
Nucleic Acids Res. 32: 598-610, 2004. [Journal]
55)  Wong K, Zhang J, Awasthi S, Sharma A, Rogers L, Matlock EF, Van Lint C, Karpova T, McNally J, Harrod R.
Nerve growth factor receptor signaling induces histone acetyltransferase domain-dependent nuclear translocation of p300/CREB-binding protein-associated factor and hGCN5 acetyltransferases.
J Biol Chem. 279: 55667-74, 2004. [Journal]
56)  Park JE, Park CJ, Sakchaisri K, Karpova T, Asano S, McNally J, Sunwoo Y, Leem SH, Lee KS.
Novel functional dissection of the localization-specific roles of budding yeast polo kinase Cdc5p.
Mol Cell Biol. 24: 9873-86, 2004. [Journal]
57)  Stavreva DA, Müller WG, Hager GL, Smith CL, McNally JG.
Rapid GR exchange at a promoter: coupling to transcription and regulation by chaperones and proteasomes.
Mol. Cell Biol. 24: 2682-2697, 2004. [Journal]
58)  He L, Olson DP, Wu X, Karpova TS, McNally JG, Lipsky PE.
A flow cytometric method to detect protein-protein interaction in living cells by directly visualizing donor fluorophore quenching during CFP-->YFP fluorescence resonance energy transfer (FRET).
Cytometry. 55A: 71-85, 2003. [Journal]
59)  Macpherson GR, Ng SS, Forbes SL, Melillo G, Karpova T, McNally J, Conrads TP, Veenstra TD, Martinez A, Cuttitta F, Price DK, Figg WD.
Anti-angiogenic activity of human endostatin is HIF-1-independent in vitro and sensitive to timing of treatment in a human saphenous vein assay.
Mol Cancer Ther. 2: 845-54, 2003. [Journal]
60)  He L, Bradrick TD, Karpova TS, Wu X, Fox MH, Fischer R, McNally JG, Knutson JR, Grammer AC, Lipsky PE.
Flow cytometric measurement of fluorescence (Forster) resonance energy transfer from cyan fluorescent protein to yellow fluorescent protein using single-laser excitation at 458 nm.
Cytometry. 53A: 39-54, 2003. [Journal]
61)  Karpova TS, Baumann CT, He L, Wu X, Grammer A, Lipsky P, Hager GL, McNally JG.
Fluorescence resonance energy transfer from cyan to yellow fluorescent protein detected by acceptor photobleaching using confocal microscopy and a single argon laser.
J. Microscopy. 209 (Pt.1): 56-70, 2003. [Journal]
62)  Harrod R, Nacsa J, Van Lint C, Hansen J, Karpova T, McNally J, Franchini G.
Human immunodeficiency virus type-1 Tat/co-activator acetyltransferase interactions inhibit p53Lys-320 acetylation and p53-responsive transcription.
J Biol Chem. 278: 12310-8, 2003. [Journal]
63)  Edghill-Smith Y, Venzon D, Karpova T, McNally J, Nacsa J, Tsai WP, Tryniszewska E, Moniuszko M, Manischewitz J, King LR, Snodgrass SJ, Parrish J, Markham P, Sowers M, Martin D, Lewis MG, Berzofsky JA, Belyakov IM, Moss B, Tartaglia J, Bray M, Hirsch V, Golding H, Franchini G.
Modeling a safer smallpox vaccination regimen, for human immunodeficiency virus type 1-infected patients, in immunocompromised macaques.
J Infect Dis. 188: 1181-91, 2003. [Journal]
64)  Felici A, Wurthner JU, Parks WT, Giam LR, Reiss M, Karpova TS, McNally JG, Roberts AB.
TLP, a novel modulator of TGF-beta signaling, has opposite effects on Smad2- and Smad3-dependent signaling.
EMBO J. 22: 4465-77, 2003. [Journal]
65)  Hel Z, Tryniszewska E, Tsai WP, Johnson JM, Harrod R, Fullen J, Kalyanaraman VS, Altman JD, McNally J, Karpova T, Felber BK, Tartaglia J, Franchini G.
Design and in vivo immunogenicity of a polyvalent vaccine based on SIVmac regulatory genes.
DNA Cell Biol. 21: 619-26, 2002. [Journal]
66)  Becker M, Baumann C, John S, Walker DA, Vigneron M, McNally JG, Hager GL.
Dynamic behavior of transcription factors on a natural promoter in living cells.
EMBO Rep. 3: 1188-94, 2002. [Journal]
67)  D'Oro U, Munitic I, Chacko G, Karpova T, McNally J, Ashwell JD.
Regulation of constitutive TCR internalization by the zeta-chain.
J Immunol. 169: 6269-78, 2002. [Journal]
68)  Joseph J, Tan SH, Karpova TS, McNally JG, Dasso M.
SUMO-1 targets RanGAP1 to kinetochores and mitotic spindles.
J Cell Biol. 156: 595-602, 2002. [Journal]
69)  Müller WG, Walker D, Hager GL, McNally JG.
Large-scale chromatin decondensation and recondensation regulated by transcription from a natural promoter.
J Cell Biol. 154: 33-48, 2001. [Journal]
70)  McNally JG, Müller WG, Walker D, Wolford R, Hager GL.
The glucocorticoid receptor: rapid exchange with regulatory sites in living cells.
Science. 287: 1262-1265, 2000. [Journal]
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This page was last updated on 5/15/2013.