Departmental Publications 2014

Identification of an actin binding surface on vinculin that mediates mechanical cell and focal adhesion properties. Thompson PM, Tolbert CE, Shen K, Kota P, Palmer SM, Plevock KM, Orlova A, Galkin VE, Burridge K, Egelman EH, Dokholyan NV, Superfine R, Campbell SL. Structure. 2014 May 6;22(5):697-706. doi: 10.1016/j.str.2014.03.002. Epub 2014 Mar 27. PMID: 24685146

Distinct docking and stabilization steps of the Pseudopilus conformational transition path suggest rotational assembly of type IV pilus-like fibers. Nivaskumar M, Bouvier G, Campos M, Nadeau N, Yu X, Egelman EH, Nilges M, Francetic O. Structure. 2014 May 6;22(5):685-96. doi: 10.1016/j.str.2014.03.001. Epub 2014 Mar 27. PMID: 24685147

A user’s guide to the ribosomal DNA in Saccharomyces cerevisiae. Johnson JM, Smith JS, Schneider DA. Methods Mol Biol. 2014;1205:303-28. doi: 10.1007/978-1-4939-1363-3_18. PMID: 25213252

Centromere licensing: Mis18 is required to Polo-ver. Barnhart-Dailey MC, Foltz DR. Curr Biol. 2014 Sep 8;24(17):R808-10. doi: 10.1016/j.cub.2014.07.026. PMID: 25202874

Chromosomal structural variations during progression of a prostate epithelial cell line to a malignant metastatic state inactivate the NF2, NIPSNAP1, UGT2B17, and LPIN2 genes. Malhotra A, Shibata Y, Hall IM, Dutta A. Cancer Biol Ther. 2013 Sep;14(9):840-52. doi: 10.4161/cbt.25329. Epub 2013 Jul 26. PMID: 23792589

Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. Kumar P, Anaya J, Mudunuri SB, Dutta A. BMC Biol. 2014 Oct 1;12:78. doi: 10.1186/s12915-014-0078-0. PMID: 25270025

Yan C, Liu D, Li L, Wempe MF, Guin S, Khanna M, Meier J, Hoffman B, Owens C, Wysoczynski CL, Nitz MD, Knabe WE, Ahmed M, Brautigan DL, Paschal BM, Schwartz MA, Jones DN, Ross D, Meroueh SO, Theodorescu D. Discovery and characterization of small molecules that target the GTPase Ral. Nature. 2014 Nov 20;515(7527):443-7. doi: 10.1038/nature13713. Epub 2014 Sep 14. PubMed PMID: 25219851.

Pang X, Fan J, Zhang Y, Zhang K, Gao B, Ma J, Li J, Deng Y, Zhou Q, Egelman EH, Hsu VW, Sun F. A PH domain in ACAP1 possesses key features of the BAR domain in promoting membrane curvature. Dev Cell. 2014 Oct 13;31(1):73-86. doi: 10.1016/j.devcel.2014.08.020. Epub 2014 Oct 2. PubMed PMID: 25284369; PubMed Central PMCID: PMC4198613.

Wu B, Peisley A, Tetrault D, Li Z, Egelman EH, Magor KE, Walz T, Penczek PA, Hur S. Molecular imprinting as a signal-activation mechanism of the viral RNA sensor RIG-I. Mol Cell. 2014 Aug 21;55(4):511-23. doi: 10.1016/j.molcel.2014.06.010. Epub 2014 Jul 10. PubMed PMID: 25018021; PubMed Central PMCID: PMC4142144.

Kuscu C, Arslan S, Singh R, Thorpe J, Adli M. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat Biotechnol. 2014 Jul;32(7):677-83. doi: 10.1038/nbt.2916. Epub 2014 May 18. PubMed PMID: 24837660.

Nivaskumar M, Bouvier G, Campos M, Nadeau N, Yu X, Egelman EH, Nilges M, Francetic O. Distinct docking and stabilization steps of the Pseudopilus conformational transition path suggest rotational assembly of type IV pilus-like fibers. Structure. 2014 May 6;22(5):685-96. doi: 10.1016/j.str.2014.03.001. Epub 2014 Mar 27. PubMed PMID: 24685147; PubMed Central PMCID: PMC4016124.

Thompson PM, Tolbert CE, Shen K, Kota P, Palmer SM, Plevock KM, Orlova A, Galkin VE, Burridge K, Egelman EH, Dokholyan NV, Superfine R, Campbell SL. Identification of an actin binding surface on vinculin that mediates mechanical cell and focal adhesion properties. Structure. 2014 May 6;22(5):697-706. doi: 10.1016/j.str.2014.03.002. Epub 2014 Mar 27. PubMed PMID: 24685146; PubMed Central PMCID: PMC4039106.

Im JS, Keaton M, Lee KY, Kumar P, Park J, Dutta A. ATR checkpoint kinase and CRL1Œ≤TRCP collaborate to degrade ASF1a and thus repress genes overlapping with clusters of stalled replication forks. Genes Dev. 2014 Apr 15;28(8):875-87. doi: 10.1101/gad.239194.114. Epub 2014 Apr 3. PubMed PMID: 24700029; PubMed Central PMCID: PMC4003279.

Lu A, Magupalli VG, Ruan J, Yin Q, Atianand MK, Vos MR, Schr√∂der GF, Fitzgerald KA, Wu H, Egelman EH. Unified polymerization mechanism for the assembly of ASC-dependent inflammasomes. Cell. 2014 Mar 13;156(6):1193-206. doi: 10.1016/j.cell.2014.02.008. PubMed PMID: 24630722; PubMed Central PMCID: PMC4000066.

Dey BK, Pfeifer K, Dutta A. The H19 long noncoding RNA gives rise to microRNAs miR-675-3p and miR-675-5p to promote skeletal muscle differentiation and regeneration. Genes Dev. 2014 Mar 1;28(5):491-501. doi: 10.1101/gad.234419.113. Epub 2014 Feb 14. PubMed PMID: 24532688; PubMed Central PMCID: PMC3950346.

Egelman EH. Ambiguities in helical reconstruction. Elife. 2014 Dec 8;3. doi: 10.7554/eLife.04969. PubMed PMID: 25486515.

Lindberg MR, Hall IM, Quinlan AR. Population-based structural variation discovery with Hydra-Multi. Bioinformatics. 2014 Dec 2. pii: btu771. [Epub ahead of print] PubMed PMID: 25527832.

Viswanathan R, Hoffman EA, Shetty SJ, Bekiranov S, Auble DT. Analysis of chromatin binding dynamics using the crosslinking kinetics (CLK) method. Methods. 2014 Dec;70(2-3):97-107. doi: 10.1016/j.ymeth.2014.10.029. Epub 2014 Nov 1. PubMed PMID: 25448301; PubMed Central PMCID: PMC4267959.

Yan C, Liu D, Li L, Wempe MF, Guin S, Khanna M, Meier J, Hoffman B, Owens C, Wysoczynski CL, Nitz MD, Knabe WE, Ahmed M, Brautigan DL, Paschal BM, Schwartz MA, Jones DN, Ross D, Meroueh SO, Theodorescu D. Discovery and characterization of small molecules that target the GTPase Ral. Nature. 2014 Nov 20;515(7527):443-7. doi: 10.1038/nature13713. Epub 2014 Sep 14. PubMed PMID: 25219851.

Kostan J, Salzer U, Orlova A, T√∂r√∂ I, Hodnik V, Senju Y, Zou J, Schreiner C, Steiner J, Meril√§inen J, Nikki M, Virtanen I, Carugo O, Rappsilber J, Lappalainen P, Lehto VP, Anderluh G, Egelman EH, Djinoviƒá-Carugo K. Direct interaction of actin filaments with F-BAR protein pacsin2. EMBO Rep. 2014 Nov;15(11):1154-62. doi: 10.15252/embr.201439267. Epub 2014 Sep 12. PubMed PMID: 25216944; PubMed Central PMCID: PMC4253489.

Dar A, Wu D, Lee N, Shibata E, Dutta A. 14-3-3 proteins play a role in the cell cycle by shielding cdt2 from ubiquitin-mediated degradation. Mol Cell Biol. 2014 Nov;34(21):4049-61. doi: 10.1128/MCB.00838-14. Epub 2014 Aug 25. PubMed PMID: 25154416.

Taylor RP, Lindorfer MA. Analyses of CD20 monoclonal antibody-mediated tumor cell killing mechanisms: rational design of dosing strategies. Mol Pharmacol. 2014 Nov;86(5):485-91. doi: 10.1124/mol.114.092684. Epub 2014 Jun 18. Review. PubMed PMID: 24944188; PubMed Central PMCID: PMC4201137.

Kumar P, Anaya J, Mudunuri SB, Dutta A. Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. BMC Biol. 2014 Oct 1;12:78. doi: 10.1186/s12915-014-0078-0. PubMed PMID: 25270025; PubMed Central PMCID: PMC4203973.

Wotton D. A CREB1-TGFŒ≤2 self-sustaining loop in glioblastoma. Cancer Discov. 2014 Oct;4(10):1123-5. doi: 10.1158/2159-8290.CD-14-0861. PubMed PMID: 25274684.

Cox KH, Bonthuis PJ, Rissman EF. Mouse model systems to study sex chromosome genes and behavior: relevance to humans. Front Neuroendocrinol. 2014 Oct;35(4):405-19. doi: 10.1016/j.yfrne.2013.12.004. Epub 2014 Jan 2. PubMed PMID: 24388960; PubMed Central PMCID: PMC4079771.

Barnhart-Dailey MC, Foltz DR. Centromere licensing: Mis18 is required to Polo-ver. Curr Biol. 2014 Sep 8;24(17):R808-10. doi: 10.1016/j.cub.2014.07.026.PubMed PMID: 25202874.

Faust GG, Hall IM. SAMBLASTER: fast duplicate marking and structural variant read extraction. Bioinformatics. 2014 Sep 1;30(17):2503-5. doi: 10.1093/bioinformatics/btu314. Epub 2014 May 7. PubMed PMID: 24812344; PubMed Central PMCID: PMC4147885.

Stolzenberg DS, Stevens JS, Rissman EF. Histone deacetylase inhibition induces long-lasting changes in maternal behavior and gene expression in female mice. Endocrinology. 2014 Sep;155(9):3674-83. doi: 10.1210/en.2013-1946. Epub 2014 Jun 16. PubMed PMID: 24932804; PubMed Central PMCID: PMC4138561.

Goodman WA, Garg RR, Reuter BK, Mattioli B, Rissman EF, Pizarro TT. Loss of estrogen-mediated immunoprotection underlies female gender bias in experimental Crohn’s-like ileitis. Mucosal Immunol. 2014 Sep;7(5):1255-65. doi: 10.1038/mi.2014.15. Epub 2014 Mar 12. PubMed PMID: 24621993; PubMed Central PMCID: PMC4139459.

Wu B, Peisley A, Tetrault D, Li Z, Egelman EH, Magor KE, Walz T, Penczek PA, Hur S. Molecular imprinting as a signal-activation mechanism of the viral RNA sensor RIG-I. Mol Cell. 2014 Aug 21;55(4):511-23. doi: 10.1016/j.molcel.2014.06.010. Epub 2014 Jul 10. PubMed PMID: 25018021; PubMed Central PMCID: PMC4142144.

Shibata E, Dar A, Dutta A. CRL4Cdt2 E3 ubiquitin ligase and proliferating cell nuclear antigen (PCNA) cooperate to degrade thymine DNA glycosylase in S phase. J Biol Chem. 2014 Aug 15;289(33):23056-64. doi: 10.1074/jbc.M114.574210. Epub 2014 Jun 24. PubMed PMID: 24962565; PubMed Central PMCID: PMC4132804.

Rissman EF, Adli M. Minireview: transgenerational epigenetic inheritance: focus on endocrine disrupting compounds. Endocrinology. 2014 Aug;155(8):2770-80. doi: 10.1210/en.2014-1123. Epub 2014 Jun 2. Review. PubMed PMID: 24885575; PubMed Central PMCID: PMC4098001.

Bjerke GA, Yang CS, Frierson HF, Paschal BM, Wotton D. Activation of Akt signaling in prostate induces a TGFŒ≤-mediated restraint on cancer progression and metastasis. Oncogene. 2014 Jul 10;33(28):3660-7. doi: 10.1038/onc.2013.342. Epub 2013 Sep 2. PubMed PMID: 23995785; PubMed Central PMCID: PMC3939071.

Kuscu C, Arslan S, Singh R, Thorpe J, Adli M. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat Biotechnol. 2014 Jul;32(7):677-83. doi: 10.1038/nbt.2916. Epub 2014 May 18. PubMed PMID: 24837660.

Matson DR, Stukenberg PT. CENP-I and Aurora B act as a molecular switch that ties RZZ/Mad1 recruitment to kinetochore attachment status. J Cell Biol. 2014 May 26;205(4):541-54. doi: 10.1083/jcb.201307137. PubMed PMID: 24862574; PubMed Central PMCID: PMC4033774.

Nivaskumar M, Bouvier G, Campos M, Nadeau N, Yu X, Egelman EH, Nilges M, Francetic O. Distinct docking and stabilization steps of the Pseudopilus conformational transition path suggest rotational assembly of type IV pilus-like fibers. Structure. 2014 May 6;22(5):685-96. doi: 10. 1016/j.str.2014.03.001. Epub 2014 Mar 27. PubMed PMID: 24685147; PubMed Central PMCID: PMC4016124.

Thompson PM, Tolbert CE, Shen K, Kota P, Palmer SM, Plevock KM, Orlova A, Galkin VE, Burridge K, Egelman EH, Dokholyan NV, Superfine R, Campbell SL. Identification of an actin binding surface on vinculin that mediates mechanical cell and focal adhesion properties. Structure. 2014 May 6;22(5):697-706. doi: 10.1016/j.str.2014.03.002. Epub 2014 Mar 27. PubMed PMID: 24685146; PubMed Central PMCID: PMC4039106.

Zhang Y, Kim J, Mueller AC, Dey B, Yang Y, Lee DH, Hachmann J, Finderle S, Park DM, Christensen J, Schiff D, Purow B, Dutta A, Abounader R. Multiple receptor tyrosine kinases converge on microRNA-134 to control KRAS, STAT5B, and glioblastoma. Cell Death Differ. 2014 May;21(5):720-34. doi: 10.1038/cdd.2013.196. Epub 2014 Jan 17. PubMed PMID: 24440911; PubMed Central PMCID: PMC3978301.

Paciorkowski AR, Weisenberg J, Kelley JB, Spencer A, Tuttle E, Ghoneim D, Thio LL, Christian SL, Dobyns WB, Paschal BM. Autosomal recessive mutations in nuclear transport factor KPNA7 are associated with infantile spasms and cerebellar malformation. Eur J Hum Genet. 2014 May;22(5):587-93. doi: 10.1038/ejhg.2013.196. Epub 2013 Sep 18. PubMed PMID: 24045845; PubMed Central PMCID: PMC3992559.

Lu G, Su G, Zhao Y, Johnston WF, Sherman NE, Rissman EF, Lau C, Ailawadi G, Upchurch GR Jr. Dietary phytoestrogens inhibit experimental aneurysm formation in male mice. J Surg Res. 2014 May 1;188(1):326-38. doi: 10.1016/j.jss.2013.11.1108. Epub 2013 Dec 3. PubMed PMID: 24388399; PubMed Central PMCID: PMC3972298.

Im JS, Keaton M, Lee KY, Kumar P, Park J, Dutta A. ATR checkpoint kinase and CRL1Œ≤TRCP collaborate to degrade ASF1a and thus repress genes overlapping with clusters of stalled replication forks. Genes Dev. 2014 Apr 15;28(8):875-87. doi: 10.1101/gad.239194.114. Epub 2014 Apr 3. PubMed PMID: 24700029; PubMed Central PMCID: PMC4003279.

Datta S, Snow CJ, Paschal BM. A pathway linking oxidative stress and the Ran GTPase system in progeria. Mol Biol Cell. 2014 Apr;25(8):1202-15. doi: 10.1091/mbc.E13-07-0430. Epub 2014 Feb 12. PubMed PMID: 24523287; PubMed Central PMCID: PMC3982987.

Banerjee B, Kestner CA, Stukenberg PT. EB1 enables spindle microtubules to regulate centromeric recruitment of Aurora B. J Cell Biol. 2014 Mar 17;204(6):947-63. doi: 10.1083/jcb.201307119. Epub 2014 Mar 10. PubMed PMID: 24616220; PubMed Central PMCID: PMC3998792.

Lu A, Magupalli VG, Ruan J, Yin Q, Atianand MK, Vos MR, Schr√∂der GF, Fitzgerald KA, Wu H, Egelman EH. Unified polymerization mechanism for the assembly of ASC-dependent inflammasomes. Cell. 2014 Mar 13;156(6):1193-206. doi: 10.1016/j.cell.2014.02.008. PubMed PMID: 24630722; PubMed Central PMCID: PMC4000066.

Sun D, Layer R, Mueller AC, Cichewicz MA, Negishi M, Paschal BM, Dutta A. Regulation of several androgen-induced genes through the repression of the miR-99a/let-7c/miR-125b-2 miRNA cluster in prostate cancer cells. Oncogene. 2014 Mar 13;33(11):1448-57. doi: 10.1038/onc.2013.77. Epub 2013 Mar 18. PubMed PMID: 23503464; PubMed Central PMCID: PMC3915043.

Gore AC, Balthazart J, Bikle D, Carpenter DO, Crews D, Czernichow P, Diamanti-Kandarakis E, Dores RM, Grattan D, Hof PR, Hollenberg AN, Lange C, Lee AV, Levine JE, Millar RP, Nelson RJ, Porta M, Poth M, Power DM, Prins GS, Ridgway EC, Rissman EF, Romijn JA, Sawchenko PE, Sly PD, S√∂der O, Taylor HS, Tena-Sempere M, Vaudry H, Wallen K, Wang Z, Wartofsky L, Watson CS. Reprint of: policy decisions on endocrine disruptors should be based on science across disciplines: a response to Dietrich et al. Horm Behav. 2014 Feb;65(2):190-3. doi: 10.1016/j.yhbeh.2013.09.001. Epub 2013 Nov 28. PubMed PMID: 24289987.

Cie≈õlik M, Bekiranov S. Combinatorial epigenetic patterns as quantitative predictors of chromatin biology. BMC Genomics. 2014 Jan 28;15:76. doi: 10.1186/1471-2164-15-76. PubMed PMID: 24472558; PubMed Central PMCID: PMC3922690.

Snow CJ, Paschal BM. Roles of the nucleoporin Tpr in cancer and aging. Adv Exp Med Biol. 2014;773:309-22. doi: 10.1007/978-1-4899-8032-8_14. Review. PubMed PMID: 24563354.

Gore AC, Balthazart J, Bikle D, Carpenter DO, Crews D, Czernichow P, Diamanti-Kandarakis E, Dores RM, Grattan D, Hof PR, Hollenberg AN, Lange C, Lee AV, Levine JE, Millar RP, Nelson RJ, Porta M, Poth M, Power DM, Prins GS, Ridgway EC, Rissman EF, Romijn JA, Sawchenko PE, Sly PD, S√∂der O, Taylor HS, Tena-Sempere M, Vaudry H, Wallen K, Wang Z, Wartofsky L, Watson CS. Reprint of: policy decisions on endocrine disruptors should be based on science across disciplines: a response to Dietrich, et al. Front Neuroendocrinol. 2014 Jan;35(1):2-5. doi: 10.1016/j.yfrne.2013.09.003. Epub 2013 Nov 21. PubMed PMID: 24268499.

Taylor RP, Lindorfer MA. The role of complement in mAb-based therapies of cancer. Methods. 2014 Jan 1;65(1):18-27. doi: 10.1016/j.ymeth.2013.07.027. Epub 2013 Jul 22. Review. PubMed PMID: 23886909.

Johnson JM, Smith JS, Schneider DA. A user’s guide to the ribosomal DNA in Saccharomyces cerevisiae. Methods Mol Biol. 2014;1205:303-28. doi: 10.1007/978-1-4939-1363-3_18. PubMed PMID: 25213252.

Zy≈Çkiewicz E, Stukenberg PT. Xenopus egg extracts as a simplified model system for structure-function studies of dynein regulators. Methods Mol Biol.2014;1136:117-33. doi: 10.1007/978-1-4939-0329-0_8. PubMed PMID: 24633797.

Pearson WR. BLAST and FASTA similarity searching for multiple sequence alignment. Methods Mol Biol. 2014;1079:75-101. doi: 10.1007/978-1-62703-646-7_5. PubMed PMID: 24170396.

Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM. The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Res. 2014 Jan;42(Database issue):D485-9. doi: 10.1093/nar/gkt1243. Epub 2013 Dec 6. PubMed PMID: 24319146; PubMed Central PMCID: PMC3964973.

Floyd DH, Zhang Y, Dey BK, Kefas B, Breit H, Marks K, Dutta A, Herold-Mende C, Synowitz M, Glass R, Abounader R, Purow BW. Novel anti-apoptotic microRNAs 582-5p and 363 promote human glioblastoma stem cell survival via direct inhibition of caspase 3, caspase 9, and Bim. PLoS One. 2014 May 7;9(5):e96239. doi: 10.1371/journal.pone.0096239. eCollection 2014. PubMed PMID: 24805821; PubMed Central PMCID: PMC4013090.

Hall EH, Liu Y, Xiao A, Shock L, Brautigan DL, Mayo MW, Adusumilli PS, Jones Inhibition of breast cancer metastasis suppressor 1 promotes a mesenchymal phenotype in lung epithelial cells that express oncogenic K-RasV12 and loss of p53. PLoS One. 2014 Apr 24;9(4):e95869. doi: 10.1371/journal.pone.0095869. eCollection 2014. PubMed PMID: 24763730; PubMed Central PMCID: PMC3999110.

Negishi M, Wongpalee SP, Sarkar S, Park J, Lee KY, Shibata Y, Reon BJ, Abounader R, Suzuki Y, Sugano S, Dutta A. A new lncRNA, APTR, associates with and represses the CDKN1A/p21 promoter by recruiting polycomb proteins. PLoS One. 2014 Apr 18;9(4):e95216. doi: 10.1371/journal.pone.0095216. eCollection 2014. PubMed PMID: 24748121; PubMed Central PMCID: PMC3991591.

Bjerke GA, Pietrzak K, Melhuish TA, Frierson HF Jr, Paschal BM, Wotton D. Prostate cancer induced by loss of Apc is restrained by TGFŒ≤ signaling. PLoS One. 2014 Mar 20;9(3):e92800. doi: 10.1371/journal.pone.0092800. eCollection 2014. PubMed PMID: 24651496; PubMed Central PMCID: PMC3961420.

Cohen JN, Tewalt EF, Rouhani SJ, Buonomo EL, Bruce AN, Xu X, Bekiranov S, Fu YX, Engelhard VH. Tolerogenic properties of lymphatic endothelial cells are controlled by the lymph node microenvironment. PLoS One. 2014 Feb 4;9(2):e87740. doi: 10.1371/journal.pone.0087740. eCollection 2014. PubMed PMID: 24503860; PubMed Central PMCID: PMC3913631.

Dey BK, Mueller AC, Dutta A. Long non-coding RNAs as emerging regulators of differentiation, development, and disease. Transcription. 2014;5(4):e944014. doi: 10.4161/21541272.2014.944014. Epub 2014 Oct 30. PubMed PMID: 25483404.

Near-atomic resolution for one state of F-actin. Galkin VE, Orlova A, Vos MR, Schröder GF, Egelman EH. Structure. 2015 Jan 6;23(1):173-82. doi: 10.1016/j.str.2014.11.006. Epub 2014 Dec 18. PMID: 25533486

Direct interaction of actin filaments with F-BAR protein pacsin2. Kostan J, Salzer U, Orlova A, Törö I, Hodnik V, Senju Y, Zou J, Schreiner C, Steiner J, Meriläinen J, Nikki M, Virtanen I, Carugo O, Rappsilber J, Lappalainen P, Lehto VP, Anderluh G, Egelman EH, Djinović-Carugo K. EMBO Rep. 2014 Nov;15(11):1154-62. doi: 10.15252/embr.201439267. Epub 2014 Sep 12. PMID: 25216944