Departmental Publications 2013

1: 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.

2: 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.

3: 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.

4: 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.

5: Wierman MB, Smith JS. Yeast sirtuins and the regulation of aging. FEMS Yeast Res. 2014 Feb;14(1):73-88. doi: 10.1111/1567-1364.12115. Epub 2013 Nov 14. PubMed PMID: 24164855.

6: 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.

7: 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.

8: 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.

9: 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.

10: Mills LJ, Pearson WR. Adjusting scoring matrices to correct overextended alignments. Bioinformatics. 2013 Dec 1;29(23):3007-13. doi: 10.1093/bioinformatics/btt517. Epub 2013 Aug 31. PubMed PMID: 23995390; PubMed Central PMCID: PMC3834790.

11: Im JS, Lee KY, Dillon LW, Dutta A. Human Primpol1: a novel guardian of stalled replication forks. EMBO Rep. 2013 Dec;14(12):1032-3. doi: 10.1038/embor.2013.171. Epub 2013 Nov 5. PubMed PMID: 24189099; PubMed Central PMCID: PMC3981087.

12: Pokrass MJ, Liu MF, Lindorfer MA, Taylor RP. Activation of complement by monoclonal antibodies that target cell-associated Œ≤‚ÇÇ-microglobulin: implications for cancer immunotherapy. Mol Immunol. 2013 Dec;56(4):549-60. doi: 10.1016/j.molimm.2013.05.242. Epub 2013 Aug 1. PubMed PMID: 23911412.

13: Burke TL, Miller JL, Grant PA. Direct inhibition of Gcn5 protein catalytic activity by polyglutamine-expanded ataxin-7. J Biol Chem. 2013 Nov 22;288(47):34266-75. doi: 10.1074/jbc.M113.487538. Epub 2013 Oct 15. PubMed PMID: 24129567; PubMed Central PMCID: PMC3837167.

14: 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. Policy decisions on endocrine disruptors should be based on science across disciplines: a response to Dietrich et¬†al. Andrology. 2013 Nov;1(6):802-5. doi: 10.1111/j.2047-2927.2013.00151.x. PubMed PMID: 24166945.

15: 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. Policy decisions on endocrine disruptors should be based on science across disciplines: a response to Dietrich et al. Endocrinology. 2013 Nov;154(11):3957-60. doi: 10.1210/en.2013-1854. Epub 2013 Sep 18. PubMed PMID: 24048095.

16: Mesner LD, Valsakumar V, Cieslik M, Pickin R, Hamlin JL, Bekiranov S. Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins. Genome Res. 2013 Nov;23(11):1774-88. doi: 10.1101/gr.155218.113. Epub 2013 Jul 16. PubMed PMID: 23861383; PubMed Central PMCID: PMC3814878.

17: Wolstenholme JT, Goldsby JA, Rissman EF. Transgenerational effects of prenatal bisphenol A on social recognition. Horm Behav. 2013 Nov;64(5):833-9. doi: 10.1016/j.yhbeh.2013.09.007. Epub 2013 Oct 5. PubMed PMID: 24100195; PubMed Central PMCID: PMC3955720.

18: Taylor RP. Gnawing at Metchnikoff’s paradigm. Blood. 2013 Oct 24;122(17):2922-4. doi: 10.1182/blood-2013-07-514083. PubMed PMID: 24159161.

19: 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. Policy decisions on endocrine disruptors should be based on science across disciplines: a response to Dietrich et al. Eur J Endocrinol. 2013 Oct 21;169(6):E1-4. doi: 10.1530/EJE-13-0763. Print 2013 Dec. PubMed PMID: 24057478.

20: Terai K, Shibata E, Abbas T, Dutta A. Degradation of p12 subunit by CRL4Cdt2 E3 ligase inhibits fork progression after DNA damage. J Biol Chem. 2013 Oct 18;288(42):30509-14. doi: 10.1074/jbc.C113.505586. Epub 2013 Sep 10. PubMed PMID: 24022480; PubMed Central PMCID: PMC3798521.

21: Poorey K, Viswanathan R, Carver MN, Karpova TS, Cirimotich SM, McNally JG, Bekiranov S, Auble DT. Measuring chromatin interaction dynamics on the second time scale at single-copy genes. Science. 2013 Oct 18;342(6156):369-72. doi: 10.1126/science.1242369. Epub 2013 Oct 3. PubMed PMID: 24091704; PubMed Central PMCID: PMC3997053.

22: Gupta A, Jha S, Engel DA, Ornelles DA, Dutta A. Tip60 degradation by adenovirus relieves transcriptional repression of viral transcriptional activator EIA. Oncogene. 2013 Oct 17;32(42):5017-25. doi: 10.1038/onc.2012.534. Epub 2012 Nov 26. PubMed PMID: 23178490; PubMed Central PMCID: PMC3955737.

23: Bonthuis PJ, Rissman EF. Neural growth hormone implicated in body weight sex differences. Endocrinology. 2013 Oct;154(10):3826-35. doi: 10.1210/en.2013-1234. Epub 2013 Jul 16. PubMed PMID: 23861378; PubMed Central PMCID: PMC3776866.

24: Abel JL, Rissman EF. Running-induced epigenetic and gene expression changes in the adolescent brain. Int J Dev Neurosci. 2013 Oct;31(6):382-90. doi: 10.1016/j.ijdevneu.2012.11.002. Epub 2012 Nov 23. PubMed PMID: 23178748; PubMed Central PMCID: PMC3686974.

25: Jazaeri AA, Shibata E, Park J, Bryant JL, Conaway MR, Modesitt SC, Smith PG, Milhollen MA, Berger AJ, Dutta A. Overcoming platinum resistance in preclinical models of ovarian cancer using the neddylation inhibitor MLN4924. Mol Cancer Ther. 2013 Oct;12(10):1958-67. doi: 10.1158/1535-7163.MCT-12-1028. Epub 2013 Aug 12 PubMed PMID: 23939375; PubMed Central PMCID: PMC3795967.

26: Wagenseller AG, Shada A, D’Auria KM, Murphy C, Sun D, Molhoek KR, Papin JA, Dutta A, Slingluff CL Jr. MicroRNAs induced in melanoma treated with combination targeted therapy of Temsirolimus and Bevacizumab. J Transl Med. 2013 Sep 18;11:218. doi: 10.1186/1479-5876-11-218. PubMed PMID: 24047116; PubMed Central PMCID: PMC3853033.

27: Cie≈õlik M, Hoang SA, Baranova N, Chodaparambil S, Kumar M, Allison DF, Xu X, Wamsley JJ, Gray L, Jones DR, Mayo MW, Bekiranov S. Epigenetic coordination of signaling pathways during the epithelial-mesenchymal transition. Epigenetics Chromatin. 2013 Sep 2;6(1):28. doi: 10.1186/1756-8935-6-28. PubMed PMID: 24004852; PubMed Central PMCID: PMC3847279.

28: Malhotra A, Shibata Y, Hall IM, Dutta A. Chromosomal structural variations during progression of a prostate epithelial cell line to a malignant metastatic state inactivate the NF2, NIPSNAP1, UGT2B17, and LPIN2 genes. Cancer Biol Ther. 2013 Sep;14(9):840-52. doi: 10.4161/cbt.25329. Epub 2013 Jul 26. PubMed PMID: 23792589; PubMed Central PMCID: PMC3909553.

29: Dar A, Shibata E, Dutta A. Deubiquitination of Tip60 by USP7 determines the activity of the p53-dependent apoptotic pathway. Mol Cell Biol. 2013 Aug;33(16):3309-20. doi: 10.1128/MCB.00358-13. Epub 2013 Jun 17. PubMed PMID: 23775119; PubMed Central PMCID: PMC3753911.

30: Zasadzi≈Ñska E, Barnhart-Dailey MC, Kuich PH, Foltz DR. Dimerization of the CENP-A assembly factor HJURP is required for centromeric nucleosome deposition. EMBO J. 2013 Jul 31;32(15):2113-24. doi: 10.1038/emboj.2013.142. Epub 2013 Jun 14 PubMed PMID: 23771058; PubMed Central PMCID: PMC3730228.

31: Kumar M, Allison DF, Baranova NN, Wamsley JJ, Katz AJ, Bekiranov S, Jones DR, Mayo MW. NF-Œ∫B regulates mesenchymal transition for the induction of non-small cell lung cancer initiating cells. PLoS One. 2013 Jul 30;8(7):e68597. doi: 10.1371/journal.pone.0068597. Print 2013. PubMed PMID: 23935876; PubMed Central PMCID: PMC3728367.

32: Bharadwaj P, McInnis C, Madden AM, Bonthuis PJ, Zup S, Rissman EF, Park JH. Increased dendritic spine density and tau expression are associated with individual differences in steroidal regulation of male sexual behavior. PLoS One. 2013 Jul 16;8(7):e69672. doi: 10.1371/journal.pone.0069672. Print 2013. PubMed PMID: 23874981; PubMed Central PMCID: PMC3713039.

33: Bailey AO, Panchenko T, Sathyan KM, Petkowski JJ, Pai PJ, Bai DL, Russell DH, Macara IG, Shabanowitz J, Hunt DF, Black BE, Foltz DR. Posttranslational modification of CENP-A influences the conformation of centromeric chromatin. Proc Natl Acad Sci U S A. 2013 Jul 16;110(29):11827-32. doi: 10.1073/pnas.1300325110. Epub 2013 Jul 1. PubMed PMID: 23818633; PubMed Central PMCID: PMC3718089.

34: Abbas T, Keaton M, Dutta A. Regulation of TGF-Œ≤ signaling, exit from the cell cycle, and cellular migration through cullin cross-regulation: SCF-FBXO11 turns off CRL4-Cdt2. Cell Cycle. 2013 Jul 15;12(14):2175-82. doi: 10.4161/cc.25314. PubMed PMID: 23892434; PubMed Central PMCID: PMC3755067.

35: Johnson JM, French SL, Osheim YN, Li M, Hall L, Beyer AL, Smith JS. Rpd3- and spt16-mediated nucleosome assembly and transcriptional regulation on yeast ribosomal DNA genes. Mol Cell Biol. 2013 Jul;33(14):2748-59. doi: 10.1128/MCB.00112-13. Epub 2013 May 20. PubMed PMID: 23689130; PubMed Central PMCID: PMC3700123.

36: Pearson WR. An introduction to sequence similarity (“homology”) searching. Curr Protoc Bioinformatics. 2013 Jun;Chapter 3:Unit3.1. doi: 10.1002/0471250953.bi0301s42. Review. PubMed PMID: 23749753; PubMed Central PMCID: PMC3820096.

37: Li M, Valsakumar V, Poorey K, Bekiranov S, Smith JS. Genome-wide analysis of functional sirtuin chromatin targets in yeast. Genome Biol. 2013 May 27;14(5):R48. doi: 10.1186/gb-2013-14-5-r48. PubMed PMID: 23710766; PubMed Central PMCID: PMC4053722.

38: Snow CJ, Dar A, Dutta A, Kehlenbach RH, Paschal BM. Defective nuclear import of Tpr in Progeria reflects the Ran sensitivity of large cargo transport. J Cell Biol. 2013 May 13;201(4):541-57. doi: 10.1083/jcb.201212117. Epub 2013 May 6. PubMed PMID: 23649804; PubMed Central PMCID: PMC3653351.

39: Burke DJ. Unbiased segregation of yeast chromatids in Saccharomyces cerevisiae. Chromosome Res. 2013 May;21(3):193-202. doi: 10.1007/s10577-013-9348-x. Review. PubMed PMID: 23681653.

40: Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, Hall IM. Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms. Genome Res. 2013 May;23(5):762-76. doi: 10.1101/gr.143677.112. Epub 2013 Feb 14. PubMed PMID: 23410887; PubMed Central PMCID: PMC3638133.

41: Galkin VE, Kolappan S, Ng D, Zong Z, Li J, Yu X, Egelman EH, Craig L. The structure of the CS1 pilus of enterotoxigenic Escherichia coli reveals structural polymorphism. J Bacteriol. 2013 Apr;195(7):1360-70. doi: 10.1128/JB.01989-12. Epub 2012 Nov 21. PubMed PMID: 23175654; PubMed Central PMCID: PMC3624524.

42: Park J, Long DT, Lee KY, Abbas T, Shibata E, Negishi M, Luo Y, Schimenti JC, Gambus A, Walter JC, Dutta A. The MCM8-MCM9 complex promotes RAD51 recruitment at DNA damage sites to facilitate homologous recombination. Mol Cell Biol. 2013 Apr;33(8):1632-44. doi: 10.1128/MCB.01503-12. Epub 2013 Feb 11. PubMed PMID: 23401855; PubMed Central PMCID: PMC3624244.

43: Abbas T, Mueller AC, Shibata E, Keaton M, Rossi M, Dutta A. CRL1-FBXO11 promotes Cdt2 ubiquitylation and degradation and regulates Pr-Set7/Set8-mediated cellular migration. Mol Cell. 2013 Mar 28;49(6):1147-58. doi: 10.1016/j.molcel.2013.02.003. Epub 2013 Mar 7. PubMed PMID: 23478445; PubMed Central PMCID: PMC3615078.

44: Abbas T, Keaton MA, Dutta A. Genomic instability in cancer. Cold Spring Harb Perspect Biol. 2013 Mar 1;5(3):a012914. doi: 10.1101/cshperspect.a012914. Review. PubMed PMID: 23335075; PubMed Central PMCID: PMC3578360.

45: Wolstenholme JT, Rissman EF, Bekiranov S. Sexual differentiation in the developing mouse brain: contributions of sex chromosome genes. Genes Brain Behav. 2013 Mar;12(2):166-80. doi: 10.1111/gbb.12010. Epub 2013 Jan 10. PubMed PMID: 23210685; PubMed Central PMCID: PMC3581734.

46: Jha S, Gupta A, Dar A, Dutta A. RVBs are required for assembling a functional TIP60 complex. Mol Cell Biol. 2013 Mar;33(6):1164-74. doi: 10.1128/MCB.01567-12. Epub 2013 Jan 7. PubMed PMID: 23297341; PubMed Central PMCID: PMC3592018.

47: Mueller AC, Sun D, Dutta A. The miR-99 family regulates the DNA damage response through its target SNF2H. Oncogene. 2013 Feb 28;32(9):1164-72. doi: 10.1038/onc.2012.131. Epub 2012 Apr 23. PubMed PMID: 22525276; PubMed Central PMCID: PMC3407337.

48: Liu Y, Mayo MW, Nagji AS, Hall EH, Shock LS, Xiao A, Stelow EB, Jones DR. BRMS1 suppresses lung cancer metastases through an E3 ligase function on histone acetyltransferase p300. Cancer Res. 2013 Feb 15;73(4):1308-17. doi: 10.1158/0008-5472.CAN-12-2489. Epub 2012 Dec 26. PubMed PMID: 23269275; PubMed Central PMCID: PMC3578176.

49: Stellfox ME, Bailey AO, Foltz DR. Putting CENP-A in its place. Cell Mol Life Sci. 2013 Feb;70(3):387-406. doi: 10.1007/s00018-012-1048-8. Epub 2012 Jun 23. Review. PubMed PMID: 22729156; PubMed Central PMCID: PMC4084702.

50: Layer RM, Skadron K, Robins G, Hall IM, Quinlan AR. Binary Interval Search: a scalable algorithm for counting interval intersections. Bioinformatics. 2013 Jan 1;29(1):1-7. doi: 10.1093/bioinformatics/bts652. Epub 2012 Nov 4. PubMed PMID: 23129298; PubMed Central PMCID: PMC3530906.

51: Pearson WR. Selecting the Right Similarity-Scoring Matrix. Curr Protoc Bioinformatics. 2013;43:3.5.1-3.5.9. PubMed PMID: 24509512; PubMed Central PMCID: PMC3848038.

52: 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. Policy decisions on endocrine disruptors should be based on science across disciplines: a response to Dietrich et al. Horm Res Paediatr. 2013;80(5):305-8. doi: 10.1159/000355668. Epub 2013 Oct 9. PubMed PMID: 24107550.

53: Hoang SA, Bekiranov S. The network architecture of the Saccharomyces cerevisiae genome. PLoS One. 2013 Dec 9;8(12):e81972. doi: 10.1371/journal.pone.0081972. eCollection 2013. PubMed PMID: 24349163; PubMed Central PMCID: PMC3857230.

54: Cox KH, So NL, Rissman EF. Foster dams rear fighters: strain-specific effects of within-strain fostering on aggressive behavior in male mice. PLoS One. 2013 Sep 10;8(9):e75037. doi: 10.1371/journal.pone.0075037. eCollection 2013. PubMed PMID: 24040381; PubMed Central PMCID: PMC3769275.

55: Miller JL, Grant PA. The role of DNA methylation and histone modifications in transcriptional regulation in humans. Subcell Biochem. 2013;61:289-317. doi: 10.1007/978-94-007-4525-4_13. Review. PubMed PMID: 23150256.

56: Human Primpol1: a novel guardian of stalled replication forks. Im JS, Lee KY, Dillon LW, Dutta A. EMBO Rep. 2013 Dec;14(12):1032-3. doi: 10.1038/embor.2013.171. Epub 2013 Nov 5. No abstract available.  PMID: 24189099