Departmental Publications 2012

1: 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.

2: 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.

3: 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.

4: 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.

5: 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.

6: 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.

7: 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.

8: McCullough SD, Xu X, Dent SY, Bekiranov S, Roeder RG, Grant PA. Reelin is a target of polyglutamine expanded ataxin-7 in human spinocerebellar ataxia type 7 (SCA7) astrocytes. Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21319-24. doi: 10.1073/pnas.1218331110. Epub 2012 Dec 10. PubMed PMID: 23236151; PubMed Central PMCID: PMC3535616.

9: Keyes BE, Sykes KD, Remington CE, Burke DJ. Sister chromatids segregate at mitosis without mother-daughter bias in Saccharomyces cerevisiae. Genetics. 2012 Dec;192(4):1553-7. doi: 10.1534/genetics.112.145680. Epub 2012 Oct 10. PubMed PMID: 23051643; PubMed Central PMCID: PMC3512160.

10: Dey BK, Mueller AC, Dutta A. Non-micro-short RNAs: the new kids on the block. Mol Biol Cell. 2012 Dec;23(24):4664-7. doi: 10.1091/mbc.E12-10-0716. PubMed PMID: 23239791; PubMed Central PMCID: PMC3521675.

11: Gagan J, Dey BK, Layer R, Yan Z, Dutta A. Notch3 and Mef2c proteins are mutually antagonistic via Mkp1 protein and miR-1/206 microRNAs in differentiating myoblasts. J Biol Chem. 2012 Nov 23;287(48):40360-70. doi: 10.1074/jbc.M112.378414. Epub 2012 Oct 10. PubMed PMID: 23055528; PubMed Central PMCID: PMC3504751.

12: Galkin VE, Orlova A, Egelman EH. Are ParM filaments polar or bipolar? J Mol Biol. 2012 Nov 2;423(4):482-5. doi: 10.1016/j.jmb.2012.08.006. Epub 2012 Aug 21. PubMed PMID: 22922064; PubMed Central PMCID: PMC3467344.

13: Locke LW, Mayo MW, Yoo AD, Williams MB, Berr SS. PET imaging of tumor associated macrophages using mannose coated 64Cu liposomes. Biomaterials. 2012 Nov;33(31):7785-93. doi: 10.1016/j.biomaterials.2012.07.022. Epub 2012 Jul 26. PubMed PMID: 22840225.

14: Allison DF, Wamsley JJ, Kumar M, Li D, Gray LG, Hart GW, Jones DR, Mayo MW. Modification of RelA by O-linked N-acetylglucosamine links glucose metabolism to NF-Œ∫B acetylation and transcription. Proc Natl Acad Sci U S A. 2012 Oct 16;109(42):16888-93. doi: 10.1073/pnas.1208468109. Epub 2012 Oct 1. PubMed PMID: 23027940; PubMed Central PMCID: PMC3479489.

15: Faust GG, Hall IM. YAHA: fast and flexible long-read alignment with optimal breakpoint detection. Bioinformatics. 2012 Oct 1;28(19):2417-24. Epub 2012 Jul PubMed PMID: 22829624; PubMed Central PMCID: PMC3463118.

16: Dey BK, Gagan J, Yan Z, Dutta A. miR-26a is required for skeletal muscle differentiation and regeneration in mice. Genes Dev. 2012 Oct 1;26(19):2180-91. doi: 10.1101/gad.198085.112. PubMed PMID: 23028144; PubMed Central PMCID: PMC3465739.

17: Demirel PB, Keyes BE, Chaterjee M, Remington CE, Burke DJ. A redundant function for the N-terminal tail of Ndc80 in kinetochore-microtubule interaction in Saccharomyces cerevisiae. Genetics. 2012 Oct;192(2):753-6. doi: 10.1534/genetics.112.143818. Epub 2012 Jul 30. PubMed PMID: 22851650; PubMed Central PMCID: PMC3454895.

18: Yu X, Goforth C, Meyer C, Rachel R, Wirth R, Schr√∂der GF, Egelman EH. Filaments from Ignicoccus hospitalis show diversity of packing in proteins containing N-terminal type IV pilin helices. J Mol Biol. 2012 Sep 14;422(2):274-81. doi: 10.1016/j.jmb.2012.05.031. Epub 2012 May 30. PubMed PMID: 22659006; PubMed Central PMCID: PMC3599786.

19: Lindorfer MA, Wiestner A, Zent CS, Taylor RP. Monoclonal antibody (mAb)-based cancer therapy: Is it time to reevaluate dosing strategies? Oncoimmunology. 2012 Sep 1;1(6):959-961. PubMed PMID: 23162771; PubMed Central PMCID: PMC3489759.

20: Abel JL, Rissman EF. Location, location, location: genetic regulation of neural sex differences. Rev Endocr Metab Disord. 2012 Sep;13(3):151-61. doi: 10.1007/s11154-011-9186-0. Review. PubMed PMID: 21607612; PubMed Central PMCID: PMC3622700.

21: Utepbergenov D, Derewenda U, Olekhnovich N, Szukalska G, Banerjee B, Hilinski MK, Lannigan DA, Stukenberg PT, Derewenda ZS. Insights into the inhibition of the p90 ribosomal S6 kinase (RSK) by the flavonol glycoside SL0101 from the 1.5 √Ö crystal structure of the N-terminal domain of RSK2 with bound inhibitor. Biochemistry. 2012 Aug 21;51(33):6499-510. doi: 10.1021/bi300620c. Epub 2012 Aug 6 PubMed PMID: 22846040; PubMed Central PMCID: PMC3462495.

22: Wolstenholme JT, Edwards M, Shetty SR, Gatewood JD, Taylor JA, Rissman EF, Connelly JJ. Gestational exposure to bisphenol a produces transgenerational changes in behaviors and gene expression. Endocrinology. 2012 Aug;153(8):3828-38. doi: 10.1210/en.2012-1195. Epub 2012 Jun 15. PubMed PMID: 22707478; PubMed Central PMCID: PMC3404345.

23: Tejada LD, Rissman EF. Sex differences in social investigation: effects of androgen receptors, hormones and test partner. J Neuroendocrinol. 2012 Aug;24(8):1144-53. doi: 10.1111/j.1365-2826.2012.02322.x. PubMed PMID: 22487205; PubMed Central PMCID: PMC3615635.

24: Stolzenberg DS, Stevens JS, Rissman EF. Experience-facilitated improvements in pup retrieval; evidence for an epigenetic effect. Horm Behav. 2012 Jul;62(2):128-35. doi: 10.1016/j.yhbeh.2012.05.012. Epub 2012 Jun 8. PubMed PMID: 22687346; PubMed Central PMCID: PMC3474355.

25: Li W, McWilliam H, Goujon M, Cowley A, Lopez R, Pearson WR. PSI-Search: iterative HOE-reduced profile SSEARCH searching. Bioinformatics. 2012 Jun 15;28(12):1650-1. doi: 10.1093/bioinformatics/bts240. Epub 2012 Apr 25. PubMed PMID: 22539666; PubMed Central PMCID: PMC3371869.

26: McClure JM, Wierman MB, Maqani N, Smith JS. Isonicotinamide enhances Sir2 protein-mediated silencing and longevity in yeast by raising intracellular NAD+ concentration. J Biol Chem. 2012 Jun 15;287(25):20957-66. doi: 10.1074/jbc.M112.367524. Epub 2012 Apr 26. PubMed PMID: 22539348; PubMed Central PMCID: PMC3375519.

27: Wotton D. TGF-Œ≤ drives DNA demethylation. Mol Cell. 2012 Jun 8;46(5):556-7. doi: 10.1016/j.molcel.2012.05.031. PubMed PMID: 22681884.

28: Gagan J, Dey BK, Dutta A. MicroRNAs regulate and provide robustness to the myogenic transcriptional network. Curr Opin Pharmacol. 2012 Jun;12(3):383-8. doi: 10.1016/j.coph.2012.02.001. Epub 2012 Mar 2. Review. PubMed PMID: 22386695; PubMed Central PMCID: PMC3369106.

29: Bassett EA, DeNizio J, Barnhart-Dailey MC, Panchenko T, Sekulic N, Rogers DJ, Foltz DR, Black BE. HJURP uses distinct CENP-A surfaces to recognize and to stabilize CENP-A/histone H4 for centromere assembly. Dev Cell. 2012 Apr 17;22(4):749-62. doi: 10.1016/j.devcel.2012.02.001. Epub 2012 Mar 8. PubMed PMID: 22406139; PubMed Central PMCID: PMC3353549.

30: Gioeli D, Paschal BM. Post-translational modification of the androgen receptor. Mol Cell Endocrinol. 2012 Apr 16;352(1-2):70-8. doi: 10.1016/j.mce.2011.07.004. Epub 2011 Jul 24. PubMed PMID: 21820033.

31: Shibata Y, Kumar P, Layer R, Willcox S, Gagan JR, Griffith JD, Dutta A. Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues. Science. 2012 Apr 6;336(6077):82-6. doi: 10.1126/science.1213307. Epub 2012 Mar 8. Erratum in: Science. 2012 Jun 22;336(6088):1506. PubMed PMID: 22403181; PubMed Central PMCID: PMC3703515.

32: Addison ML, Rissman EF. Sexual dimorphism of growth hormone in the hypothalamus: regulation by estradiol. Endocrinology. 2012 Apr;153(4):1898-907. doi: 10.1210/en.2011-1982. Epub 2012 Feb 7. PubMed PMID: 22315455; PubMed Central PMCID: PMC3320260.

33: Bonthuis PJ, Cox KH, Rissman EF. X-chromosome dosage affects male sexual behavior. Horm Behav. 2012 Apr;61(4):565-72. doi: 10.1016/j.yhbeh.2012.02.003. Epub 2012 Feb 10. PubMed PMID: 22349083; PubMed Central PMCID: PMC3319230.

34: Niedzialkowska E, Wang F, Porebski PJ, Minor W, Higgins JM, Stukenberg PT. Molecular basis for phosphospecific recognition of histone H3 tails by Survivin paralogues at inner centromeres. Mol Biol Cell. 2012 Apr;23(8):1457-66. doi: 10.1091/mbc.E11-11-0904. Epub 2012 Feb 22. PubMed PMID: 22357620; PubMed Central PMCID: PMC3327328.

35: Moyle-Heyrman G, Viswanathan R, Widom J, Auble DT. Two-step mechanism for modifier of transcription 1 (Mot1) enzyme-catalyzed displacement of TATA-binding protein (TBP) from DNA. J Biol Chem. 2012 Mar 16;287(12):9002-12. doi: 10.1074/jbc.M111.333484. Epub 2012 Feb 1. PubMed PMID: 22298788; PubMed Central PMCID: PMC3308732.

36: Matson DR, Demirel PB, Stukenberg PT, Burke DJ. A conserved role for COMA/CENP-H/I/N kinetochore proteins in the spindle checkpoint. Genes Dev. 2012 Mar 15;26(6):542-7. doi: 10.1101/gad.184184.111. PubMed PMID: 22426531; PubMed Central PMCID: PMC3315115.

37: Liu Y, Mayo MW, Nagji AS, Smith PW, Ramsey CS, Li D, Jones DR. Phosphorylation of RelA/p65 promotes DNMT-1 recruitment to chromatin and represses transcription of the tumor metastasis suppressor gene BRMS1. Oncogene. 2012 Mar 1;31(9):1143-54. doi: 10.1038/onc.2011.308. Epub 2011 Jul 18. PubMed PMID: 21765477; PubMed Central PMCID: PMC3219802.

38: Galkin VE, Orlova A, Egelman EH. Actin filaments as tension sensors. Curr Biol. 2012 Feb 7;22(3):R96-101. doi: 10.1016/j.cub.2011.12.010. Review. PubMed PMID: 22321312; PubMed Central PMCID: PMC3277726.

39: Foltz DR, Stukenberg PT. A new histone at the centromere? Cell. 2012 Feb 3;148(3):394-6. doi: 10.1016/j.cell.2012.01.023. PubMed PMID: 22304909; PubMed Central PMCID: PMC3404608.

40: Silva MC, Bodor DL, Stellfox ME, Martins NM, Hochegger H, Foltz DR, Jansen 1. Cdk activity couples epigenetic centromere inheritance to cell cycle progression. Dev Cell. 2012 Jan 17;22(1):52-63. doi: 10.1016/j.devcel.2011.10.014. Epub 2011 Dec 8. PubMed PMID: 22169070.

41: Glidden EJ, Gray LG, Vemuru S, Li D, Harris TE, Mayo MW. Multiple site acetylation of Rictor stimulates mammalian target of rapamycin complex 2 (mTORC2)-dependent phosphorylation of Akt protein. J Biol Chem. 2012 Jan 2;287(1):581-8. doi: 10.1074/jbc.M111.304337. Epub 2011 Nov 14. PubMed PMID: 22084251; PubMed Central PMCID: PMC3249112.

42: Zhang Y, Dutta A, Abounader R. The role of microRNAs in glioma initiation and progression. Front Biosci (Landmark Ed). 2012 Jan 1;17:700-12. Review. PubMed PMID: 22201769; PubMed Central PMCID: PMC3278211.

43: Keene KL, Quinlan AR, Hou X, Hall IM, Mychaleckyj JC, Onengut-Gumuscu S, Concannon P. Evidence for two independent associations with type 1 diabetes at the 12q13 locus. Genes Immun. 2012 Jan;13(1):66-70. doi: 10.1038/gene.2011.56. Epub 2011 Aug 18. PubMed PMID: 21850031; PubMed Central PMCID: PMC3285513.

44: Hall IM, Quinlan AR. Detection and interpretation of genomic structural variation in mammals. Methods Mol Biol. 2012;838:225-48. doi: 10.1007/978-1-61779-507-7_11. Review. PubMed PMID: 22228015.

45: Holliday GL, Andreini C, Fischer JD, Rahman SA, Almonacid DE, Williams ST, Pearson WR. MACiE: exploring the diversity of biochemical reactions. Nucleic Acids Res. 2012 Jan;40(Database issue):D783-9. doi: 10.1093/nar/gkr799. Epub 2011 Nov 3. PubMed PMID: 22058127; PubMed Central PMCID: PMC3244993.

46: Taniguchi K, Anderson AE, Sutherland AE, Wotton D. Loss of Tgif function causes holoprosencephaly by disrupting the SHH signaling pathway. PLoS Genet. 2012;8(2):e1002524. doi: 10.1371/journal.pgen.1002524. Epub 2012 Feb 23. PubMed PMID: 22383895; PubMed Central PMCID: PMC3285584.

47: Dutta P, Tanti GK, Sharma S, Goswami SK, Komath SS, Mayo MW, Hockensmith JW, Muthuswami R. Global epigenetic changes induced by SWI2/SNF2 inhibitors characterize neomycin-resistant mammalian cells. PLoS One. 2012;7(11):e49822. doi: 10.1371/journal.pone.0049822. Epub 2012 Nov 28. PubMed PMID: 23209606; PubMed Central PMCID: PMC3509132.

48: Zerlanko BJ, Bartholin L, Melhuish TA, Wotton D. Premature senescence and increased TGFŒ≤ signaling in the absence of Tgif1. PLoS One. 2012;7(4):e35460. doi: 10.1371/journal.pone.0035460. Epub 2012 Apr 13. PubMed PMID: 22514746; PubMed Central PMCID: PMC3325954.

49: Quinlan AR, Hall IM. Characterizing complex structural variation in germline and somatic genomes. Trends Genet. 2012 Jan;28(1):43-53. doi: 10.1016/j.tig.2011.10.002. Epub 2011 Nov 15. Review. PubMed PMID: 22094265; PubMed Central PMCID: PMC3249479.