Departmental Publications 2017

CK2α’ Drives Lung Cancer Metastasis by Targeting BRMS1 Nuclear Export and Degradation. Liu Y, Amin EB, Mayo MW, Chudgar NP, Bucciarelli PR, Kadota K, Adusumilli PS, Jones DR. Cancer Res. 2016 May 1;76(9):2675-86. doi: 10.1158/0008-5472.CAN-15-2888. Epub 2016 Mar 15. PMID: 26980766
Structural basis of TIR-domain-assembly formation in MAL- and MyD88-dependent TLR4 signaling. Ve T, Vajjhala PR, Hedger A, Croll T, DiMaio F, Horsefield S, Yu X, Lavrencic P, Hassan Z, Morgan GP, Mansell A, Mobli M, O’Carroll A, Chauvin B, Gambin Y, Sierecki E, Landsberg MJ, Stacey KJ, Egelman EH, Kobe B. Nat Struct Mol Biol. 2017 Jul 31. doi: 10.1038/nsmb.3444.  PMID: 28759049
Refined Cryo-EM Structure of the T4 Tail Tube: Exploring the Lowest Dose Limit. Zheng W, Wang F, Taylor NMI, Guerrero-Ferreira RC, Leiman PG, Egelman EH. Structure. 2017 Jul 10. pii: S0969-2126(17)30213-7. doi: 10.1016/j.str.2017.06.017. PMID: 28757144
Genome-Wide Identification of Basic Helix-Loop-Helix and NF-1 Motifs Underlying GR Binding Sites in Male Rat Hippocampus. Pooley JR, Flynn BP, Grøntved L, Baek S, Guertin MJ, Kershaw YM, Birnie MT, Pellatt A, Rivers CA, Schiltz RL, Hager GL, Lightman SL, Conway-Campbell BL. Endocrinology. 2017 May 1;158(5):1486-1501. doi: 10.1210/en.2016-1929. PMID: 28200020
Complement C5a-induced changes in neutrophil morphology during inflammation. Denk S, Taylor RP, Wiegner R, Cook EM, Lindorfer MA, Pfeiffer K, Paschke S, Eiseler T, Weiss M, Barth E, Lambris JD, Kalbitz M, Martin T, Barth H, Messerer DAC, Gebhard F, Huber-Lang MS. Scand J Immunol. 2017 Jun 30. doi: 10.1111/sji.12580.  PMID: 28671713
Pericytes and immune cells contribute to complement activation in tubulointerstitial fibrosis. Xavier S, Sahu RK, Landes SG, Yu J, Taylor RP, Ayyadevara S, Megyesi J, Stallcup WB, Duffield JS, Reis ES, Lambris JD, Portilla D. Am J Physiol Renal Physiol. 2017 Mar 1;312(3):F516-F532. doi: 10.1152/ajprenal.00604.2016. Epub 2017 Jan 4. PMID: 28052876
Tgif1 and Tgif2 Repress Expression of the RabGAP Evi5l. Anderson AE, Taniguchi K, Hao Y, Melhuish TA, Shah A, Turner SD, Sutherland AE, Wotton D. Mol Cell Biol. 2017 Feb 15;37(5). pii: e00527-16. doi: 10.1128/MCB.00527-16. Print 2017 Mar 1. PMID: 27956704
Genetic and Molecular Analyses indicate independent effects of TGIFs on Nodal and Gli3 in neural tube patterning. Taniguchi K, Anderson AE, Melhuish TA, Carlton AL, Manukyan A, Sutherland AE, Wotton D. Eur J Hum Genet. 2017 Feb;25(2):208-215. doi: 10.1038/ejhg.2016.164. Epub 2016 Dec 7. PMID: 27924807
Tgif1 and Tgif2 Regulate Axial Patterning in Mouse. Melhuish TA, Taniguchi K, Wotton D. PLoS One. 2016 May 17;11(5):e0155837. doi: 10.1371/journal.pone.0155837. eCollection 2016. PMID: 27187787
Transcriptomes of six mutants in the Sen1 pathway reveal combinatorial control of transcription termination across the Saccharomyces cerevisiae genome. Chen X, Poorey K, Carver MN, Müller U, Bekiranov S, Auble DT, Brow DA. PLoS Genet. 2017 Jun 30;13(6):e1006863. doi: 10.1371/journal.pgen.1006863. eCollection 2017 Jun. PMID: 28665995
IgG Fc domains that bind C1q but not effector Fcγ receptors delineate the importance of complement-mediated effector functions. Lee CH, Romain G, Yan W, Watanabe M, Charab W, Todorova B, Lee J, Triplett K, Donkor M, Lungu OI, Lux A, Marshall N, Lindorfer MA, Goff OR, Balbino B, Kang TH, Tanno H, Delidakis G, Alford C, Taylor RP, Nimmerjahn F, Varadarajan N, Bruhns P, Zhang YJ, Georgiou G. Nat Immunol. 2017 Jun 12. doi: 10.1038/ni.3770. PMID: 28604720
RNA Polymerase I and Fob1 contributions to transcriptional silencing at the yeast rDNA locus.Buck SW, Maqani N, Matecic M, Hontz RD, Fine RD, Li M, Smith JS. Nucleic Acids Res. 2016 Jul 27;44(13):6173-84. doi: 10.1093/nar/gkw212. Epub 2016 Apr 8. PMID: 27060141
Model for a novel membrane envelope in a filamentous hyperthermophilic virus. Egelman EH, Kasson PM, DiMaio F, Yu X, Lucas-Staat S, Krupovic M, Schouten S, Prangishvili D. Elife. 2017 Jun 22;6. pii: e26268. doi: 10.7554/eLife.26268. PMID: 28639939  
RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps. Frenz B, Walls AC, Egelman EH, Veesler D, DiMaio F. Nat Methods. 2017 Jun 19. doi: 10.1038/nmeth.4340. PMID: 28628127
Cryo-EM of bacterial pili and archaeal flagellar filaments. Egelman EH. Curr Opin Struct Biol. 2017 Jun 10;46:31-37. doi: 10.1016/j.sbi.2017.05.012. Review. PMID: 28609682
CRISPR-STOP: gene silencing through base-editing-induced nonsense mutations. Kuscu C, Parlak M, Tufan T, Yang J, Szlachta K, Wei X, Mammadov R, Adli M. Nat Methods. 2017 Jul;14(7):710-712. doi: 10.1038/nmeth.4327. Epub 2017 Jun 5. PMID: 28581493
Transcriptomes of six mutants in the Sen1 pathway reveal combinatorial control of transcription termination across the Saccharomyces cerevisiae genome. Chen X, Poorey K, Carver MN, Müller U, Bekiranov S, Auble DT, Brow DA. PLoS Genet. 2017 Jun 30;13(6):e1006863. doi: 10.1371/journal.pgen.1006863.  PMID: 28665995
Transcriptomes of six mutants in the Sen1 pathway reveal combinatorial control of transcription termination across the Saccharomyces cerevisiae genome. Chen X, Poorey K, Carver MN, Müller U, Bekiranov S, Auble DT, Brow DA. PLoS Genet. 2017 Jun 30;13(6):e1006863. doi: 10.1371/journal.pgen.1006863. PMID: 28665995
  Mislocalization of centromeric histone H3 variant CENP-A contributes to chromosomal instability (CIN) in human cells. Shrestha RL, Ahn GS, Staples MI, Sathyan KM, Karpova TS, Foltz DR, Basrai MA. Oncotarget. 2017 May 23. doi: 10.18632/oncotarget.18108. PMID: 28596481
Neonatal expression of RNA-binding protein IGF2BP3 regulates the human fetal-adult megakaryocyte transition. Elagib KE, Lu CH, Mosoyan G, Khalil S, Zasadzińska E, Foltz DR, Balogh P, Gru AA, Fuchs DA, Rimsza LM, Verhoeyen E, Sansó M, Fisher RP, Iancu-Rubin C, Goldfarb AN. J Clin Invest. 2017 Jun 1;127(6):2365-2377. doi: 10.1172/JCI88936. Epub 2017 May 8. PMID: 28481226
The Modifier of Transcription 1 (Mot1) ATPase and Spt16 Histone Chaperone Co-regulate Transcription through Preinitiation Complex Assembly and Nucleosome Organization.
True JD, Muldoon JJ, Carver MN, Poorey K, Shetty SJ, Bekiranov S, Auble DT. J Biol Chem. 2016 Jul 15;291(29):15307-19. doi: 10.1074/jbc.M116.735134. Epub 2016 May 16. PMID: 27226635
Neutrophils: positive or negative? Taylor RP. Blood. 2017 May 11;129(19):2596-2597. doi: 10.1182/blood-2017-03-774695. PMID: 28495923
Ubiquitin Modification by the E3 Ligase/ADP-Ribosyltransferase Dtx3L/Parp9.Yang CS, Jividen K, Spencer A, Dworak N, Ni L, Oostdyk LT, Chatterjee M, Kuśmider B, Reon B, Parlak M, Gorbunova V, Abbas T, Jeffery E, Sherman NE, Paschal BM. Mol Cell. 2017 May 18;66(4):503-516.e5. doi: 10.1016/j.molcel.2017.04.028. PMID: 28525742
Normal and Cancerous Tissues Release extrachromosomal circular DNA (eccDNA) into the Circulation. Kumar P, Dillon L, Shibata Y, Jazaeri AA, Jones DR, Dutta A. Mol Cancer Res. 2017 May 26. pii: molcanres.0095.2016. doi: 10.1158/1541-7786.MCR-17-0095. PMID: 28550083
Expression of lncRNAs in Low-Grade Gliomas and Glioblastoma Multiforme: An In Silico Analysis. Reon BJ, Anaya J, Zhang Y, Mandell J, Purow B, Abounader R, Dutta A. PLoS Med. 2016 Dec 6;13(12):e1002192. doi: 10.1371/journal.pmed.1002192. eCollection 2016 Dec. PMID: 27923049
Molecular Mechanism of Mot1, a TATA-binding Protein (TBP)-DNA Dissociating Enzyme. Viswanathan R, True JD, Auble DT. J Biol Chem. 2016 Jul 22;291(30):15714-26. doi: 10.1074/jbc.M116.730366. Epub 2016 Jun 2. PMID: 27255709
Mechanism of Ska Recruitment by Ndc80 Complexes to Kinetochores. Janczyk PŁ, Skorupka KA, Tooley JG, Matson DR, Kestner CA, West T, Pornillos O, Stukenberg PT. Dev Cell. 2017 May 22;41(4):438-449.e4. doi: 10.1016/j.devcel.2017.04.020. PMID: 28535377
Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation. Duarte FM, Fuda NJ, Mahat DB, Core LJ, Guertin MJ, Lis JT. Genes Dev. 2016 Aug 1;30(15):1731-46. doi: 10.1101/gad.284430.116. Epub 2016 Aug 4. PMID: 27492368
Caloric restriction extends yeast chronological lifespan by optimizing the Snf1 (AMPK) signaling pathway. Wierman MB, Maqani N, Strickler E, Li M, Smith JS. Mol Cell Biol. 2017 Apr 3. pii: MCB.00562-16. doi: 10.1128/MCB.00562-16. PMID: 28373292
Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9. Qin P, Parlak M, Kuscu C, Bandaria J, Mir M, Szlachta K, Singh R, Darzacq X, Yildiz A, Adli M. Nat Commun. 2017 Mar 14;8:14725. doi: 10.1038/ncomms14725. PMID: 28290446
α-amino trimethylation of CENP-A by NRMT is required for full recruitment of the centromere. Sathyan KM, Fachinetti D, Foltz DR. Nat Commun. 2017 Mar 7;8:14678. doi: 10.1038/ncomms14678. PMID: 28266506
SUMO and Chromatin Remodeling. Wotton D, Pemberton LF, Merrill-Schools J. Adv Exp Med Biol. 2017;963:35-50. doi: 10.1007/978-3-319-50044-7_3. PMID: 28197905
Genome-wide identification of basic helix-loop helix and NF-1 motifs underlying GR binding sites in male rat hippocampus. Pooley JR, Flynn BP, Grøntved L, Baek S, Guertin MJ, Kershaw YM, Birnie MT, Pellatt A, Rivers CA, Schiltz RL, Hager GL, Lightman SL, Conway-Campbell BL. Endocrinology. 2017 Feb 13. doi: 10.1210/en.2016-1929. No abstract available. PMID: 28200020
Small Molecule Inhibitor of CBFβ-RUNX Binding for RUNX Transcription Factor Driven Cancers. Illendula A, Gilmour J, Grembecka J, Tirumala VS, Boulton A, Kuntimaddi A, Schmidt C, Wang L, Pulikkan JA, Zong H, Parlak M, Kuscu C, Pickin A, Zhou Y, Gao Y, Mishra L, Adli M, Castilla LH, Rajewski RA, Janes KA, Guzman ML, Bonifer C, Bushweller JH. EBioMedicine. 2016 Jun;8:117-31. doi: 10.1016/j.ebiom.2016.04.032. PMID: 27428424
The human SKA complex drives the metaphase-anaphase cell cycle transition by recruiting protein phosphatase 1 to kinetochores. Sivakumar S, Janczyk PŁ, Qu Q, Brautigam CA, Stukenberg PT, Yu H, Gorbsky GJ. Elife. 2016 Mar 16;5. pii: e12902. doi: 10.7554/eLife.12902. PMID: 26981768
DNA Fragile Site Breakage as a Measure of Chemical Exposure and Predictor of Individual Susceptibility to Form Oncogenic Rearrangements. Lehman CE, Dillon LW, Nikiforov YE, Wang YH. Carcinogenesis. 2017 Jan 9. pii: bgw210. doi: 10.1093/carcin/bgw210.  PMID: 28069693
RNA synthesis is associated with multiple TBP-chromatin binding events. Zaidi HA, Auble DT, Bekiranov S. Sci Rep. 2017 Jan 4;7:39631. doi: 10.1038/srep39631. PMID: 28051102
Pericyte and immune cells contribute to complement activation in tubulointerstitial fibrosis.Xavier S, Sahu RK, Landes SG, Yu J, Taylor RP, Ayyadevara S, Megyesi J, Stallcup WB, Duffield JS, Reis ES, Lambris JD, Portilla D. Am J Physiol Renal Physiol. 2017 Jan 4:ajprenal.00604.2016. doi: 10.1152/ajprenal.00604.2016. PMID: 28052876
Single neuron transcriptome analysis can reveal more than cell type classification: Does it matter if every neuron is unique? Harbom LJ, Chronister WD, McConnell MJ. Bioessays. 2016 Feb;38(2):157-61. doi: 10.1002/bies.201500097. Review. PMID: 26749010