Departmental Publications 2019

An improved auxin-inducible degron system preserves native protein levels and enables rapid and specific protein depletion. Sathyan KM, McKenna BD, Anderson WD, Duarte FM, Core L, Guertin MJ. Genes Dev. 2019 Aug 29. doi: 10.1101/gad.328237.119. PMID: 31467088

Mapping and Making Sense of Noncoding Mutations in the Genome.Yang J, Adli M. Cancer Res. 2019 Aug 6. doi: 10.1158/0008-5472.CAN-19-0905. Review. PMID: 31387922

Assessing work-related risk factors for musculoskeletal knee disorders in construction roofing tasks. Breloff SP, Dutta A, Dai F, Sinsel EW, Warren CM, Ning X, Wu JZ. Appl Ergon. 2019 Nov;81:102901. doi: 10.1016/j.apergo.2019.102901. Epub 2019 Jul 17. PMID: 31422268

Functional role of the type 1 pilus rod structure in mediating host-pathogen interactions. Spaulding CN, Schreiber HL 4th, Zheng W, Dodson KW, Hazen JE, Conover MS, Wang F, Svenmarker P, Luna-Rico A, Francetic O, Andersson M, Hultgren S, Egelman EH. Elife. 2018 Jan 18;7. pii: e31662. doi: 10.7554/eLife.31662. PMID: 29345620

NF-κB upregulates glutamine-fructose-6-phosphate transaminase 2 to promote migration in non-small cell lung cancer. Szymura SJ, Zaemes JP, Allison DF, Clift SH, D’Innocenzi JM, Gray LG, McKenna BD, Morris BB, Bekiranov S, LeGallo RD, Jones DR, Mayo MW. Cell Commun Signal. 2019 Mar 18;17(1):24. doi: 10.1186/s12964-019-0335-5. PMID: 30885209

Detection of ADP-Ribosylation of the Androgen Receptor Using the Recombinant Macrodomain AF1521 from Archaeoglobus fulgidus. Kamata T, Yang CS, Jividen K, Spencer A, Dworak N, Oostdyk LT, Paschal BM. Methods Mol Biol. 2019;1966:107-124. doi: 10.1007/978-1-4939-9195-2_9. PMID: 31041742

A Sir2-regulated locus control region in the recombination enhancer of Saccharomyces cerevisiae specifies chromosome III structure. Li M, Fine RD, Dinda M, Bekiranov S, Smith JS. PLoS Genet. 2019 Aug 28;15(8):e1008339. doi: 10.1371/journal.pgen.1008339. PMID: 31461456

AT-dinucleotide rich sequences drive fragile site formation. Irony-Tur Sinai M, Salamon A, Stanleigh N, Goldberg T, Weiss A, Wang YH, Kerem B. Nucleic Acids Res. 2019 Aug 14. pii: gkz689. doi: 10.1093/nar/gkz689. PMID: 31410468

Complex DNA structures trigger copy number variation across the Plasmodium falciparum genome. Huckaby AC, Granum CS, Carey MA, Szlachta K, Al-Barghouthi B, Wang YH, Guler JL. Nucleic Acids Res. 2019 Feb 28;47(4):1615-1627. doi: 10.1093/nar/gky1268. PMID: 30576466

Antitumor effect of insulin-like growth factor-1 receptor inhibition in head and neck squamous cell carcinoma. Lehman CE, Khalil AA, Axelrod MJ, Dougherty MI, Schoeff SS, Taniguchi LE, Mendez RE, David AP, McGarey PO Jr.,, Hubbard MA, Donaldson L, Frierson HF Jr.,, Stelow EB, Bekiranov S, Wulfkuhle JD, Petricoin EF, Gioeli DG, Jameson MJ.Laryngoscope. 2019 Aug 21. doi: 10.1002/lary.28236. PMID: 31433065

Shah KK, Whitaker RH, Busby T, Hu J, Shi B, Wang Z, Zang C, Placzek WJ, Jiang H. Specific inhibition of DPY30 activity by ASH2L-derived peptides suppresses blood cancer cell growth. Exp Cell Res. 2019 Sep 15;382(2):111485. doi: 10.1016/j.yexcr.2019.06.030. Epub 2019 Jun 26. PubMed PMID: 31251903; PubMed Central PMCID: PMC6717027.

Yang Z, Shah K, Khodadadi-Jamayran A, Jiang H. Control of Hematopoietic Stem and Progenitor Cell Function through Epigenetic Regulation of Energy Metabolism and Genome Integrity. Stem Cell Reports. 2019 Jul 9;13(1):61-75. doi: 10.1016/j.stemcr.2019.05.023. Epub 2019 Jun 20. PubMed PMID: 31231026; PubMed Central PMCID: PMC6627005.

Shah K, King GD, Jiang H. A chromatin modulator sustains self-renewal and enables differentiation of postnatal neural stem and progenitor cells. J Mol Cell Biol. 2019 May 8;. doi: 10.1093/jmcb/mjz036. PubMed PMID: 31065682.

Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq. Guertin MJ, Cullen AE, Markowetz F, Holding AN. Nucleic Acids Res. 2018 Jul 6;46(12):e75. doi: 10.1093/nar/gky252. PMID: 29672735

Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions. Martins AL, Walavalkar NM, Anderson WD, Zang C, Guertin MJ. Nucleic Acids Res. 2018 Jan 25;46(2):e9. doi: 10.1093/nar/gkx1053. PMID: 29126307

Chemotherapy-induced distal enhancers drive transcriptional program to maintain the chemoresistant state in ovarian cancer. Shang S, Yang J, Jazaeri AA, Duval AJ, Tufan T, Lopes Fischer N, Benamar M, Guessous F, Lee I, Campbell RM, Ebert PJ, Abbas T, Landen CN, DiFeo A, Scacheri PC, Adli M. Cancer Res. 2019 Jul 29. pii: canres.0215.2019. doi: 10.1158/0008-5472.CAN-19-0215. PMID: 31358529

<i>LINC00152</i> Promotes Invasion through a 3′-Hairpin Structure and Associates with Prognosis in Glioblastoma. Reon BJ, Takao Real Karia B, Kiran M, Dutta A. Mol Cancer Res. 2018 Oct;16(10):1470-1482. doi: 10.1158/1541-7786.MCR-18-0322. Epub 2018 Jul 10. PMID: 29991527

The AAA + ATPase TorsinA polymerizes into hollow helical tubes with 8.5 subunits per turn. Demircioglu FE, Zheng W, McQuown AJ, Maier NK, Watson N, Cheeseman IM, Denic V, Egelman EH, Schwartz TU. Nat Commun. 2019 Jul 22;10(1):3262. doi: 10.1038/s41467-019-11194-w. PMID: 31332180

Ambidextrous helical nanotubes from self-assembly of designed helical hairpin motifs. Hughes SA, Wang F, Wang S, Kreutzberger MAB, Osinski T, Orlova A, Wall JS, Zuo X, Egelman EH, Conticello VP. Proc Natl Acad Sci U S A. 2019 Jul 16;116(29):14456-14464. doi: 10.1073/pnas.1903910116. Epub 2019 Jul 1. PMID: 31262809

Functional reconstitution of the type IVa pilus assembly system from enterohaemorrhagic Escherichia coli. Luna Rico A, Zheng W, Petiot N, Egelman EH, Francetic O. Mol Microbiol. 2019 Mar;111(3):732-749. doi: 10.1111/mmi.14188. Epub 2019 Jan 21. PMID: 30561149

Genetic and epigenetic determinants establish a continuum of Hsf1 occupancy and activity across the yeast genome. Pincus D, Anandhakumar J, Thiru P, Guertin MJ, Erkine AM, Gross DS. Mol Biol Cell. 2018 Dec 15;29(26):3168-3182. doi: 10.1091/mbc.E18-06-0353. Epub 2018 Oct 17. PMID: 30332327

A Non-random Mouse Model for Pharmacological Reactivation of Mecp2 on the Inactive X Chromosome. Przanowski P, Zheng Z, Wasko U, Bhatnagar S. J Vis Exp. 2019 May 22;(147). doi: 10.3791/59449. PMID: 31180354

A Single-Agent Dual-Specificity Targeting of FOLR1 and DR5 as an Effective Strategy for Ovarian Cancer. Shivange G, Urbanek K, Przanowski P, Perry JSA, Jones J, Haggart R, Kostka C, Patki T, Stelow E, Petrova Y, Llaneza D, Mayo M, Ravichandran KS, Landen CN, Bhatnagar S, Tushir-Singh J. Cancer Cell. 2018 Aug 13;34(2):331-345.e11. doi: 10.1016/j.ccell.2018.07.005. PMID: 30107179

MUNC, an Enhancer RNA Upstream from the <i>MYOD</i> Gene, Induces a Subgroup of Myogenic Transcripts in <i>trans</i> Independently of MyoD. Cichewicz MA, Kiran M, Przanowska RK, Sobierajska E, Shibata Y, Dutta A. Mol Cell Biol. 2018 Sep 28;38(20). pii: e00655-17. doi: 10.1128/MCB.00655-17. Print 2018 Oct 15. PMID: 30037979

Mechanisms underlying the efficacy of exercise as an intervention for cocaine relapse: a focus on mGlu5 in the dorsal medial prefrontal cortex. Abel JM, Nesil T, Bakhti-Suroosh A, Grant PA, Lynch WJ. Psychopharmacology (Berl). 2019 Jun 3. doi: 10.1007/s00213-019-05208-0. PMID: 31161451

Complement alone drives efficacy of a chimeric antigonococcal monoclonal antibody. Gulati S, Beurskens FJ, de Kreuk BJ, Roza M, Zheng B, DeOliveira RB, Shaughnessy J, Nowak NA, Taylor RP, Botto M, He X, Ingalls RR, Woodruff TM, Song WC, Schuurman J, Rice PA, Ram S. PLoS Biol. 2019 Jun 19;17(6):e3000323. doi: 10.1371/journal.pbio.3000323. PMID: 31216278

Myt1 and Myt1l transcription factors limit proliferation in GBM cells by repressing YAP1 expression. Melhuish TA, Kowalczyk I, Manukyan A, Zhang Y, Shah A, Abounader R, Wotton D. Biochim Biophys Acta Gene Regul Mech. 2018 Nov;1861(11):983-995. doi: 10.1016/j.bbagrm.2018.10.005. Epub 2018 Oct 10. PMID: 30312684

Imaging Flow Cytometry Quantifies Neural Genome Dynamics. Michel N, Majumdar UB, Lannigan J, McConnell MJ. Cytometry A. 2019 May 7. doi: 10.1002/cyto.a.23783. PMID: 31063256

An extensively glycosylated archaeal pilus survives extreme conditions. Wang F, Cvirkaite-Krupovic V, Kreutzberger MAB, Su Z, de Oliveira GAP, Osinski T, Sherman N, DiMaio F, Wall JS, Prangishvili D, Krupovic M, Egelman EH. Nat Microbiol. 2019 May 20. doi: 10.1038/s41564-019-0458-x. PMID: 31110358

The Deubiquitinase USP46 Is Essential for Proliferation and Tumor Growth of HPV-Transformed Cancers. Kiran S, Dar A, Singh SK, Lee KY, Dutta A. Mol Cell. 2018 Dec 6;72(5):823-835.e5. doi: 10.1016/j.molcel.2018.09.019. Epub 2018 Nov 8. PMID: 30415951

Targeting HER2 beyond breast cancer. Bhatnagar S, Tushir-Singh J. Mol Cell Oncol. 2019 Mar 20;6(3):1571984. doi: 10.1080/23723556.2019.1571984. eCollection 2019. PMID: 31131305

Visualization of Xist Long Noncoding RNA with a Fluorescent CRISPR/Cas9 System. Waśko U, Zheng Z, Bhatnagar S. Methods Mol Biol. 2019;1870:41-50. doi: 10.1007/978-1-4939-8808-2_3. PMID: 30539545

Detection of ADP-Ribosylation of the Androgen Receptor Using the Recombinant Macrodomain AF1521 from Archaeoglobus fulgidus. Kamata T, Yang CS, Jividen K, Spencer A, Dworak N, Oostdyk LT, Paschal BM. Methods Mol Biol. 2019;1966:107-124. doi: 10.1007/978-1-4939-9195-2_9. PMID: 31041742

Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers. Wang F, Gu Y, O’Brien JP, Yi SM, Yalcin SE, Srikanth V, Shen C, Vu D, Ing NL, Hochbaum AI, Egelman EH, Malvankar NS. Cell. 2019 Apr 4;177(2):361-369.e10. doi: 10.1016/j.cell.2019.03.029. PMID: 30951668

Molecular mechanism for NLRP6 inflammasome assembly and activation. Shen C, Lu A, Xie WJ, Ruan J, Negro R, Egelman EH, Fu TM, Wu H. Proc Natl Acad Sci U S A. 2019 Feb 5;116(6):2052-2057. doi: 10.1073/pnas.1817221116. Epub 2019 Jan 23. PMID: 30674671

Cryo-EM structure of the NLRC4<sup>CARD</sup> filament provides insights into how symmetric and asymmetric supramolecular structures drive inflammasome assembly. Matyszewski M, Zheng W, Lueck J, Antiochos B, Egelman EH, Sohn J. J Biol Chem. 2018 Dec 28;293(52):20240-20248. doi: 10.1074/jbc.RA118.006050. Epub 2018 Nov 1. PMID: 30385506

The binding of Borealin to microtubules underlies a tension independent kinetochore-microtubule error correction pathway. Trivedi P, Zaytsev AV, Godzi M, Ataullakhanov FI, Grishchuk EL, Stukenberg PT. Nat Commun. 2019 Feb 8;10(1):682. doi: 10.1038/s41467-019-08418-4. PMID: 30737408

TGIF transcription factors repress acetyl CoA metabolic gene expression and promote intestinal tumor growth. Shah A, Melhuish TA, Fox TE, Frierson HF Jr, Wotton D. Genes Dev. 2019 Apr 1;33(7-8):388-402. doi: 10.1101/gad.320127.118. Epub 2019 Feb 26. PMID: 30808659

Mechanisms of Complement-Mediated Damage in Hematological Disorders. Taylor RP, Lindorfer MA. Semin Hematol. 2018 Jul;55(3):118-123. doi: 10.1053/j.seminhematol.2018.02.003. Epub 2018 Feb 14. Review. PMID: Similar articles

Evaluation of various risk factors associated with multidrug-resistant organisms isolated from diabetic foot ulcer patients. Datta P, Chander J, Gupta V, Mohi GK, Attri AK. J Lab Physicians. 2019 Jan-Mar;11(1):58-62. doi: 10.4103/JLP.JLP_106_18. PMID: 30983804

Methods in Nuclear Architecture and Transport. Paschal BM. Methods. 2019 Mar 15;157:1-2. doi: 10.1016/j.ymeth.2019.02.020. No abstract available. PMID: 30832896

Depletion of Limiting rDNA Structural Complexes Triggers Chromosomal Instability and Replicative Aging of <i>Saccharomyces cerevisiae</i>. Fine RD, Maqani N, Li M, Franck E, Smith JS. Genetics. 2019 Mar 6. pii: genetics.302047.2019. doi: 10.1534/genetics.119.302047. PMID: 30842210

P190RhoGAP prevents mitotic spindle fragmentation and is required to activate Aurora A kinase at acentriolar poles. Manukyan A, Sargsyan L, Parsons SJ, Stukenberg PT. Chromosoma. 2018 Sep;127(3):375-386. doi: 10.1007/s00412-018-0670-0. Epub 2018 Apr 14. PMID: 29656322

Null donors favor prepared immunologists. Taylor RP. Blood. 2019 Mar 28;133(13):1389-1390. doi: 10.1182/blood-2019-01-898775. No abstract available. PMID: 30923104

Histone H3 lysine 4 methylation signature associated with human undernutrition. Uchiyama R, Kupkova K, Shetty SJ, Linford AS, Pray-Grant MG, Wagar LE, Davis MM, Haque R, Gaultier A, Mayo MW, Grant PA, Petri WA Jr, Bekiranov S, Auble DT. Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):E11264-E11273. doi: 10.1073/pnas.1722125115. Epub 2018 Nov 12. PMID: 30420518

NF-κB upregulates glutamine-fructose-6-phosphate transaminase 2 to promote migration in non-small cell lung cancer. Szymura SJ, Zaemes JP, Allison DF, Clift SH, D’Innocenzi JM, Gray LG, McKenna BD, Morris BB, Bekiranov S, LeGallo RD, Jones DR, Mayo MW. Cell Commun Signal. 2019 Mar 18;17(1):24. doi: 10.1186/s12964-019-0335-5. PMID: 30885209

Histone H3 lysine 4 methylation signature associated with human undernutrition. Uchiyama R, Kupkova K, Shetty SJ, Linford AS, Pray-Grant MG, Wagar LE, Davis MM, Haque R, Gaultier A, Mayo MW, Grant PA, Petri WA Jr, Bekiranov S, Auble DT. Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):E11264-E11273. doi: 10.1073/pnas.1722125115. Epub 2018 Nov 12. PMID: 30420518

Small extrachromosomal circular DNAs, microDNA, produce short regulatory RNAs that suppress gene expression independent of canonical promotersPaulsen T, Shibata Y, Kumar P, Dillon L, Dutta A. Nucleic Acids Res. 2019 Mar 4. pii: gkz155. doi: 10.1093/nar/gkz155. [Epub ahead of print] PMID: 30828735

Improved molecular karyotyping in glioblastoma. Burbulis IE, Wierman MB, Wolpert M, Haakenson M, Lopes MB, Schiff D, Hicks J, Loe J, Ratan A, McConnell MJ. Mutat Res. 2018 Sep;811:16-26. doi: 10.1016/j.mrfmmm.2018.06.002. Epub 2018 Jul 8. PMID: 30055482

Dissecting the Genetics of Osteoporosis using Systems Approaches. Al-Barghouthi BM, Farber CR. Trends Genet. 2019 Jan;35(1):55-67. doi: 10.1016/j.tig.2018.10.004. Epub 2018 Nov 20. PMID: 30470485

TGIF transcription factors repress acetyl CoA metabolic gene expression and promote intestinal tumor growth. Shah A, Melhuish TA, Fox TE, Frierson HF Jr, Wotton D. Genes Dev. 2019 Feb 26. doi: 10.1101/gad.320127.118. PMID: 30808659

Analysis of transcriptional activity by the Myt1 and Myt1l transcription factors. Manukyan A, Kowalczyk I, Melhuish TA, Lemiesz A, Wotton D. J Cell Biochem. 2018 Jun;119(6):4644-4655. doi: 10.1002/jcb.26636. Epub 2018 Mar 9. PMID: 29291346

CD20 and CD37 antibodies synergize to activate complement by Fc-mediated clustering. Oostindie SC, van der Horst HJ, Lindorfer MA, Cook EM, Tupitza JC, Zent CS, Burack R, VanDerMeid KR, Strumane K, Chamuleau MED, Mutis T, de Jong RN, Schuurman J, Breij ECW, Beurskens FJ, Parren PWHI, Taylor RP. Haematologica. 2019 Feb 21. pii: haematol.2018.207266. doi: 10.3324/haematol.2018.207266. PMID: 30792198

Recurrent mutations at estrogen receptor binding sites alter chromatin topology and distal gene expression in breast cancer. Yang J, Wei X, Tufan T, Kuscu C, Unlu H, Farooq S, Demirtas E, Paschal BM, Adli M. Genome Biol. 2018 Nov 7;19(1):190. doi: 10.1186/s13059-018-1572-4. PMID: 30404658

The binding of Borealin to microtubules underlies a tension independent kinetochore-microtubule error correction pathway. Trivedi P, Zaytsev AV, Godzi M, Ataullakhanov FI, Grishchuk EL, Stukenberg PT. Nat Commun. 2019 Feb 8;10(1):682. doi: 10.1038/s41467-019-08418-4. PMID: 30737408

STAT3 mutations are not sufficient to induce large granular lymphocytic leukaemia in mice. Dutta A, Yan D, Hutchison RE, Mohi G. Br J Haematol. 2018 Mar;180(6):911-915. doi: 10.1111/bjh.14487. Epub 2016 Dec 26. No abstract available. PMID: 28025836

Conformational changes and catalytic inefficiency associated with Mot1-mediated TBP-DNA dissociation. Heiss G, Ploetz E, Voith von Voithenberg L, Viswanathan R, Glaser S, Schluesche P, Madhira S, Meisterernst M, Auble DT, Lamb DC. Nucleic Acids Res. 2019 Jan 15. doi: 10.1093/nar/gky1322. PMID: 30649478

BRG1 is a prognostic indicator and a potential therapeutic target for prostate cancer. Muthuswami R, Bailey L, Rakesh R, Imbalzano AN, Nickerson JA, Hockensmith JW J Cell Physiol. 2019 Jan 22. doi: 10.1002/jcp.28161. PMID: 30667054

Neurons with Complex Karyotypes Are Rare in Aged Human Neocortex. Chronister WD, Burbulis IE, Wierman MB, Wolpert MJ, Haakenson MF, Smith ACB, Kleinman JE, Hyde TM, Weinberger DR, Bekiranov S, McConnell MJ. Cell Rep. 2019 Jan 22;26(4):825-835.e7. doi: 10.1016/j.celrep.2018.12.107. PMID: 30673605

Molecular mechanism for NLRP6 inflammasome assembly and activation. Shen C, Lu A, Xie WJ, Ruan J, Negro R, Egelman EH, Fu TM, Wu H. Proc Natl Acad Sci U S A. 2019 Jan 23. pii: 201817221. doi: 10.1073/pnas.1817221116. PMID: 30674671

The Germline Variants rs61757955 and rs34988193 are Predictive of Survival in Lower Grade Glioma Patients. Chatrath A, Kiran M, Kumar P, Ratan A, Dutta A. Mol Cancer Res. 2019 Jan 16. pii: molcanres.0996.2018. doi: 10.1158/1541-7786.MCR-18-0996. PMID: 30651372