Departmental Publications 2018

TGFβ signaling limits lineage plasticity in prostate cancer. Hao Y, Bjerke GA, Pietrzak K, Melhuish TA, Han Y, Turner SD, Frierson HF Jr, Wotton D. PLoS Genet. 2018 May 21;14(5):e1007409. doi: 10.1371/journal.pgen.1007409. eCollection 2018 May. PMID: 29782499
Functions of TGIF homeodomain proteins and their roles in normal brain development and holoprosencephaly. Wotton D, Taniguchi K. Am J Med Genet C Semin Med Genet. 2018 May 11. doi: 10.1002/ajmg.c.31612. PMID: 29749689
Spontaneous mutations in <i>CYC8</i> and <i>MIG1</i> suppress the short chronological lifespan of budding yeast lacking SNF1/AMPK. Maqani N, Fine RD, Shahid M, Li M, Enriquez-Hesles E, Smith JS. Microb Cell. 2018 Feb 19;5(5):233-248. doi: 10.15698/mic2018.05.630. PMID: 29796388
The RNA-editing enzyme ADAR promotes lung adenocarcinoma migration and invasion by stabilizing <i>FAK</i>. Amin EM, Liu Y, Deng S, Tan KS, Chudgar N, Mayo MW, Sanchez-Vega F, Adusumilli PS, Schultz N, Jones DR. Sci Signal. 2017 Sep 19;10(497). pii: eaah3941. doi: 10.1126/scisignal.aah3941. PMID: 28928239
tRNA fragments (tRFs) guide Ago to regulate gene expression post-transcriptionally in a Dicer independent manner. Kuscu C, Kumar P, Kiran M, Su Z, Malik A, Dutta A. RNA. 2018 May 29. pii: rna.066126.118. doi: 10.1261/rna.066126.118. PMID: 29844106
Normal and Cancerous Tissues Release Extrachromosomal Circular DNA (eccDNA) into the Circulation. Kumar P, Dillon LW, Shibata Y, Jazaeri AA, Jones DR, Dutta A. Mol Cancer Res. 2017 Sep;15(9):1197-1205. doi: 10.1158/1541-7786.MCR-17-0095. Epub 2017 May 26. PMID: 28550083
The CRISPR tool kit for genome editing and beyond.  Adli M. Nat Commun. 2018 May 15;9(1):1911. doi: 10.1038/s41467-018-04252-2. Review. PMID: 29765029
Identification of Drivers of Aneuploidy in Breast Tumors. Pfister K, Pipka JL, Chiang C, Liu Y, Clark RA, Keller R, Skoglund P, Guertin MJ, Hall IM, Stukenberg PT. Cell Rep. 2018 May 29;23(9):2758-2769. doi: 10.1016/j.celrep.2018.04.102. PMID: 29847804
An Improved Method for Measuring Chromatin-binding Dynamics Using Time-dependent Formaldehyde Crosslinking. Hoffman EA, Zaidi H, Shetty SJ, Bekiranov S, Auble DT. Bio Protoc. 2018 Feb 20;8(4). pii: e2905. doi: 10.21769/bioprotoc.2905. PMID: 29682595
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 Apr 14. doi: 10.1007/s00412-018-0670-0. PMID: 29656322
Posttranslational mechanisms controlling centromere function and assembly. Srivastava S, Zasadzińska E, Foltz DR. Curr Opin Cell Biol. 2018 Apr 2;52:126-135. doi: 10.1016/ PMID: 29621654
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 Jul 18;8(29):46781-46800. doi: 10.18632/oncotarget.18108. PMID: 28596481
Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq. Guertin MJ, Cullen AE, Markowetz F, Holding AN. Nucleic Acids Res. 2018 Apr 17. doi: 10.1093/nar/gky252. PMID: 29672735
BART: a transcription factor prediction tool with query gene sets or epigenomic profiles. Wang Z, Civelek M, Miller CL, Sheffield NC, Guertin MJ, Zang C. Bioinformatics. 2018 Mar 28. doi: 10.1093/bioinformatics/bty194. PMID: 29608647
A structural model of flagellar filament switching across multiple bacterial species. Wang F, Burrage AM, Postel S, Clark RE, Orlova A, Sundberg EJ, Kearns DB, Egelman EH. Nat Commun. 2017 Oct 16;8(1):960. doi: 10.1038/s41467-017-01075-5. PMID: 29038601
Cryoelectron Microscopy Reconstructions of the Pseudomonas aeruginosa and Neisseria gonorrhoeae Type IV Pili at Sub-nanometer Resolution. Wang F, Coureuil M, Osinski T, Orlova A, Altindal T, Gesbert G, Nassif X, Egelman EH, Craig L. Structure. 2017 Sep 5;25(9):1423-1435.e4. doi: 10.1016/j.str.2017.07.016. PMID: 28877506
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 Sep 5;25(9):1436-1441.e2. doi: 10.1016/j.str.2017.06.017. Epub 2017 Jul 27. PMID: 28757144
Model for a novel membrane envelope in a filamentous hyperthermophilic virus. Kasson P, DiMaio F, Yu X, Lucas-Staat S, Krupovic M, Schouten S, Prangishvili D, Egelman EH. Elife. 2017 Jun 22;6. pii: e26268. doi: 10.7554/eLife.26268. PMID: 28639939
Small molecule inhibition of the CBFβ/RUNX interaction decreases ovarian cancer growth and migration through alterations in genes related to epithelial-to-mesenchymal transition. Carlton AL, Illendula A, Gao Y, Llaneza DC, Boulton A, Shah A, Rajewski RA, Landen CN, Wotton D, Bushweller JH. Gynecol Oncol. 2018 Mar 15. pii: S0090-8258(18)30174-4. doi: 10.1016/j.ygyno.2018.03.005. PMID: 29551565
Archaeal flagellin combines a bacterial type IV pilin domain with an Ig-like domain. Braun T, Vos MR, Kalisman N, Sherman NE, Rachel R, Wirth R, Schröder GF, Egelman EH. Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10352-7. doi: 10.1073/pnas.1607756113. Epub 2016 Aug 30. PMID: 27578865
Transgenerational Effects of Bisphenol A on Gene Expression and DNA Methylation of Imprinted Genes in Brain. Drobná Z, Henriksen AD, Wolstenholme JT, Montiel C, Lambeth PS, Shang S, Harris EP, Zhou C, Flaws JA, Adli M, Rissman EF. Endocrinology. 2018 Jan 1;159(1):132-144. doi: 10.1210/en.2017-00730. PMID: 29165653
Neutrophils: positive or negative? Taylor RP. Blood. 2017 May 11;129(19):2596-2597. doi: 10.1182/blood-2017-03-774695. No abstract available. PMID: 28495923
Functional role of the type 1 pilus rod structure in mediating host-pathogen interactions.
Spaulding CN, Schreiber HL, 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
Regulation of Mammalian DNA Replication via the Ubiquitin-Proteasome System. Abbas T, Dutta A. Adv Exp Med Biol. 2017;1042:421-454. doi: 10.1007/978-981-10-6955-0_19. PMID: 29357069
Discoveries of Extrachromosomal Circles of DNA in Normal and Tumor Cells. Paulsen T, Kumar P, Koseoglu MM, Dutta A. Trends Genet. 2018 Jan 9. pii: S0168-9525(17)30230-5. doi: 10.1016/j.tig.2017.12.010.  PMID: 29329720
Second-generation method for analysis of chromatin binding with formaldehyde-cross-linking kinetics. Zaidi H, Hoffman EA, Shetty SJ, Bekiranov S, Auble DT. J Biol Chem. 2017 Nov 24;292(47):19338-19355. doi: 10.1074/jbc.M117.796441. Epub 2017 Sep 26. PMID: 28972159
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 Jan 1. doi: 10.1002/jcb.26636.  PMID: 29291346
In Vitro Assay to Study Histone Ubiquitination During Transcriptional Regulation. Tushir-Singh J, Bhatnagar S. Methods Mol Biol. 2017;1507:235-244. PMID: 27832544
Up For A Challenge (U4C): Stimulating innovation in breast cancer genetic epidemiology. Mechanic LE, Lindström S, Daily KM, Sieberts SK, Amos CI, Chen HS, Cox NJ, Dathe M, Feuer EJ, Guertin MJ, Hoffman J, Liu Y, Moore JH, Myers CL, Ritchie MD, Schildkraut J, Schumacher F, Witte JS, Wang W, Williams SM; U4C Challenge Participants; U4C Challenge Data Contributors, Gillanders EM. PLoS Genet. 2017 Sep 28;13(9):e1006945. doi: 10.1371/journal.pgen.1006945. eCollection 2017 Sep. No abstract available.  PMID: 28957327
Transcriptional response to stress is pre-wired by promoter and enhancer architecture. Vihervaara A, Mahat DB, Guertin MJ, Chu T, Danko CG, Lis JT, Sistonen L. Nat Commun. 2017 Aug 15;8(1):255. doi: 10.1038/s41467-017-00151-0. PMID: 28811569