Departmental Publications 2018

The Biology and Application Areas of CRISPR Technologies.Adli M. J Mol Biol. 2018 Nov 14. pii: S0022-2836(18)31237-3. doi: 10.1016/j.jmb.2018.11.012. PMID: 30447221
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  
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
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
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
Fluorescence-based Quantification of Nucleocytoplasmic Transport. Kelley JB, Paschal BM. Methods. 2018 Nov 9. pii: S1046-2023(18)30123-3. doi: 10.1016/j.ymeth.2018.11.002. PMID: 30419335
Towards improving proximity labeling by the biotin ligase BirA. Oostdyk LT, Shank L, Jividen K, Dworak N, Sherman NE, Paschal BM. Methods. 2018 Nov 10. pii: S1046-2023(18)30115-4. doi: 10.1016/j.ymeth.2018.11.003. PMID: 30419333
The effect of rho kinase inhibition on morphological and electrophysiological maturity in iPSC-derived neurons. Harbom LJ, Rudisill TL, Michel N, Litwa KA, Beenhakker MP, McConnell MJ. Cell Tissue Res. 2018 Nov 8. doi: 10.1007/s00441-018-2942-7. PMID: 30406823
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 Nov 1. pii: jbc.RA118.006050. doi: 10.1074/jbc.RA118.006050. PMID: 30385506
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 Oct 30. pii: S1097-2765(18)30790-1. doi: 10.1016/j.molcel.2018.09.019. PMID: 30415951
A Prognostic Signature for Lower Grade Gliomas Based on Expression of Long Non-Coding RNAs. Kiran M, Chatrath A, Tang X, Keenan DM, Dutta A. Mol Neurobiol. 2018 Nov 3. doi: 10.1007/s12035-018-1416-y. PMID: 3039213
CRISPR knockout screening identifies combinatorial drug targets in pancreatic cancer and models cellular drug response. Szlachta K, Kuscu C, Tufan T, Adair SJ, Shang S, Michaels AD, Mullen MG, Fischer NL, Yang J, Liu L, Trivedi P, Stelow EB, Stukenberg PT, Parsons JT, Bauer TW, Adli M. Nat Commun. 2018 Oct 15;9(1):4275. doi: 10.1038/s41467-018-06676-2. PMID: 30323222
Crystal structure of the full Swi2/Snf2 remodeler Mot1 in the resting state. Butryn A, Woike S, Shetty SJ, Auble DT, Hopfner KP. Elife. 2018 Oct 5;7. pii: e37774. doi: 10.7554/eLife.37774. PMID: 30289385
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
Alternative DNA secondary structure formation affects RNA polymerase II promoter-proximal pausing in human. Szlachta K, Thys RG, Atkin ND, Pierce LCT, Bekiranov S, Wang YH. Genome Biol. 2018 Jul 12;19(1):89. doi: 10.1186/s13059-018-1463-8. PMID: 30001206
Inheritance of CENP-A Nucleosomes during DNA Replication Requires HJURP. Zasadzińska E, Huang J, Bailey AO, Guo LY, Lee NS, Srivastava S, Wong KA, French BT, Black BE, Foltz DR. Dev Cell. 2018 Oct 3. pii: S1534-5807(18)30732-9. doi: 10.1016/j.devcel.2018.09.003. PMID: 30293838
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
Genomic analysis of DNA repair genes and androgen signaling in prostate cancer. Jividen K, Kedzierska KZ, Yang CS, Szlachta K, Ratan A, Paschal BM. BMC Cancer. 2018 Oct 10;18(1):960. doi: 10.1186/s12885-018-4848-x. PMID: 30305041
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 Nov 1. pii: jbc.RA118.006050. doi: 10.1074/jbc.RA118.006050. PMID: 30385506
Structure of the Neisseria meningitidis Type IV pilus. Kolappan S, Coureuil M, Yu X, Nassif X, Egelman EH, Craig L. Nat Commun. 2016 Oct 4;7:13015. doi: 10.1038/ncomms13015. PMID: 27698424  
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 Oct 17:mbcE18060353. doi: 10.1091/mbc.E18-06-0353. PMID: 30332327
Structural basis for high-affinity actin binding revealed by a β-III-spectrin SCA5 missense mutation. Avery AW, Fealey ME, Wang F, Orlova A, Thompson AR, Thomas DD, Hays TS, Egelman EH. Nat Commun. 2017 Nov 7;8(1):1350. doi: 10.1038/s41467-017-01367-w. PMID: 29116080
CRISPR-Cas9-AID base editor is a powerful gain-of-function screening tool. Kuscu C, Adli M. Nat Methods. 2016 Nov 29;13(12):983-984. doi: 10.1038/nmeth.4076. No abstract available. PMID: 27898061
Pharmacological reactivation of inactive X-linked <i>Mecp2</i> in cerebral cortical neurons of living mice. Przanowski P, Wasko U, Zheng Z, Yu J, Sherman R, Zhu LJ, McConnell MJ, Tushir-Singh J, Green MR, Bhatnagar S. Proc Natl Acad Sci U S A. 2018 Jul 31;115(31):7991-7996. doi: 10.1073/pnas.1803792115. Epub 2018 Jul 16. PMID: 30012595
Hijacking a key chromatin modulator creates epigenetic vulnerability for MYC-driven cancer. Yang Z, Shah K, Busby T, Giles K, Khodadadi-Jamayran A, Li W, Jiang H. The Journal of clinical investigation. 2018; 128(8):3605-3618. PMID:29870403
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
Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota. Van Deynze A, Zamora P, Delaux PM, Heitmann C, Jayaraman D, Rajasekar S, Graham D, Maeda J, Gibson D, Schwartz KD, Berry AM, Bhatnagar S, Jospin G, Darling A, Jeannotte R, Lopez J, Weimer BC, Eisen JA, Shapiro HY, Ané JM, Bennett AB. PLoS Biol. 2018 Aug 7;16(8):e2006352. doi: 10.1371/journal.pbio.2006352. eCollection 2018 Aug. PMID: 30086128
Single-cell analysis of diversity in human stem cell-derived neurons. Harbom LJ, Michel N, McConnell MJ. Cell Tissue Res. 2018 Jan;371(1):171-179. doi: 10.1007/s00441-017-2728-3. Epub 2017 Nov 29. Review. PMID: 29185070
Temporal and Spatial Epigenome Editing Allows Precise Gene Regulation in Mammalian Cells. Kuscu C, Mammeadov R, Czikora A, Unlu H, Tufan T, Fischer NL, Arslan S, Bekiranov S, Kanemaki M, Adli M. J Mol Biol. 2018 Aug 9. pii: S0022-2836(18)30892-1. doi: 10.1016/j.jmb.2018.08.001. PMID: 30098338
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 Aug;24(8):1093-1105. doi: 10.1261/rna.066126.118. Epub 2018 May 29. PMID: 29844106
Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile. Liu Y, Osinski T, Wang F, Krupovic M, Schouten S, Kasson P, Prangishvili D, Egelman EH. Nat Commun. 2018 Aug 22;9(1):3360. doi: 10.1038/s41467-018-05684-6. PMID: 30135568
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 Jul 8;811:16-26. doi: 10.1016/j.mrfmmm.2018.06.002. PMID: 30055482
Pharmacological reactivation of inactive X-linked <i>Mecp2</i> in cerebral cortical neurons of living mice. Przanowski P, Wasko U, Zheng Z, Yu J, Sherman R, Zhu LJ, McConnell MJ, Tushir-Singh J, Green MR, Bhatnagar S. Proc Natl Acad Sci U S A. 2018 Jul 31;115(31):7991-7996. doi: 10.1073/pnas.1803792115. Epub 2018 Jul 16. PMID: 30012595
Structure of the calcium-dependent type 2 secretion pseudopilus. López-Castilla A, Thomassin JL, Bardiaux B, Zheng W, Nivaskumar M, Yu X, Nilges M, Egelman EH, Izadi-Pruneyre N, Francetic O. Nat Microbiol. 2017 Dec;2(12):1686-1695. doi: 10.1038/s41564-017-0041-2. Epub 2017 Oct 9. PMID: 28993624
MUNC, an eRNA upstream from the <i>MYOD</i> gene, induces a subgroup of myogenic transcripts <i>in trans</i>, independently of MyoD. Cichewicz MA, Kiran M, Przanowska RK, Sobierajska E, Shibata Y, Dutta A. Mol Cell Biol. 2018 Jul 23. pii: MCB.00655-17. doi: 10.1128/MCB.00655-17. PMID: 30037979
LINC00152 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 Jul 10. pii: molcanres.0322.2018. doi: 10.1158/1541-7786.MCR-18-0322. PMID: 29991527
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. Review. PMID: 29357069
Alternative DNA secondary structure formation affects RNA polymerase II promoter-proximal pausing in human. Szlachta K, Thys RG, Atkin ND, Pierce LCT, Bekiranov S, Wang YH. Genome Biol. 2018 Jul 12;19(1):89. doi: 10.1186/s13059-018-1463-8. PMID: 30001206
Overexpression of transforming growth factor β induced factor homeobox 1 represses NPC1L1 and lowers markers of intestinal cholesterol absorption. Parini P, Melhuish TA, Wotton D, Larsson L, Ahmed O, Eriksson M, Pramfalk C. Atherosclerosis. 2018 Jun 19;275:246-255. doi: 10.1016/j.atherosclerosis.2018.06.867. PMID: 29980051
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 May;149(2):350-360. doi: 10.1016/j.ygyno.2018.03.005. Epub 2018 Mar 16. PMID: 29551565
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: 30032747
Endothelial Microparticles and Systemic Complement Activation in Patients With Chronic Kidney Disease. Jalal D, Renner B, Laskowski J, Stites E, Cooper J, Valente K, You Z, Perrenoud L, Le Quintrec M, Muhamed I, Christians U, Klawitter J, Lindorfer MA, Taylor RP, Holers VM, Thurman JM. J Am Heart Assoc. 2018 Jul 13;7(14). pii: e007818. doi: 10.1161/JAHA.117.007818. PMID: 30006493
 Differential Expression of Homing Receptor Ligands on Tumor-Associated Vasculature that Control CD8 Effector T-cell Entry. Woods AN, Wilson AL, Srivinisan N, Zeng J, Dutta AB, Peske JD, Tewalt EF, Gregg RK, Ferguson AR, Engelhard VH. Cancer Immunol Res. 2017 Dec;5(12):1062-1073. doi: 10.1158/2326-6066.CIR-17-0190. Epub 2017 Nov 2. PMID: 29097419
CRISPR Ethics: Moral Considerations for Applications of a Powerful Tool. Brokowski C, Adli M. J Mol Biol. 2018 Jun 7. pii: S0022-2836(18)30586-2. doi: 10.1016/j.jmb.2018.05.044. PMID: 29885329
Correction to: Multiple receptor tyrosine kinases converge on microRNA-134 to control KRAS, STAT5B, and glioblastoma. Zhang Y, Kim J, Mueller AC, Dey B, Yang Y, Lee DH, Hachmann J, Finderle S, Park DM, Christensen J, Schiff D, Purow B, Dutta A, Abounader R.
Cell Death Differ. 2018 Jun 13. doi: 10.1038/s41418-018-0145-0. PMID: 29899381 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
Cryo-EM of bacterial pili and archaeal flagellar filaments. Egelman EH. Curr Opin Struct Biol. 2017 Oct;46:31-37. doi: 10.1016/j.sbi.2017.05.012. Epub 2017 Jun 10. Review. PMID: 28609682
Deletion of Ptpn1 induces myeloproliferative neoplasm. Jobe F, Patel B, Kuzmanovic T, Makishima H, Yang Y, Przychodzen B, Hutchison RE, Bence KK, Maciejewski JP, Mohi G. Leukemia. 2017 May;31(5):1229-1234. doi: 10.1038/leu.2017.31. Epub 2017 Jan 23. No abstract available. PMID:
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/j.ceb.2018.03.003. 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