Departmental Publications 2020

The Biology and Application Areas of CRISPR Technologies. Adli M. J Mol Biol. 2019 Jan 4;431(1):1-2. doi: 10.1016/j.jmb.2018.11.012. Epub 2018 Nov 14. No abstract available. PMID: 30447221

Temporal and Spatial Epigenome Editing Allows Precise Gene Regulation in Mammalian Cells.Kuscu C, Mammadov R, Czikora A, Unlu H, Tufan T, Fischer NL, Arslan S, Bekiranov S, Kanemaki M, Adli M. J Mol Biol. 2019 Jan 4;431(1):111-121. doi: 10.1016/j.jmb.2018.08.001. Epub 2018 Aug 9. PMID: 30098338

CRISPR Ethics: Moral Considerations for Applications of a Powerful Tool. Brokowski C, Adli M. J Mol Biol. 2019 Jan 4;431(1):88-101. doi: 10.1016/j.jmb.2018.05.044. Epub 2018 Jun 7. Review. PMID: 29885329

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

An epilepsy-associated mutation in the nuclear import receptor KPNA7 reduces nuclear localization signal binding. Oostdyk LT, Wang Z, Zang C, Li H, McConnell MJ, Paschal BM Sci Rep. 2020 Mar 16;10(1):4844. doi: 10.1038/s41598-020-61369-5. PMID: 32179771

A nuclear lamina-chromatin-Ran GTPase axis modulates nuclear import and DNA damage signaling. Dworak N, Makosa D, Chatterjee M, Jividen K, Yang CS, Snow C, Simke WC, Johnson IG, Kelley JB, Paschal BM. Aging Cell. 2019 Feb;18(1):e12851. doi: 10.1111/acel.12851. Epub 2018 Dec 19. PMID: 30565836

A three-dimensional dementia model reveals spontaneous cell cycle re-entry and a senescence-associated secretory phenotype. Porterfield V, Khan SS, Foff EP, Koseoglu MM, Blanco IK, Jayaraman S, Lien E, McConnell MJ, Bloom GS, Lazo JS, Sharlow ER. Neurobiol Aging. 2020 Feb 19. pii: S0197-4580(20)30038-5. doi: 10.1016/j.neurobiolaging.2020.02.011. PMID: 32184029

An epilepsy-associated mutation in the nuclear import receptor KPNA7 reduces nuclear localization signal binding. Oostdyk LT, Wang Z, Zang C, Li H, McConnell MJ, Paschal BM. Sci Rep. 2020 Mar 16;10(1):4844. doi: 10.1038/s41598-020-61369-5. PMID: 32179771

A deletion in Eml1 leads to bilateral subcortical heterotopia in the tish rat. Grosenbaugh DK, Joshi S, Fitzgerald MP, Lee KS, Wagley PK, Koeppel AF, Turner SD, McConnell MJ, Goodkin HP. Neurobiol Dis. 2020 Mar 13:104836. doi: 10.1016/j.nbd.2020.104836. PMID: 32179177

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

Ant-icipating Change: An Epigenetic Switch in Reprogramming the Social Lives of Ants. Pray-Grant MG, Grant PA. Mol Cell. 2020 Jan 16;77(2):205-206. doi: 10.1016/j.molcel.2019.12.006. PMID: 31951544

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

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

Barriers to integration of bioinformatics into undergraduate life sciences education: A national study of US life sciences faculty uncover significant barriers to integrating bioinformatics into undergraduate instruction. Williams JJ, Drew JC, Galindo-Gonzalez S, Robic S, Dinsdale E, Morgan WR, Triplett EW, Burnette JM 3rd, Donovan SS, Fowlks ER, Goodman AL, Grandgenett NF, Goller CC, Hauser C, Jungck JR, Newman JD, Pearson WR, Ryder EF, Sierk M, Smith TM, Tosado-Acevedo R, Tapprich W, Tobin TC, Toro-Martínez A, Welch LR, Wilson MA, Ebenbach D, McWilliams M, Rosenwald AG, Pauley MA. PLoS One. 2019 Nov 18;14(11):e0224288. doi: 10.1371/journal.pone.0224288. eCollection 2019. PMID: 31738797

Cryo-EM: Ice Is Nice, but Good Ice Can Be Hard to Find. Egelman EH. Biophys J. 2020 Feb 1. pii: S0006-3495(20)30099-0. doi: 10.1016/j.bpj.2020.01.026. No abstract available. PMID: 32061273

Hooked on motility. Egelman EH. Nat Struct Mol Biol. 2019 Oct;26(10):848-849. doi: 10.1038/s41594-019-0302-2. No abstract available.  PMID: 31570876

The pan-cancer landscape of prognostic germline variants in 10,582 patients. Chatrath A, Przanowska R, Kiran S, Su Z, Saha S, Wilson B, Tsunematsu T, Ahn JH, Lee KY, Paulsen T, Sobierajska E, Kiran M, Tang X, Li T, Kumar P, Ratan A, Dutta A. Genome Med. 2020 Feb 17;12(1):15. doi: 10.1186/s13073-020-0718-7. PMID: 32066500

Pausing sites of RNA polymerase II on actively transcribed genes are enriched with DNA double-stranded breaks. Singh S, Szlachta K, Manukyan A, Raimer HM, Dinda M, Bekiranov S, Wang YH. J Biol Chem. 2020 Feb 6. pii: jbc.RA119.011665. doi: 10.1074/jbc.RA119.011665.

PMID: 32029477

Broken by the Cut: A Journey into the Role of Topoisomerase II in DNA Fragility. Atkin ND, Raimer HM, Wang YH. Genes (Basel). 2019 Oct 12;10(10). pii: E791. doi: 10.3390/genes10100791. Review. PMID: 31614754

Ant-icipating Change: An Epigenetic Switch in Reprogramming the Social Lives of Ants. Pray-Grant MG, Grant PA. Mol Cell. 2020 Jan 16;77(2):205-206. doi: 10.1016/j.molcel.2019.12.006.PMID: 31951544

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 Aug;4(8):1401-1410. doi: 10.1038/s41564-019-0458-x. Epub 2019 May 20. PMID: 31110358

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

 tRNA-derived fragments and microRNAs in the maternal-fetal interface of a mouse maternal-immune-activation autism model. Su Z, Frost EL, Lammert CR, Przanowska RK, Lukens JR, Dutta A. RNA Biol. 2020 Jan 31:1-13. doi: 10.1080/15476286.2020.1721047. PMID: 31983265

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. eCollection 2019 Aug. PMID: 31461456  

High-content phenotypic assay for proliferation of human iPSC-derived cardiomyocytes identifies L-type calcium channels as targets. Woo LA, Tkachenko S, Ding M, Plowright AT, Engkvist O, Andersson H, Drowley L, Barrett I, Firth M, Akerblad P, Wolf MJ, Bekiranov S, Brautigan DL, Wang QD, Saucerman JJ. J Mol Cell Cardiol. 2019 Feb;127:204-214. doi: 10.1016/j.yjmcc.2018.12.015. Epub 2018 Dec 28. PMID: 30597148

CNCC: an analysis tool to determine genome-wide DNA break end structure at single-nucleotide resolution. Szlachta K, Raimer HM, Comeau LD, Wang YH. BMC Genomics. 2020 Jan 8;21(1):25. doi: 10.1186/s12864-019-6436-0. PMID: 31914926

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. eCollection 2019 Jun. PMID: 31216278

Defining data-driven primary transcript annotations with primaryTranscriptAnnotation in R. Anderson WD, Duarte FM, Civelek M, Guertin MJ. Bioinformatics. 2020 Jan 9. pii: btaa011. doi: 10.1093/bioinformatics/btaa011. PMID: 31917388