Publications
2023
Meagher RB, Lewis ZA, Ambati S, Lin X. DectiSomes: C-type lectin receptor-targeted liposomes as pan-antifungal drugs. Adv Drug Deliv Rev. 2023;196:114776. Epub 20230317. doi: 10.1016/j.addr.2023.114776. PubMed PMID: 36934519; PMCID: PMC10133202
Lewis ZA. Expanding the proteome: A-to-I RNA editing provides an adaptive advantage. Proc Natl Acad Sci U S A. 2023;120(16):e2303563120. Epub 20230410. doi: 10.1073/pnas.2303563120. PubMed PMID: 37036963; PMCID: PMC10120046
Choudhury QJ, Ambati S, Link CD, Lin X, Lewis ZA, Meagher RB. Dectin-3-targeted antifungal liposomes efficiently bind and kill diverse fungal pathogens. Mol Microbiol. 2023;120(5):723-39. Epub 20231006. doi: 10.1111/mmi.15174. PubMed PMID: 37800599; PMCID: PMC10823756
2022
Peixoto E, Khan A, Lewis ZA, Contreras-Galindo R, Czaja W. The Chromatin Remodeler HELLS: A New Regulator in DNA Repair, Genome Maintenance, and Cancer. Int J Mol Sci. 2022;23(16). Epub 20220818. doi: 10.3390/ijms23169313. PubMed PMID: 36012581; PMCID: PMC9409174
Choudhury QJ, Ambati S, Lewis ZA, Meagher RB. Targeted Delivery of Antifungal Liposomes to Rhizopus delemar. J Fungi (Basel). 2022;8(4). Epub 20220330. doi: 10.3390/jof8040352. PubMed PMID: 35448583; PMCID: PMC9026866
Ambati S, Pham T, Lewis ZA, Lin X, Meagher RB. DectiSomes: Glycan Targeting of Liposomal Drugs Improves the Treatment of Disseminated Candidiasis. Antimicrob Agents Chemother. 2022;66(1):e0146721. Epub 20211011. doi: 10.1128/aac.01467-21. PubMed PMID: 34633846; PMCID: PMC8765427
2021
Meagher RB, Lewis ZA, Ambati S, Lin X. Aiming for a bull's-eye: Targeting antifungals to fungi with dectin-decorated liposomes. PLoS Pathog. 2021;17(7):e1009699. Epub 20210722. doi: 10.1371/journal.ppat.1009699. PubMed PMID: 34293050; PMCID: PMC8297870
Ma Y, Zhang X, Alsaidan OA, Yang X, Sulejmani E, Zha J, Beharry Z, Huang H, Bartlett M, Lewis Z, Cai H. Long-Chain Acyl-CoA Synthetase 4-Mediated Fatty Acid Metabolism Sustains Androgen Receptor Pathway-Independent Prostate Cancer. Mol Cancer Res. 2021;19(1):124-35. Epub 20201019. doi: 10.1158/1541-7786.Mcr-20-0379. PubMed PMID: 33077484; PMCID: PMC7785683
Li Y, Mao P, Basenko EY, Lewis Z, Smerdon MJ, Czaja W. Versatile cell-based assay for measuring DNA alkylation damage and its repair. Sci Rep. 2021;11(1):18393. Epub 20210915. doi: 10.1038/s41598-021-97523-w. PubMed PMID: 34526526; PMCID: PMC8443546
Kamei M, Ameri AJ, Ferraro AR, Bar-Peled Y, Zhao F, Ethridge CL, Lail K, Amirebrahimi M, Lipzen A, Ng V, Grigoriev IV, Schmitz RJ, Liu Y, Lewis ZA. IMITATION SWITCH is required for normal chromatin structure and gene repression in PRC2 target domains. Proc Natl Acad Sci U S A. 2021;118(4). doi: 10.1073/pnas.2010003118. PubMed PMID: 33468665; PMCID: PMC7848606
Ferraro AR, Ameri AJ, Lu Z, Kamei M, Schmitz RJ, Lewis ZA. Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin. BMC Genomics. 2021;22(1):459. Epub 20210619. doi: 10.1186/s12864-021-07774-0. PubMed PMID: 34147068; PMCID: PMC8214302
Ameri AJ, Lewis ZA. Shannon entropy as a metric for conditional gene expression in Neurospora crassa. G3 (Bethesda). 2021;11(4). doi: 10.1093/g3journal/jkab055. PubMed PMID: 33751112; PMCID: PMC8049430
Ambati S, Pham T, Lewis ZA, Lin X, Meagher RB. DC-SIGN targets amphotericin B-loaded liposomes to diverse pathogenic fungi. Fungal Biol Biotechnol. 2021;8(1):22. Epub 20211224. doi: 10.1186/s40694-021-00126-3. PubMed PMID: 34952645; PMCID: PMC8709943
Ambati S, Ellis EC, Pham T, Lewis ZA, Lin X, Meagher RB. Antifungal Liposomes Directed by Dectin-2 Offer a Promising Therapeutic Option for Pulmonary Aspergillosis. mBio. 2021;12(1). Epub 20210223. doi: 10.1128/mBio.00030-21. PubMed PMID: 33622715; PMCID: PMC8545082
2020
Courtney AJ, Kamei M, Ferraro AR, Gai K, He Q, Honda S, Lewis ZA. Normal Patterns of Histone H3K27 Methylation Require the Histone Variant H2A.Z in Neurospora crassa. Genetics. 2020;216(1):51-66. Epub 20200710. doi: 10.1534/genetics.120.303442. PubMed PMID: 32651262; PMCID: PMC7463285
2019
Schmitz RJ, Lewis ZA, Goll MG. DNA Methylation: Shared and Divergent Features across Eukaryotes. Trends Genet. 2019;35(11):818-27. Epub 20190806. doi: 10.1016/j.tig.2019.07.007. PubMed PMID: 31399242; PMCID: PMC6825889
Lin J, Zhao Y, Ferraro AR, Yang E, Lewis ZA, Lin X. Transcription factor Znf2 coordinates with the chromatin remodeling SWI/SNF complex to regulate cryptococcal cellular differentiation. Commun Biol. 2019;2:412. Epub 20191114. doi: 10.1038/s42003-019-0665-2. PubMed PMID: 31754642; PMCID: PMC6856107
Laue K, Rajshekar S, Courtney AJ, Lewis ZA, Goll MG. The maternal to zygotic transition regulates genome-wide heterochromatin establishment in the zebrafish embryo. Nat Commun. 2019;10(1):1551. Epub 20190404. doi: 10.1038/s41467-019-09582-3. PubMed PMID: 30948728; PMCID: PMC6449393
Ambati S, Ferarro AR, Kang SE, Lin J, Lin X, Momany M, Lewis ZA, Meagher RB. Dectin-1-Targeted Antifungal Liposomes Exhibit Enhanced Efficacy. mSphere. 2019;4(1). Epub 20190213. doi: 10.1128/mSphere.00025-19. PubMed PMID: 30760610; PMCID: PMC6374590
Ambati S, Ferarro AR, Kang SE, Lin J, Lin X, Momany M, Lewis ZA, Meagher RB. Erratum for Ambati et al., "Dectin-1-Targeted Antifungal Liposomes Exhibit Enhanced Efficacy". mSphere. 2019;4(2). Epub 20190306. doi: 10.1128/mSphere.00121-19. PubMed PMID: 30842270; PMCID: PMC6403456
Ambati S, Ellis EC, Lin J, Lin X, Lewis ZA, Meagher RB. Dectin-2-Targeted Antifungal Liposomes Exhibit Enhanced Efficacy. mSphere. 2019;4(5). Epub 20191030. doi: 10.1128/mSphere.00715-19. PubMed PMID: 31666315; PMCID: PMC6821932
2018
Ferraro AR, Lewis ZA. ChIP-Seq Analysis in Neurospora crassa. Methods Mol Biol. 2018;1775:241-50. doi: 10.1007/978-1-4939-7804-5_19. PubMed PMID: 29876822; PMCID: PMC10911069
2017
Lewis ZA. Polycomb Group Systems in Fungi: New Models for Understanding Polycomb Repressive Complex 2. Trends Genet. 2017;33(3):220-31. Epub 20170211. doi: 10.1016/j.tig.2017.01.006. PubMed PMID: 28196760
2016
Seymour M, Ji L, Santos AM, Kamei M, Sasaki T, Basenko EY, Schmitz RJ, Zhang X, Lewis ZA. Histone H1 Limits DNA Methylation in Neurospora crassa. G3 (Bethesda). 2016;6(7):1879-89. Epub 20160707. doi: 10.1534/g3.116.028324. PubMed PMID: 27172195; PMCID: PMC4938642
Gacek-Matthews A, Berger H, Sasaki T, Wittstein K, Gruber C, Lewis ZA, Strauss J. KdmB, a Jumonji Histone H3 Demethylase, Regulates Genome-Wide H3K4 Trimethylation and Is Required for Normal Induction of Secondary Metabolism in Aspergillus nidulans. PLoS Genet. 2016;12(8):e1006222. Epub 20160822. doi: 10.1371/journal.pgen.1006222. PubMed PMID: 27548260; PMCID: PMC4993369
Basenko EY, Kamei M, Ji L, Schmitz RJ, Lewis ZA. The LSH/DDM1 Homolog MUS-30 Is Required for Genome Stability, but Not for DNA Methylation in Neurospora crassa. PLoS Genet. 2016;12(1):e1005790. Epub 20160115. doi: 10.1371/journal.pgen.1005790. PubMed PMID: 26771905; PMCID: PMC4714748
2015
Basenko EY, Sasaki T, Ji L, Prybol CJ, Burckhardt RM, Schmitz RJ, Lewis ZA. Genome-wide redistribution of H3K27me3 is linked to genotoxic stress and defective growth. Proc Natl Acad Sci U S A. 2015;112(46):E6339-48. Epub 20151102. doi: 10.1073/pnas.1511377112. PubMed PMID: 26578794; PMCID: PMC4655558
Adhvaryu KK, Gessaman JD, Honda S, Lewis ZA, Grisafi PL, Selker EU. The cullin-4 complex DCDC does not require E3 ubiquitin ligase elements to control heterochromatin in Neurospora crassa. Eukaryot Cell. 2015;14(1):25-8. Epub 20141031. doi: 10.1128/ec.00212-14. PubMed PMID: 25362134; PMCID: PMC4279019
2014
Sasaki T, Lynch KL, Mueller CV, Friedman S, Freitag M, Lewis ZA. Heterochromatin controls γH2A localization in Neurospora crassa. Eukaryot Cell. 2014;13(8):990-1000. Epub 20140530. doi: 10.1128/ec.00117-14. PubMed PMID: 24879124; PMCID: PMC4135800
Ji L, Sasaki T, Sun X, Ma P, Lewis ZA, Schmitz RJ. Methylated DNA is over-represented in whole-genome bisulfite sequencing data. Front Genet. 2014;5:341. Epub 20141021. doi: 10.3389/fgene.2014.00341. PubMed PMID: 25374580; PMCID: PMC4204604
2013
Jamieson K, Rountree MR, Lewis ZA, Stajich JE, Selker EU. Regional control of histone H3 lysine 27 methylation in Neurospora. Proc Natl Acad Sci U S A. 2013;110(15):6027-32. Epub 20130325. doi: 10.1073/pnas.1303750110. PubMed PMID: 23530226; PMCID: PMC3625340
2012
Honda S, Lewis ZA, Shimada K, Fischle W, Sack R, Selker EU. Heterochromatin protein 1 forms distinct complexes to direct histone deacetylation and DNA methylation. Nat Struct Mol Biol. 2012;19(5):471-7, s1. Epub 20120415. doi: 10.1038/nsmb.2274. PubMed PMID: 22504884; PMCID: PMC4957970
2011
Belden WJ, Lewis ZA, Selker EU, Loros JJ, Dunlap JC. CHD1 remodels chromatin and influences transient DNA methylation at the clock gene frequency. PLoS Genet. 2011;7(7):e1002166. Epub 20110721. doi: 10.1371/journal.pgen.1002166. PubMed PMID: 21811413; PMCID: PMC3140994
2010
Lewis ZA, Adhvaryu KK, Honda S, Shiver AL, Selker EU. Identification of DIM-7, a protein required to target the DIM-5 H3 methyltransferase to chromatin. Proc Natl Acad Sci U S A. 2010;107(18):8310-5. Epub 20100419. doi: 10.1073/pnas.1000328107. PubMed PMID: 20404183; PMCID: PMC2889519
Lewis ZA, Adhvaryu KK, Honda S, Shiver AL, Knip M, Sack R, Selker EU. DNA methylation and normal chromosome behavior in Neurospora depend on five components of a histone methyltransferase complex, DCDC. PLoS Genet. 2010;6(11):e1001196. Epub 20101104. doi: 10.1371/journal.pgen.1001196. PubMed PMID: 21079689; PMCID: PMC2973830
Lee HC, Li L, Gu W, Xue Z, Crosthwaite SK, Pertsemlidis A, Lewis ZA, Freitag M, Selker EU, Mello CC, Liu Y. Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi. Mol Cell. 2010;38(6):803-14. Epub 20100422. doi: 10.1016/j.molcel.2010.04.005. PubMed PMID: 20417140; PMCID: PMC2902691
Honda S, Lewis ZA, Huarte M, Cho LY, David LL, Shi Y, Selker EU. The DMM complex prevents spreading of DNA methylation from transposons to nearby genes in Neurospora crassa. Genes Dev. 2010;24(5):443-54. Epub 20100205. doi: 10.1101/gad.1893210. PubMed PMID: 20139222; PMCID: PMC2827840
2009
Lewis ZA, Honda S, Khlafallah TK, Jeffress JK, Freitag M, Mohn F, Schübeler D, Selker EU. Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa. Genome Res. 2009;19(3):427-37. Epub 20081217. doi: 10.1101/gr.086231.108. PubMed PMID: 19092133; PMCID: PMC2661801
2008
Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One. 2008;3(10):e3376. Epub 20081013. doi: 10.1371/journal.pone.0003376. PubMed PMID: 18852878; PMCID: PMC2557064
2007
Lewis ZA, Shiver AL, Stiffler N, Miller MR, Johnson EA, Selker EU. High-density detection of restriction-site-associated DNA markers for rapid mapping of mutated loci in Neurospora. Genetics. 2007;177(2):1163-71. Epub 20070729. doi: 10.1534/genetics.107.078147. PubMed PMID: 17660537; PMCID: PMC2034621
2006
de Paula RM, Lewis ZA, Greene AV, Seo KS, Morgan LW, Vitalini MW, Bennett L, Gomer RH, Bell-Pedersen D. Two circadian timing circuits in Neurospora crassa cells share components and regulate distinct rhythmic processes. J Biol Rhythms. 2006;21(3):159-68. doi: 10.1177/0748730406288338. PubMed PMID: 16731655
2004
Xie X, Wilkinson HH, Correa A, Lewis ZA, Bell-Pedersen D, Ebbole DJ. Transcriptional response to glucose starvation and functional analysis of a glucose transporter of Neurospora crassa. Fungal Genet Biol. 2004;41(12):1104-19. doi: 10.1016/j.fgb.2004.08.009. PubMed PMID: 15531214
2003
Correa A, Lewis ZA, Greene AV, March IJ, Gomer RH, Bell-Pedersen D. Multiple oscillators regulate circadian gene expression in Neurospora. Proc Natl Acad Sci U S A. 2003;100(23):13597-602. Epub 20031103. doi: 10.1073/pnas.2233734100. PubMed PMID: 14597725; PMCID: PMC263859
2002
Lewis ZA, Correa A, Schwerdtfeger C, Link KL, Xie X, Gomer RH, Thomas T, Ebbole DJ, Bell-Pedersen D. Overexpression of White Collar-1 (WC-1) activates circadian clock-associated genes, but is not sufficient to induce most light-regulated gene expression in Neurospora crassa. Mol Microbiol. 2002;45(4):917-31. doi: 10.1046/j.1365-2958.2002.03074.x. PubMed PMID: 12180913
2001
Shrode LB, Lewis ZA, White LD, Bell-Pedersen D, Ebbole DJ. vvd is required for light adaptation of conidiation-specific genes of Neurospora crassa, but not circadian conidiation. Fungal Genet Biol. 2001;32(3):169-81. doi: 10.1006/fgbi.2001.1264. PubMed PMID: 11343403
Bell-Pedersen D, Lewis ZA, Loros JJ, Dunlap JC. The Neurospora circadian clock regulates a transcription factor that controls rhythmic expression of the output eas(ccg-2) gene. Mol Microbiol. 2001;41(4):897-909. doi: 10.1046/j.1365-2958.2001.02558.x. PubMed PMID: 11532152