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A natural histone H2A variant lacking the Bub1 phosphorylation site and regulated depletion of centromeric histone CENP-A foster evolvability in Candida albicans.

Brimacombe CA, Burke JE, Parsa JY, Catania S, O'Meara TR, Witchley JN, Burrack LS, Madhani HD, Noble SM.

PLoS Biol. 2019 Jun 21;17(6):e3000331. doi: 10.1371/journal.pbio.3000331. eCollection 2019 Jun.


A Non-Dicer RNase III and Four Other Novel Factors Required for RNAi-Mediated Transposon Suppression in the Human Pathogenic Yeast Cryptococcus neoformans.

Burke JE, Longhurst AD, Natarajan P, Rao B, Liu J, Sales-Lee J, Mortensen Y, Moresco JJ, Diedrich JK, Yates JR 3rd, Madhani HD.

G3 (Bethesda). 2019 Jul 9;9(7):2235-2244. doi: 10.1534/g3.119.400330.


Real-Time Genetic Compensation Defines the Dynamic Demands of Feedback Control.

Harrigan P, Madhani HD, El-Samad H.

Cell. 2018 Oct 18;175(3):877-886.e10. doi: 10.1016/j.cell.2018.09.044.


Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance.

Mavor D, Barlow KA, Asarnow D, Birman Y, Britain D, Chen W, Green EM, Kenner LR, Mensa B, Morinishi LS, Nelson CA, Poss EM, Suresh P, Tian R, Arhar T, Ary BE, Bauer DP, Bergman ID, Brunetti RM, Chio CM, Dai SA, Dickinson MS, Elledge SK, Helsell CVM, Hendel NL, Kang E, Kern N, Khoroshkin MS, Kirkemo LL, Lewis GR, Lou K, Marin WM, Maxwell AM, McTigue PF, Myers-Turnbull D, Nagy TL, Natale AM, Oltion K, Pourmal S, Reder GK, Rettko NJ, Rohweder PJ, Schwarz DMC, Tan SK, Thomas PV, Tibble RW, Town JP, Tsai MK, Ugur FS, Wassarman DR, Wolff AM, Wu TS, Bogdanoff D, Li J, Thorn KS, O'Conchúir S, Swaney DL, Chow ED, Madhani HD, Redding S, Bolon DN, Kortemme T, DeRisi JL, Kampmann M, Fraser JS.

Biol Open. 2018 Jul 23;7(7). pii: bio036103. doi: 10.1242/bio.036103.


Polymerase pausing induced by sequence-specific RNA-binding protein drives heterochromatin assembly.

Parsa JY, Boudoukha S, Burke J, Homer C, Madhani HD.

Genes Dev. 2018 Jul 1;32(13-14):953-964. doi: 10.1101/gad.310136.117.


Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution.

Burke JE, Longhurst AD, Merkurjev D, Sales-Lee J, Rao B, Moresco JJ, Yates JR 3rd, Li JJ, Madhani HD.

Cell. 2018 May 3;173(4):1014-1030.e17. doi: 10.1016/j.cell.2018.03.020.


Total RNA Isolation and Quantification of Specific RNAs in Fission Yeast.

Roth R, Madhani HD, Garcia JF.

Methods Mol Biol. 2018;1721:63-72. doi: 10.1007/978-1-4939-7546-4_6. Review.


Ten principles of heterochromatin formation and function.

Allshire RC, Madhani HD.

Nat Rev Mol Cell Biol. 2018 Apr;19(4):229-244. doi: 10.1038/nrm.2017.119. Epub 2017 Dec 13. Review.


Integrated Activity and Genetic Profiling of Secreted Peptidases in Cryptococcus neoformans Reveals an Aspartyl Peptidase Required for Low pH Survival and Virulence.

Clarke SC, Dumesic PA, Homer CM, O'Donoghue AJ, La Greca F, Pallova L, Majer P, Madhani HD, Craik CS.

PLoS Pathog. 2016 Dec 15;12(12):e1006051. doi: 10.1371/journal.ppat.1006051. eCollection 2016 Dec.


Phospho-site mutants of the RNA Polymerase II C-terminal domain alter subtelomeric gene expression and chromatin modification state in fission yeast.

Inada M, Nichols RJ, Parsa JY, Homer CM, Benn RA, Hoxie RS, Madhani HD, Shuman S, Schwer B, Pleiss JA.

Nucleic Acids Res. 2016 Nov 2;44(19):9180-9189. Epub 2016 Jul 8.


Sensitive and Quantitative Three-Color Protein Imaging in Fission Yeast Using Spectrally Diverse, Recoded Fluorescent Proteins with Experimentally-Characterized In Vivo Maturation Kinetics.

Al-Sady B, Greenstein RA, El-Samad HJ, Braun S, Madhani HD.

PLoS One. 2016 Aug 1;11(8):e0159292. doi: 10.1371/journal.pone.0159292. eCollection 2016.


Intracellular Action of a Secreted Peptide Required for Fungal Virulence.

Homer CM, Summers DK, Goranov AI, Clarke SC, Wiesner DL, Diedrich JK, Moresco JJ, Toffaletti D, Upadhya R, Caradonna I, Petnic S, Pessino V, Cuomo CA, Lodge JK, Perfect J, Yates JR 3rd, Nielsen K, Craik CS, Madhani HD.

Cell Host Microbe. 2016 Jun 8;19(6):849-64. doi: 10.1016/j.chom.2016.05.001. Epub 2016 May 19.


Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans.

Dumesic PA, Rosenblad MA, Samuelsson T, Nguyen T, Moresco JJ, Yates JR 3rd, Madhani HD.

Nucleic Acids Res. 2015 Oct 15;43(18):9017-27. doi: 10.1093/nar/gkv819. Epub 2015 Aug 14.


Contrasting host-pathogen interactions and genome evolution in two generalist and specialist microsporidian pathogens of mosquitoes.

Desjardins CA, Sanscrainte ND, Goldberg JM, Heiman D, Young S, Zeng Q, Madhani HD, Becnel JJ, Cuomo CA.

Nat Commun. 2015 May 13;6:7121. doi: 10.1038/ncomms8121.


Intrinsic Toxicity of Unchecked Heterochromatin Spread Is Suppressed by Redundant Chromatin Boundary Functions in Schizosacchromyces pombe.

Garcia JF, Al-Sady B, Madhani HD.

G3 (Bethesda). 2015 May 8;5(7):1453-61. doi: 10.1534/g3.115.018663.


Product binding enforces the genomic specificity of a yeast polycomb repressive complex.

Dumesic PA, Homer CM, Moresco JJ, Pack LR, Shanle EK, Coyle SM, Strahl BD, Fujimori DG, Yates JR 3rd, Madhani HD.

Cell. 2015 Jan 15;160(1-2):204-18. doi: 10.1016/j.cell.2014.11.039. Epub 2014 Dec 18.


Unraveling the biology of a fungal meningitis pathogen using chemical genetics.

Brown JCS, Nelson J, VanderSluis B, Deshpande R, Butts A, Kagan S, Polacheck I, Krysan DJ, Myers CL, Madhani HD.

Cell. 2014 Nov 20;159(5):1168-1187. doi: 10.1016/j.cell.2014.10.044.


Functional profiling of human fungal pathogen genomes.

Goranov AI, Madhani HD.

Cold Spring Harb Perspect Med. 2014 Nov 6;5(3):a019596. doi: 10.1101/cshperspect.a019596. Review.


Estrogen receptor antagonists are anti-cryptococcal agents that directly bind EF hand proteins and synergize with fluconazole in vivo.

Butts A, Koselny K, Chabrier-Roselló Y, Semighini CP, Brown JC, Wang X, Annadurai S, DiDone L, Tabroff J, Childers WE Jr, Abou-Gharbia M, Wellington M, Cardenas ME, Madhani HD, Heitman J, Krysan DJ.

MBio. 2014 Feb 11;5(1):e00765-13. doi: 10.1128/mBio.00765-13.


The spliceosome as a transposon sensor.

Dumesic PA, Madhani HD.

RNA Biol. 2013 Nov;10(11):1653-60. doi: 10.4161/rna.26800. Review.


snRNA catalysts in the spliceosome's ancient core.

Madhani HD.

Cell. 2013 Dec 5;155(6):1213-5. doi: 10.1016/j.cell.2013.11.022.


Recognizing the enemy within: licensing RNA-guided genome defense.

Dumesic PA, Madhani HD.

Trends Biochem Sci. 2014 Jan;39(1):25-34. doi: 10.1016/j.tibs.2013.10.003. Epub 2013 Nov 23. Review.


The frustrated gene: origins of eukaryotic gene expression.

Madhani HD.

Cell. 2013 Nov 7;155(4):744-9. doi: 10.1016/j.cell.2013.10.003.


A conserved ncRNA-binding protein recruits silencing factors to heterochromatin through an RNAi-independent mechanism.

Marina DB, Shankar S, Natarajan P, Finn KJ, Madhani HD.

Genes Dev. 2013 Sep 1;27(17):1851-6. doi: 10.1101/gad.226019.113.


Division of labor between the chromodomains of HP1 and Suv39 methylase enables coordination of heterochromatin spread.

Al-Sady B, Madhani HD, Narlikar GJ.

Mol Cell. 2013 Jul 11;51(1):80-91. doi: 10.1016/j.molcel.2013.06.013.


A conformational switch in HP1 releases auto-inhibition to drive heterochromatin assembly.

Canzio D, Liao M, Naber N, Pate E, Larson A, Wu S, Marina DB, Garcia JF, Madhani HD, Cooke R, Schuck P, Cheng Y, Narlikar GJ.

Nature. 2013 Apr 18;496(7445):377-81. doi: 10.1038/nature12032. Epub 2013 Mar 13.


Stalled spliceosomes are a signal for RNAi-mediated genome defense.

Dumesic PA, Natarajan P, Chen C, Drinnenberg IA, Schiller BJ, Thompson J, Moresco JJ, Yates JR 3rd, Bartel DP, Madhani HD.

Cell. 2013 Feb 28;152(5):957-68. doi: 10.1016/j.cell.2013.01.046. Epub 2013 Feb 14.


Approaching the functional annotation of fungal virulence factors using cross-species genetic interaction profiling.

Brown JC, Madhani HD.

PLoS Genet. 2012;8(12):e1003168. doi: 10.1371/journal.pgen.1003168. Epub 2012 Dec 27.


Timing of transcriptional quiescence during gametogenesis is controlled by global histone H3K4 demethylation.

Xu M, Soloveychik M, Ranger M, Schertzberg M, Shah Z, Raisner R, Venkatasubrahmanyan S, Tsui K, Gebbia M, Hughes T, van Bakel H, Nislow C, Madhani HD, Meneghini MD.

Dev Cell. 2012 Nov 13;23(5):1059-71. doi: 10.1016/j.devcel.2012.10.005. Epub 2012 Nov 1.


Ers1 links HP1 to RNAi.

Rougemaille M, Braun S, Coyle S, Dumesic PA, Garcia JF, Isaac RS, Libri D, Narlikar GJ, Madhani HD.

Proc Natl Acad Sci U S A. 2012 Jul 10;109(28):11258-63. doi: 10.1073/pnas.1204947109. Epub 2012 Jun 25.


Shaping the landscape: mechanistic consequences of ubiquitin modification of chromatin.

Braun S, Madhani HD.

EMBO Rep. 2012 Jun 29;13(7):619-30. doi: 10.1038/embor.2012.78. Review. Erratum in: EMBO Rep. 2012 Dec;13(12):1152.


Quorum sensing in fungi: Q&A.

Madhani HD.

PLoS Pathog. 2011 Oct;7(10):e1002301. doi: 10.1371/journal.ppat.1002301. Epub 2011 Oct 27. No abstract available.


Spt6 is required for heterochromatic silencing in the fission yeast Schizosaccharomyces pombe.

Kiely CM, Marguerat S, Garcia JF, Madhani HD, Bähler J, Winston F.

Mol Cell Biol. 2011 Oct;31(20):4193-204. doi: 10.1128/MCB.05568-11. Epub 2011 Aug 15.


Can a systems perspective help us appreciate the biological meaning of small effects?

El-Samad H, Madhani HD.

Dev Cell. 2011 Jul 19;21(1):11-3. doi: 10.1016/j.devcel.2011.06.005.


Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress.

Charles GM, Chen C, Shih SC, Collins SR, Beltrao P, Zhang X, Sharma T, Tan S, Burlingame AL, Krogan NJ, Madhani HD, Narlikar GJ.

Proc Natl Acad Sci U S A. 2011 Jun 28;108(26):10620-5. doi: 10.1073/pnas.1019735108. Epub 2011 Jun 14.


A major role for capsule-independent phagocytosis-inhibitory mechanisms in mammalian infection by Cryptococcus neoformans.

Chun CD, Brown JCS, Madhani HD.

Cell Host Microbe. 2011 Mar 17;9(3):243-251. doi: 10.1016/j.chom.2011.02.003.


The Cul4-Ddb1(Cdt)² ubiquitin ligase inhibits invasion of a boundary-associated antisilencing factor into heterochromatin.

Braun S, Garcia JF, Rowley M, Rougemaille M, Shankar S, Madhani HD.

Cell. 2011 Jan 7;144(1):41-54. doi: 10.1016/j.cell.2010.11.051.


Chromodomain-mediated oligomerization of HP1 suggests a nucleosome-bridging mechanism for heterochromatin assembly.

Canzio D, Chang EY, Shankar S, Kuchenbecker KM, Simon MD, Madhani HD, Narlikar GJ, Al-Sady B.

Mol Cell. 2011 Jan 7;41(1):67-81. doi: 10.1016/j.molcel.2010.12.016.


Applying genetics and molecular biology to the study of the human pathogen Cryptococcus neoformans.

Chun CD, Madhani HD.

Methods Enzymol. 2010;470:797-831. doi: 10.1016/S0076-6879(10)70033-1. Epub 2010 Mar 1.


Coordinate control of gene expression noise and interchromosomal interactions in a MAP kinase pathway.

McCullagh E, Seshan A, El-Samad H, Madhani HD.

Nat Cell Biol. 2010 Oct;12(10):954-62. doi: 10.1038/ncb2097. Epub 2010 Sep 19.


Combinatorial, site-specific requirement for heterochromatic silencing factors in the elimination of nucleosome-free regions.

Garcia JF, Dumesic PA, Hartley PD, El-Samad H, Madhani HD.

Genes Dev. 2010 Aug 15;24(16):1758-71. doi: 10.1101/gad.1946410. Epub 2010 Jul 30.


Nonredundant requirement for multiple histone modifications for the early anaphase release of the mitotic exit regulator Cdc14 from nucleolar chromatin.

Hwang WW, Madhani HD.

PLoS Genet. 2009 Aug;5(8):e1000588. doi: 10.1371/journal.pgen.1000588. Epub 2009 Aug 7.


Mechanisms that specify promoter nucleosome location and identity.

Hartley PD, Madhani HD.

Cell. 2009 May 1;137(3):445-58. doi: 10.1016/j.cell.2009.02.043.


Hog1 mitogen-activated protein kinase (MAPK) interrupts signal transduction between the Kss1 MAPK and the Tec1 transcription factor to maintain pathway specificity.

Shock TR, Thompson J, Yates JR 3rd, Madhani HD.

Eukaryot Cell. 2009 Apr;8(4):606-16. doi: 10.1128/EC.00005-09. Epub 2009 Feb 13.


Systematic genetic analysis of virulence in the human fungal pathogen Cryptococcus neoformans.

Liu OW, Chun CD, Chow ED, Chen C, Madhani HD, Noble SM.

Cell. 2008 Oct 3;135(1):174-88. doi: 10.1016/j.cell.2008.07.046.


Epigenomics: a roadmap, but to where?

Madhani HD, Francis NJ, Kingston RE, Kornberg RD, Moazed D, Narlikar GJ, Panning B, Struhl K.

Science. 2008 Oct 3;322(5898):43-4. doi: 10.1126/science.322.5898.43b. No abstract available.


Genomewide screen for negative regulators of sirtuin activity in Saccharomyces cerevisiae reveals 40 loci and links to metabolism.

Raisner RM, Madhani HD.

Genetics. 2008 Aug;179(4):1933-44. doi: 10.1534/genetics.108.088443. Epub 2008 Aug 9.


Ers1, a rapidly diverging protein essential for RNA interference-dependent heterochromatic silencing in Schizosaccharomyces pombe.

Rougemaille M, Shankar S, Braun S, Rowley M, Madhani HD.

J Biol Chem. 2008 Sep 19;283(38):25770-3. doi: 10.1074/jbc.C800140200. Epub 2008 Jul 25.

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