Aaron Johnson, PhD

Publications

• Heterochromatin protein Sir3 induces contacts between the amino terminus of histone H4 and nucleosomal DNA
• Wang F, Li G, Altaf M, Lu C, Currie MA, Johnson A, Moazed D. Heterochromatin protein Sir3 induces contacts between the amino terminus of histone H4 and nucleosomal DNA. Proc Natl Acad Sci U S A. 2013 May 21;110(21):8495-500. PubMed PMID: 23650358
• Johnson A, Wu R, Peetz M, Gygi SP, Moazed D. Heterochromatic gene silencing by activator interference and a transcription elongation barrier. J Biol Chem. 2013 Oct 4;288(40):28771-82. PubMed PMID: 23940036
• Tatavosian R, Zhen CY, Duc HN, Balas MM, Johnson AM, Ren X. Distinct Cellular Assembly Stoichiometry of Polycomb Complexes on Chromatin Revealed by Single-molecule Chromatin Immunoprecipitation Imaging. J Biol Chem. 2015 Nov 20;290(47):28038-54. PubMed PMID: 26381410
• Meredith EK, Balas MM, Sindy K, Haislop K, Johnson AM. An RNA matchmaker protein regulates the activity of the long noncoding RNA HOTAIR. RNA. 2016 Jul;22(7):995-1010. PubMed PMID: 27146324
• Liu H, Wang C, Lee S, Deng Y, Wither M, Oh S, Ning F, Dege C, Zhang Q, Liu X, Johnson AM, Zang J, Chen Z, Janknecht R, Hansen K, Marrack P, Li CY, Kappler JW, Hagman J, Zhang G. Clipping of arginine-methylated histone tails by JMJD5 and JMJD7. Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):E7717-E7726. PubMed PMID: 28847961
• Zukowski A, Al-Afaleq NO, Duncan ED, Yao T, Johnson AM. Recruitment and allosteric stimulation of a histone deubiquitinating enzyme during heterochromatin assembly. J Biol Chem. 2017 Dec 29. [Epub ahead of print] PubMed PMID: 29288197
• Balas MM, Porman AM, Hansen KC, Johnson AM. SILAC-MS Profiling of Reconstituted Human Chromatin Platforms for the Study of Transcription and RNA Regulation. J Proteome Res. 2018 Oct 5;17(10):3475-3484. PubMed PMID: 30192551
• Zukowski A, Phillips J, Park S, Wu R, Gygi SP, Johnson AM. Proteomic profiling of yeast heterochromatin connects direct physical and genetic interactions. Curr Genet. 2018 Oct 12. [Epub ahead of print] PubMed PMID: 30310994
• Vogler TO, Wheeler JR, Nguyen ED, Hughes MP, Britson KA, Lester E, Rao B, Betta ND, Whitney ON, Ewachiw TE, Gomes E, Shorter J, Lloyd TE, Eisenberg DS, Taylor JP, Johnson AM, Olwin BB, Parker R. TDP-43 and RNA form amyloid-like myo-granules in regenerating muscle. Nature. 2018 Nov;563(7732):508-513. PubMed PMID: 30464263
• Zukowski A, Johnson AM. The interplay of histone H2B ubiquitination with budding and fission yeast heterochromatin. Curr Genet. 2018 Aug;64(4):799-806. PubMed PMID: 29464330
• Nguyen ED, Balas MM, Griffin AM, Roberts JT, Johnson AM. Global profiling of hnRNP A2/B1-RNA binding on chromatin highlights LncRNA interactions. RNA Biol. 2018;15(7):901-913. PubMed PMID: 29938567
• Balas MM, Johnson AM. Exploring the mechanisms behind long noncoding RNAs and cancer. Noncoding RNA Res. 2018 Sep;3(3):108-117. PubMed PMID: 30175284
• Zukowski A, Al-Afaleq NO, Duncan ED, Yao T, Johnson AM. Recruitment and allosteric stimulation of a histone-deubiquitinating enzyme during heterochromatin assembly. J Biol Chem. 2018 Feb 16;293(7):2498-2509. PubMed PMID: 29288197
• Zukowski A, Phillips J, Park S, Wu R, Gygi SP, Johnson AM. Proteomic profiling of yeast heterochromatin connects direct physical and genetic interactions. Curr Genet. 2019 Apr;65(2):495-505. PubMed PMID: 30310994
• Roberts JT, Porman AM, Johnson AM. Identification of m6A residues at single-nucleotide resolution using eCLIP and an accessible custom analysis pipeline. RNA. 2020 Dec 29. [Epub ahead of print] PubMed PMID: 33376190
• Wu SK, Roberts JT, Balas MM, Johnson AM. RNA matchmaking in chromatin regulation. Biochem Soc Trans. 2020 Dec 18;48(6):2467-2481. PubMed PMID: 33245317
• Balas MM, Hartwick EW, Barrington C, Roberts JT, Wu SK, Bettcher R, Griffin AM, Kieft JS, Johnson AM. Establishing RNA-RNA interactions remodels lncRNA structure and promotes PRC2 activity. Sci Adv. 2021 Apr;7(16). PubMed PMID: 33853770
• Roberts JT, Porman AM, Johnson AM. Identification of m(6)A residues at single-nucleotide resolution using eCLIP and an accessible custom analysis pipeline. RNA. 2021 Apr;27(4):527-541. PubMed PMID: 33376190
• Wheeler JR, Whitney ON, Vogler TO, Nguyen ED, Pawlikowski B, Lester E, Cutler A, Elston T, Dalla Betta N, Parker KR, Yost KE, Vogel H, Rando TA, Chang HY, Johnson AM, Parker R, Olwin BB. RNA-binding proteins direct myogenic cell fate decisions. Elife. 2022 Jun 13;11. PubMed PMID: 35695839
• Porman AM, Roberts JT, Duncan ED, Chrupcala ML, Levine AA, Kennedy MA, Williams MM, Richer JK, Johnson AM. A single N6-methyladenosine site regulates lncRNA HOTAIR function in breast cancer cells. PLoS Biol. 2022 Nov;20(11):e3001885. PubMed PMID: 36441764