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A
Liszczak G, Diehl KL, Dann GP, Muir TW. Acetylation blocks DNA damage-induced chromatin ADP-ribosylation. Nat Chem Biol. 2018 ;14(9):837-840.
C
Jack A, Kim Y, Strom AR, Lee DSW, Williams B, Schaub JM, et al. Compartmentalization of telomeres through DNA-scaffolded phase separation. Dev Cell. 2022 ;57(2):277-290.e9.
D
Valastyan JS, Tota MR, Taylor IR, Stergioula V, Hone GAB, Smith CD, et al. Discovery of PqsE Thioesterase Inhibitors for Using DNA-Encoded Small Molecule Library Screening. ACS Chem Biol. 2020 ;15(2):446-456.
Etzion-Fuchs A, Todd DA, Singh M. dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains. Nucleic Acids Res. 2021 ;49(13):e78.
E
David Y, Muir TW. Emerging Chemistry Strategies for Engineering Native Chromatin. J Am Chem Soc. 2017 ;139(27):9090-9096.
Chen PJ, Hussmann JA, Yan J, Knipping F, Ravisankar P, Chen P-F, et al. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell. 2021 ;184(22):5635-5652.e29.
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Geronimo CL, Zakian VA. Getting it done at the ends: Pif1 family DNA helicases and telomeres. DNA Repair (Amst). 2016 ;44:151-158.
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Garcia HG, Gregor T. Live Imaging of mRNA Synthesis in Drosophila. Methods Mol Biol. 2018 ;1649:349-357.
Anlas AA, Nelson CM. Living under Strain: How Epithelia Protect Their Genomes from Repeated Stretching. Biochemistry. 2020 ;59(30):2761-2763.
M
Huang X, Duddy OP, Silpe JE, Paczkowski JE, Cong J, Henke BR, et al. Mechanism underlying autoinducer recognition in the DPO-VqmA quorum-sensing pathway. J Biol Chem. 2020 ;295(10):2916-2931.
Su X, Wellen KE, Rabinowitz JD. Metabolic control of methylation and acetylation. Curr Opin Chem Biol. 2016 ;30:52-60.
Wang X, Paucek RD, Gooding AR, Brown ZZ, Ge EJ, Muir TW, et al. Molecular analysis of PRC2 recruitment to DNA in chromatin and its inhibition by RNA. Nat Struct Mol Biol. 2017 ;24(12):1028-1038.
P
Kachaev ZM, Lebedeva LA, Shaposhnikov AV, Moresco JJ, Yates JR, Schedl P, et al. Paip2 cooperates with Cbp80 at an active promoter and participates in RNA Polymerase II phosphorylation in Drosophila. FEBS Lett. 2019 ;593(10):1102-1112.
Yan J, Cirincione A, Adamson B. Prime Editing: Precision Genome Editing by Reverse Transcription. Mol Cell. 2020 ;77(2):210-212.
R
Deng D, Yin P, Yan C, Pan X, Gong X, Qi S, et al. Recognition of methylated DNA by TAL effectors. Cell Res. 2012 ;22(10):1502-4.
Deng D, Yan C, Wu J, Pan X, Yan N. Revisiting the TALE repeat. Protein Cell. 2014 ;5(4):297-306.
S
Yin P, Deng D, Yan C, Pan X, Xi JJeff, Yan N, et al. Specific DNA-RNA hybrid recognition by TAL effectors. Cell Rep. 2012 ;2(4):707-13.
Snir S, vonHoldt BM, Pellegrini M. A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging. PLoS Comput Biol. 2016 ;12(11):e1005183.
Chen G, Swem LR, Swem DL, Stauff DL, O'Loughlin CT, Jeffrey PD, et al. A strategy for antagonizing quorum sensing. Mol Cell. 2011 ;42(2):199-209.
Deng D, Yan C, Pan X, Mahfouz M, Wang J, Zhu J-K, et al. Structural basis for sequence-specific recognition of DNA by TAL effectors. Science. 2012 ;335(6069):720-3.
Strawn R, Melichercik M, Green M, Stockner T, Carey J, Ettrich R. Symmetric allosteric mechanism of hexameric Escherichia coli arginine repressor exploits competition between L-arginine ligands and resident arginine residues. PLoS Comput Biol. 2010 ;6(6):e1000801.
Dao HT, Liu H, Mashtalir N, Kadoch C, Muir TW. Synthesis of Oriented Hexasomes and Asymmetric Nucleosomes Using a Template Editing Process. J Am Chem Soc. 2022 ;144(5):2284-2291.
Kobren SNadimpalli, Singh M. Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions. Nucleic Acids Res. 2019 ;47(2):582-593.