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Transcription Factors

  • 1.
    Menon T, Burdine R. A twist in Pitx2 regulation of gut looping. Dev Cell. 2022;57(21):2445–2446. PMID: 36347237
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    Prentice J, Bridges A, Bassler B. Synergy between c-di-GMP and Quorum-Sensing Signaling in Vibrio cholerae Biofilm Morphogenesis. J Bacteriol. 2022;204(10):e0024922. PMCID: PMC9578409
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    Nguyen T, Costa E, Deibert T, Reyes J, Keber F, Tomschik M, Stadlmeier M, Gupta M, Kumar C, Cruz E, Amodeo A, Gatlin J, Wühr M. Differential nuclear import sets the timing of protein access to the embryonic genome. Nat Commun. 2022;13(1):5887. PMCID: PMC9537182
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    Taylor I, Murray-Nerger L, Greco T, Liu D, Cristea I, Bassler B. Protein Interaction Networks of Catalytically Active and Catalytically Inactive PqsE in Pseudomonas aeruginosa. mBio. 2022;13(5):e0155922. PMCID: PMC9600345
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    Ibragimov A, Bylino O, Kyrchanova O, Shidlovskii Y, White R, Schedl P, Georgiev P. The Variable CTCF Site from Drosophila melanogaster Ubx Gene is Redundant and Has no Insulator Activity. Dokl Biochem Biophys. 2022;505(1):173–175. PMCID: PMC9613721
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    Voortman L, Anderson C, Urban E, Yuan L, Tran S, Neuhaus-Follini A, Derrick J, Gregor T, Johnston R. Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification in flies. Dev Cell. 2022;57(15):1817–1832.e5. PMCID: PMC9378680
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    Robbe Z, Shi W, Wasson L, Scialdone A, Wilczewski C, Sheng X, Hepperla A, Akerberg B, Pu W, Cristea I, Davis I, Conlon F. CHD4 is recruited by GATA4 and NKX2-5 to repress noncardiac gene programs in the developing heart. Genes Dev. 2022;36(7-8):468–482. PMCID: PMC9067406
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    Zhang Z, Zamojski M, Smith G, Willis T, Yianni V, Mendelev N, Pincas H, Seenarine N, Amper M, Vasoya M, Cheng W, Zaslavsky E, Nair V, Turgeon J, Bernard D, Troyanskaya O, Andoniadou C, Sealfon S, Ruf-Zamojski F. Single nucleus transcriptome and chromatin accessibility of postmortem human pituitaries reveal diverse stem cell regulatory mechanisms. Cell Rep. 2022;38(10):110467. PMCID: PMC8957708
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    Shen M, Wei Y, Kim H, Wan L, Jiang Y-Z, Hang X, Raba M, Remiszewski S, Rowicki M, Wu C-G, Wu S, Zhang L, Lu X, Yuan M, Smith H, Zheng A, Bertino J, Jin J, Xing Y, Shao Z-M, Kang Y. Small-molecule inhibitors that disrupt the MTDH-SND1 complex suppress breast cancer progression and metastasis. Nat Cancer. 2022;3(1):43–59. PMCID: PMC8818087
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    Shen M, Smith H, Wei Y, Jiang Y-Z, Zhao S, Wang N, Rowicki M, Tang Y, Hang X, Wu S, Wan L, Shao Z-M, Kang Y. Pharmacological disruption of the MTDH-SND1 complex enhances tumor antigen presentation and synergizes with anti-PD-1 therapy in metastatic breast cancer. Nat Cancer. 2022;3(1):60–74. PMCID: PMC8818088
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    Chacha P, Horie R, Kusakabe T, Sasakura Y, Singh M, Horie T, Levine M. Neuronal identities derived by misexpression of the POU IV sensory determinant in a protovertebrate. Proc Natl Acad Sci U S A. 2022;119(4). PMCID: PMC8794889
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    Bauer M, Petkova M, Gregor T, Wieschaus E, Bialek W. Trading bits in the readout from a genetic network. Proc Natl Acad Sci U S A. 2021;118(46). PMCID: PMC8609648
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    Huang S-K, Whitney P, Dutta S, Shvartsman S, Rushlow C. Spatial organization of transcribing loci during early genome activation in Drosophila. Curr Biol. 2021;31(22):5102–5110.e5. PMCID: PMC8612988
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  • 1.
    Mashtalir N, Dao H, Sankar A, Liu H, Corin A, Bagert J, Ge E, D’Avino A, Filipovski M, Michel B, Dann G, Muir T, Kadoch C. Chromatin landscape signals differentially dictate the activities of mSWI/SNF family complexes. Science. 2021;373(6552):306–315. PMCID: PMC8390793
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  • 1.
    Gilmutdinov R, Kozlov E, Yakovlev K, Olenina L, Kotov A, Barr J, Zhukova M, Schedl P, Shidlovskii Y. The 3’UTR of the Drosophila CPEB translation factor gene orb2 plays a crucial role in spermatogenesis. Development. 2021;148(17). PMCID: PMC8513165
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    Lim B, Levine M. Enhancer-promoter communication: hubs or loops?. Curr Opin Genet Dev. 2021;67:5–9. PMCID: PMC8653970
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    Bagert J, Muir T. Molecular Epigenetics: Chemical Biology Tools Come of Age. Annu Rev Biochem. 2021;90:287–320. PMCID: PMC8284505
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  • 1.
    Zhao E, Lalwani M, Chen J-M, Orillac P, Toettcher J, Avalos J. Optogenetic Amplification Circuits for Light-Induced Metabolic Control. ACS Synth Biol. 2021;10(5):1143–1154. PMCID: PMC8721662
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    Treen N, Shimobayashi S, Eeftens J, Brangwynne C, Levine M. Properties of repression condensates in living Ciona embryos. Nat Commun. 2021;12(1):1561. PMCID: PMC7946874
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    Bagert J, Mitchener M, Patriotis A, Dul B, Wojcik F, Nacev B, Feng L, Allis D, Muir T. Oncohistone mutations enhance chromatin remodeling and alter cell fates. Nat Chem Biol. 2021;17(4):403–411. PMCID: PMC8174649
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  • 1.
    Shidlovskii Y, Bylino O, Shaposhnikov A, Kachaev Z, Lebedeva L, Kolesnik V, Amendola D, De Simone G, Formicola N, Schedl P, Digilio F, Giordano E. Subunits of the PBAP Chromatin Remodeler Are Capable of Mediating Enhancer-Driven Transcription in . Int J Mol Sci. 2021;22(6). PMCID: PMC7999800
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    Prior M, Selvanayagam J, Kim J-G, Tomar M, Jonikas M, Mudgett M, Smeekens S, Hanson J, Frommer W. bZIP11 Is a Susceptibility Factor During Infection. Mol Plant Microbe Interact. 2021;34(4):439–447. PMID: 33400562
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    Chetverina D, Erokhin M, Schedl P. GAGA factor: a multifunctional pioneering chromatin protein. Cell Mol Life Sci. 2021;78(9):4125–4141. PMCID: PMC8815297
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    McBride M, Mashtalir N, Winter E, Dao H, Filipovski M, D’Avino A, Seo H-S, Umbreit N, St Pierre R, Valencia A, Qian K, Zullow H, Jaffe J, Dhe-Paganon S, Muir T, Kadoch C. The nucleosome acidic patch and H2A ubiquitination underlie mSWI/SNF recruitment in synovial sarcoma. Nat Struct Mol Biol. 2020;27(9):836–845. PMCID: PMC7714695
    Reference Link
  • 1.
    Murawska M, Schauer T, Matsuda A, Wilson M, Pysik T, Wojcik F, Muir T, Hiraoka Y, Straub T, Ladurner A. The Chaperone FACT and Histone H2B Ubiquitination Maintain S. pombe Genome Architecture through Genic and Subtelomeric Functions. Mol Cell. 2020;77(3):501–513.e7. PMCID: PMC7007867
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  • 1.
    Mukherjee S, Jemielita M, Stergioula V, Tikhonov M, Bassler B. Photosensing and quorum sensing are integrated to control Pseudomonas aeruginosa collective behaviors. PLoS Biol. 2019;17(12):e3000579. PMCID: PMC6932827
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  • 1.
    Dao H, Dul B, Dann G, Liszczak G, Muir T. A basic motif anchoring ISWI to nucleosome acidic patch regulates nucleosome spacing. Nat Chem Biol. 2020;16(2):134–142. PMCID: PMC6982587
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  • 1.
    Ueberschär M, Wang H, Zhang C, Kondo S, Aoki T, Schedl P, Lai E, Wen J, Dai Q. BEN-solo factors partition active chromatin to ensure proper gene activation in Drosophila. Nat Commun. 2019;10(1):5700. PMCID: PMC6911014
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  • 1.
    Smits C, Shvartsman S. The design and logic of terminal patterning in Drosophila. Curr Top Dev Biol. 2020;137:193–217. PMID: 32143743
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  • 1.
    Wan L, Chong S, Xuan F, Liang A, Cui X, Gates L, Carroll T, Li Y, Feng L, Chen G, Wang S-P, Ortiz M, Daley S, Wang X, Xuan H, Kentsis A, Muir T, Roeder R, Li H, Li W, Tjian R, Wen H, Allis D. Impaired cell fate through gain-of-function mutations in a chromatin reader. Nature. 2020;577(7788):121–126. PMCID: PMC7061414
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  • 1.
    Huang X, Duddy O, Silpe J, Paczkowski J, Cong J, Henke B, Bassler B. Mechanism underlying autoinducer recognition in the DPO-VqmA quorum-sensing pathway. J Biol Chem. 2020;295(10):2916–2931. PMCID: PMC7062168
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  • 1.
    Park J-D, Moon K, Miller C, Rose J, Xu F, Ebmeier C, Jacobsen J, Mao D, Old W, DeShazer D, Seyedsayamdost M. Thailandenes, Cryptic Polyene Natural Products Isolated from Using Phenotype-Guided Transposon Mutagenesis. ACS Chem Biol. 2020;15(5):1195–1203. PMCID: PMC9106368
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  • 1.
    Seo K, Kleiner R. YTHDF2 Recognition of N-Methyladenosine (mA)-Modified RNA Is Associated with Transcript Destabilization. ACS Chem Biol. 2020;15(1):132–139. PMCID: PMC7025767
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  • 1.
    Valencia A, Collings C, Dao H, St Pierre R, Cheng Y-C, Huang J, Sun Z-Y, Seo H-S, Mashtalir N, Comstock D, Bolonduro O, Vangos N, Yeoh Z, Dornon M, Hermawan C, Barrett L, Dhe-Paganon S, Woolf C, Muir T, Kadoch C. Recurrent SMARCB1 Mutations Reveal a Nucleosome Acidic Patch Interaction Site That Potentiates mSWI/SNF Complex Chromatin Remodeling. Cell. 2019;179(6):1342–1356.e23. PMCID: PMC7175411
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  • 1.
    Kuroda K, Hammer S, Watanabe Y, López J, Fink G, Stephanopoulos G, Ueda M, Avalos J. Critical Roles of the Pentose Phosphate Pathway and GLN3 in Isobutanol-Specific Tolerance in Yeast. Cell Syst. 2019;9(6):534–547.e5. PMID: 31734159
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    Stine R, Sakers A, TeSlaa T, Kissig M, Stine Z, Kwon C, Cheng L, Lim H-W, Kaestner K, Rabinowitz J, Seale P. PRDM16 Maintains Homeostasis of the Intestinal Epithelium by Controlling Region-Specific Metabolism. Cell Stem Cell. 2019;25(6):830–845.e8. PMCID: PMC6898778
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    Zhu Q, Tekpli X, Troyanskaya O, Kristensen V. Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations. Bioinformatics. 2020;36(4):994–999. PMCID: PMC7031777
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    Wang W, Ishibashi J, Trefely S, Shao M, Cowan A, Sakers A, Lim H-W, O’Connor S, Doan M, Cohen P, Baur J, King T, Veech R, Won K-J, Rabinowitz J, Snyder N, Gupta R, Seale P. A PRDM16-Driven Metabolic Signal from Adipocytes Regulates Precursor Cell Fate. Cell Metab. 2019;30(1):174–189.e5. PMCID: PMC6836679
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    Aedo S, Orman M, Brynildsen M. Stationary phase persister formation in Escherichia coli can be suppressed by piperacillin and PBP3 inhibition. BMC Microbiol. 2019;19(1):140. PMCID: PMC6591824
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    Heimbucher T, Murphy C. A PBX/MEIS Complex Balances Reproduction and Somatic Resilience. Dev Cell. 2019;49(2):157–158. PMCID: PMC7452753
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    Postika N, Metzler M, Affolter M, Müller M, Schedl P, Georgiev P, Kyrchanova O. Boundaries mediate long-distance interactions between enhancers and promoters in the Drosophila Bithorax complex. PLoS Genet. 2018;14(12):e1007702. PMCID: PMC6306242
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    Barr J, Charania S, Gilmutdinov R, Yakovlev K, Shidlovskii Y ii, Schedl P. The CPEB translational regulator, Orb, functions together with Par proteins to polarize the Drosophila oocyte. PLoS Genet. 2019;15(3):e1008012. PMCID: PMC6433291
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    Petkova M, Tkačik G, Bialek W, Wieschaus E, Gregor T. Optimal Decoding of Cellular Identities in a Genetic Network. Cell. 2019;176(4):844–855.e15. PMCID: PMC6526179
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    Adamson B, Smogorzewska A, Sigoillot F, King R, Elledge S. A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response. Nat Cell Biol. 2012;14(3):318–28. PMCID: PMC3290715
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    Izhar L, Adamson B, Ciccia A, Lewis J, Pontano-Vaites L, Leng Y, Liang A, Westbrook T, Harper W, Elledge S. A Systematic Analysis of Factors Localized to Damaged Chromatin Reveals PARP-Dependent Recruitment of Transcription Factors. Cell Rep. 2015;11(9):1486–500. PMCID: PMC4464939
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    Dixit A, Parnas O, Li B, Chen J, Fulco C, Jerby-Arnon L, Marjanovic N, Dionne D, Burks T, Raychowdhury R, Adamson B, Norman T, Lander E, Weissman J, Friedman N, Regev A iv. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Cell. 2016;167(7):1853–1866.e17. PMCID: PMC5181115
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    Munro D, Ghersi D, Singh M. Two critical positions in zinc finger domains are heavily mutated in three human cancer types. PLoS Comput Biol. 2018;14(6):e1006290. PMCID: PMC6040777
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    Cande J, Namiki S, Qiu J, Korff W, Card G, Shaevitz J, Stern D, Berman G. Optogenetic dissection of descending behavioral control in . Elife. 2018;7. PMCID: PMC6031430
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    Fedotova A, Aoki T, Rossier M, Mishra R, Clendinen C, Kyrchanova O, Wolle D, Bonchuk A, Maeda R, Mutero A, Cleard F, Mogila V, Karch F, Georgiev P, Schedl P. The BEN Domain Protein Insensitive Binds to the Chromatin Boundary To Establish Proper Segmental Identity in . Genetics. 2018;210(2):573–585. PMCID: PMC6216583
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  • 1.
    Konovalova A, Grabowicz M, Balibar C, Malinverni J, Painter R, Riley D, Mann P, Wang H, Garlisi C, Sherborne B, Rigel N, Ricci D, Black T, Roemer T, Silhavy T, Walker S. Inhibitor of intramembrane protease RseP blocks the σ response causing lethal accumulation of unfolded outer membrane proteins. Proc Natl Acad Sci U S A. 2018;115(28):E6614-E6621. PMCID: PMC6048503
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