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Chromatin

  • 1.
    Lukasak B, Mitchener M, Kong L, Dul B, Lazarus C, Ramakrishnan A, Ni J, Shen L, Maze I, Muir T. TGM2-mediated histone transglutamination is dictated by steric accessibility. Proc Natl Acad Sci U S A. 2022;119(43):e2208672119. PMCID: PMC9618071
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    Mitchener M, Muir T. Oncohistones: Exposing the nuances and vulnerabilities of epigenetic regulation. Mol Cell. 2022;82(16):2925–2938. PMCID: PMC9482148
    Reference Link
  • 1.
    Lim A, McFadden T, Link V, Han S-J, Karlsson R-M, Stacy A, Farley T, Lima-Junior D, Harrison O, Desai J, Lionakis M, Shih H-Y, Cameron H, Belkaid Y. Prenatal maternal infection promotes tissue-specific immunity and inflammation in offspring. Science. 2021;373(6558). PMID: 34446580
    Reference Link
  • 1.
    Chen K, Wong A, Troyanskaya O, Zhou J. A sequence-based global map of regulatory activity for deciphering human genetics. Nat Genet. 2022;54(7):940–949. PMCID: PMC9279145
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    Howard T, Lum K, Kennedy M, Cristea I. The Nuclear DNA Sensor IFI16 Indiscriminately Binds to and Diminishes Accessibility of the HSV-1 Genome to Suppress Infection. mSystems. 2022;7(3):e0019822. PMCID: PMC9239196
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    Batut P, Bing X, Sisco Z, Raimundo J, Levo M, Levine M. Genome organization controls transcriptional dynamics during development. Science. 2022;375(6580):566–570. PMID: 35113722
    Reference Link
  • 1.
    Jack A, Kim Y, Strom A, Lee D, Williams B, Schaub J, Kellogg E, Finkelstein I, Ferro L, Yildiz A, Brangwynne C. Compartmentalization of telomeres through DNA-scaffolded phase separation. Dev Cell. 2022;57(2):277–290.e9. PMCID: PMC8988007
    Reference Link
  • 1.
    Dao H, Liu H, Mashtalir N, Kadoch C, Muir T. Synthesis of Oriented Hexasomes and Asymmetric Nucleosomes Using a Template Editing Process. J Am Chem Soc. 2022;144(5):2284–2291. PMCID: PMC8935522
    Reference Link
  • 1.
    Eeftens J, Kapoor M, Michieletto D, Brangwynne C. Polycomb condensates can promote epigenetic marks but are not required for sustained chromatin compaction. Nat Commun. 2021;12(1):5888. PMCID: PMC8497513
    Reference Link
  • 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
    Reference Link
  • 1.
    Hananya N, Daley S, Bagert J, Muir T. Synthesis of ADP-Ribosylated Histones Reveals Site-Specific Impacts on Chromatin Structure and Function. J Am Chem Soc. 2021;143(29):10847–10852. PMID: 34264659
    Reference Link
  • 1.
    Zhao S, Chuh K, Zhang B, Dul B, Thompson R, Farrelly L, Liu X, Xu N, Xue Y, Roeder R, Maze I, Muir T, Li H. Histone H3Q5 serotonylation stabilizes H3K4 methylation and potentiates its readout. Proc Natl Acad Sci U S A. 2021;118(6). PMCID: PMC8017887
    Reference Link
  • 1.
    Ing-Simmons E, Vaid R, Bing X, Levine M, Mannervik M, Vaquerizas J. Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning. Nat Genet. 2021;53(4):487–499. PMCID: PMC8035076
    Reference Link
  • 1.
    Murray-Nerger L, Cristea I. Lamin post-translational modifications: emerging toggles of nuclear organization and function. Trends Biochem Sci. 2021;46(10):832–847. PMCID: PMC8793286
    Reference Link
  • 1.
    Zhang Y, Lee D, Meir Y, Brangwynne C, Wingreen N. Mechanical Frustration of Phase Separation in the Cell Nucleus by Chromatin. Phys Rev Lett. 2021;126(25):258102. PMCID: PMC8604804
    Reference Link
  • 1.
    Strom A, Biggs R, Banigan E, Wang X, Chiu K, Herman C, Collado J, Yue F, Politz J, Tait L, Scalzo D, Telling A, Groudine M, Brangwynne C, Marko J, Stephens A. HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics. Elife. 2021;10. PMCID: PMC8233041
    Reference Link
  • 1.
    Wu A, Zhi J, Tian T, Cihan A, Cevher M, Liu Z, David Y, Muir T, Roeder R, Yu M. DOT1L complex regulates transcriptional initiation in human erythroleukemic cells. Proc Natl Acad Sci U S A. 2021;118(27). PMCID: PMC8271641
    Reference Link
  • 1.
    Erokhin M, Gorbenko F, Lomaev D, Mazina M, Mikhailova A, Garaev A, Parshikov A, Vorobyeva N, Georgiev P, Schedl P, Chetverina D. Boundaries potentiate polycomb response element-mediated silencing. BMC Biol. 2021;19(1):113. PMCID: PMC8170967
    Reference Link
  • 1.
    Ruf-Zamojski F, Zhang Z, Zamojski M, Smith G, Mendelev N, Liu H, Nudelman G, Moriwaki M, Pincas H, Castanon R, Nair V, Seenarine N, Amper M, Zhou X, Ongaro L, Toufaily C, Schang G, Nery J, Bartlett A, Aldridge A, Jain N, Childs G, Troyanskaya O, Ecker J, Turgeon J, Welt C, Bernard D, Sealfon S. Single nucleus multi-omics regulatory landscape of the murine pituitary. Nat Commun. 2021;12(1):2677. PMCID: PMC8113460
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    Murray-Nerger L, Justice J, Rekapalli P, Hutton J, Cristea I. Lamin B1 acetylation slows the G1 to S cell cycle transition through inhibition of DNA repair. Nucleic Acids Res. 2021;49(4):2044–2064. PMCID: PMC7913768
    Reference Link
  • 1.
    Chetverina D, Erokhin M, Schedl P. GAGA factor: a multifunctional pioneering chromatin protein. Cell Mol Life Sci. 2021;78(9):4125–4141. PMCID: PMC8815297
    Reference Link
  • 1.
    Leicher R, Ge E, Lin X, Reynolds M, Xie W, Walz T, Zhang B, Muir T, Liu S. Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin. Proc Natl Acad Sci U S A. 2020;117(48):30465–30475. PMCID: PMC7720148
    Reference Link
  • 1.
    Chen H, Gregor T. Using RNA Tags for Multicolor Live Imaging of Chromatin Loci and Transcription in Drosophila Embryos. Methods Mol Biol. 2020;2166:373–384. PMCID: PMC8130451
    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
    Reference Link
  • 1.
    Diehl K, Muir T. Chromatin as a key consumer in the metabolite economy. Nat Chem Biol. 2020;16(6):620–629. PMCID: PMC7258299
    Reference Link
  • 1.
    Burton A, Haugbro M, Gates L, Bagert J, Allis D, Muir T. In situ chromatin interactomics using a chemical bait and trap approach. Nat Chem. 2020;12(6):520–527. PMCID: PMC7331920
    Reference Link
  • 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
    Reference Link
  • 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
    Reference Link
  • 1.
    Albig C, Wang C, Dann G, Wojcik F, Schauer T, Krause S, Maenner S, Cai W, Li Y, Girton J, Muir T, Johansen J, Johansen K, Becker P, Regnard C. JASPer controls interphase histone H3S10 phosphorylation by chromosomal kinase JIL-1 in Drosophila. Nat Commun. 2019;10(1):5343. PMCID: PMC6877644
    Reference Link
  • 1.
    Kyrchanova O, Wolle D, Sabirov M, Kurbidaeva A, Aoki T, Maksimenko O, Kyrchanova M, Georgiev P, Schedl P. Distinct Elements Confer the Blocking and Bypass Functions of the Bithorax Boundary. Genetics. 2019;213(3):865–876. PMCID: PMC6827379
    Reference Link
  • 1.
    Chen C-F, Pohl T, Chan A, Slocum J, Zakian V. Centromere RNA Is Negatively Regulated by Cbf1 and Its Unscheduled Synthesis Impacts CenH3 Binding. Genetics. 2019;213(2):465–479. PMCID: PMC6781895
    Reference Link
  • 1.
    Jain S, Do T, Lund P, Rashoff A, Diehl K, Cieslik M, Bajic A, Juretic N, Deshmukh S, Venneti S, Muir T, Garcia B, Jabado N, Lewis P. PFA ependymoma-associated protein EZHIP inhibits PRC2 activity through a H3 K27M-like mechanism. Nat Commun. 2019;10(1):2146. PMCID: PMC6513997
    Reference Link
  • 1.
    Shin Y, Chang Y-C, Lee D, Berry J, Sanders D, Ronceray P, Wingreen N, Haataja M, Brangwynne C. Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome. Cell. 2018;175(6):1481–1491.e13. PMCID: PMC6724728
    Reference Link
  • 1.
    Jeon J, McGinty R, Muir T, Kim J-A, Kim J. Crosstalk among Set1 complex subunits involved in H2B ubiquitylation-dependent H3K4 methylation. Nucleic Acids Res. 2018;46(21):11129–11143. PMCID: PMC6265457
    Reference Link
  • 1.
    Kachaev Z, Lebedeva L, Kozlov E, Toropygin I, Schedl P, Shidlovskii Y. Paip2 is localized to active promoters and loaded onto nascent mRNA in Drosophila. Cell Cycle. 2018;17(14):1708–1720. PMCID: PMC6133343
    Reference Link
  • 1.
    Chou D, Adamson B, Dephoure N, Tan X, Nottke A, Hurov K, Gygi S, Colaiácovo M, Elledge S. A chromatin localization screen reveals poly (ADP ribose)-regulated recruitment of the repressive polycomb and NuRD complexes to sites of DNA damage. Proc Natl Acad Sci U S A. 2010;107(43):18475–80. PMCID: PMC2972950
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    Kyrchanova O, Kurbidaeva A, Sabirov M, Postika N, Wolle D, Aoki T, Maksimenko O, Mogila V, Schedl P, Georgiev P. The bithorax complex iab-7 Polycomb response element has a novel role in the functioning of the Fab-7 chromatin boundary. PLoS Genet. 2018;14(8):e1007442. PMCID: PMC6110506
    Reference Link
  • 1.
    Liszczak G, Diehl K, Dann G, Muir T. Acetylation blocks DNA damage-induced chromatin ADP-ribosylation. Nat Chem Biol. 2018;14(9):837–840. PMCID: PMC6505472
    Reference Link
  • 1.
    Chen H, Levo M, Barinov L, Fujioka M, Jaynes J, Gregor T. Dynamic interplay between enhancer-promoter topology and gene activity. Nat Genet. 2018;50(9):1296–1303. PMCID: PMC6119122
    Reference Link
  • 1.
    Sauls K, Greco T, Wang L, Zou M, Villasmil M, Qian L, Cristea I, Conlon F. Initiating Events in Direct Cardiomyocyte Reprogramming. Cell Rep. 2018;22(7):1913–1922. PMCID: PMC6045814
    Reference Link
  • 1.
    Jenness C, Giunta S, Müller M, Kimura H, Muir T, Funabiki H. HELLS and CDCA7 comprise a bipartite nucleosome remodeling complex defective in ICF syndrome. Proc Natl Acad Sci U S A. 2018;115(5):E876-E885. PMCID: PMC5798369
    Reference Link
  • 1.
    Wang X, Paucek R, Gooding A, Brown Z, Ge E, Muir T, Cech T. Molecular analysis of PRC2 recruitment to DNA in chromatin and its inhibition by RNA. Nat Struct Mol Biol. 2017;24(12):1028–1038. PMCID: PMC5771497
    Reference Link
  • 1.
    Hannon C, Blythe S, Wieschaus E. Concentration dependent chromatin states induced by the bicoid morphogen gradient. Elife. 2017;6. PMCID: PMC5624782
    Reference Link
  • 1.
    Santos J, Josling G, Ross P, Joshi P, Orchard L, Campbell T, Schieler A, Cristea I, Llinás M. Red Blood Cell Invasion by the Malaria Parasite Is Coordinated by the PfAP2-I Transcription Factor. Cell Host Microbe. 2017;21(6):731–741.e10. PMCID: PMC5855115
    Reference Link
  • 1.
    David Y, Muir T. Emerging Chemistry Strategies for Engineering Native Chromatin. J Am Chem Soc. 2017;139(27):9090–9096. PMCID: PMC5752102
    Reference Link

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