Selected publications

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• Gail HE, Healy E, Flanigan SF, Jones N, Ng XH, Uckelmann M, Levina V, Zhang Q, Davidovich C. Inseparable RNA binding and chromatin modification activities of a nucleosome-interacting surface in EZH2. Nature Genetics. 2024 May 14. doi: 10.1038/s41588-024-01740-8. PMID: 38744974.

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• Uckelmann M, Davidovich C. Chromatin compaction by Polycomb group proteins revisited. Current Opinion in Structural Biology. 2024 86, 102806. doi: 10.1016/j.sbi.2024.102806. PMID: 38537534.

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• Bi Y, Li F, Wang C, Pan T, Davidovich C, Webb GI, Song J. Advancing microRNA Target Site Prediction with Transformer and Base-Pairing Patterns. bioRxiv, 2024.05. 05.592612. doi: https://doi.org/10.1101/2024.05.05.592612.

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• Healy E, Zhang Q, Gail EH, Agius SC, Sun G, Bullen M, Pandey V, Das PP, Polo JM, Davidovich C. The apparent loss of PRC2 chromatin occupancy as an artefact of RNA depletion. Cell Rep. 2024 Feb 27;43(3):113858. doi: 10.1016/j.celrep.2024.113858. PMID: 38416645.

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• Gilan O, Talarmain L, Bell CC, Neville D, Knezevic K, Ferguson DT, Boudes M, Chan YC, Davidovich C, Lam EYN, Dawson MA. CRISPR–ChIP reveals selective regulation of H3K79me2 by Menin in MLL leukemia. Nature Struct Mol Biol. 2023 Sep 7. doi: 10.1038/s41594-023-01087-4. PMID: 37679565.

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• Ohtomo H, Ito S, McKenzie NJ, Uckelmann M, Wakamori M, Ehara H, Furukawa A, Tsunaka Y, Shibata M, Sekine S, Umehara T, Davidovich C, Koseki H, Nishimura Y. J Mol Biol. 2023 Feb 28;435(4):167936. doi: 10.1016/j.jmb.2022.167936. PMID: 36610636.

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• Deevy O, Monger C, Matra F, Tuck E, Conway E, Rodighiero S, Zhang Q, Davidovich C, Pasini D, Bracken AP. Dominant negative and directional dysregulation of Polycomb function in EZH2-mutant human growth disorders. bioRxiv. doi: https://doi.org/10.1101/2023.06.01.543208.

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• Uckelmann M, Levina V, Taveneau C, Ng XH, Pandey V, Zhang Q, Flanigan S, Li M, Das PP, de Marco A, Davidovich C. Dynamic PRC1-CBX8 stabilizes a porous structure of chromatin condensates. bioRxiv. doi: https://doi.org/10.1101/2023.05.08.539931.

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• Trovato M, Bunina D, Yildiz U, Fernandez-Novel Marx N, Uckelmann M, Levina V, Kori Y, Janeva A, Garcia B, Davidovich C, Zaugg JB, Noh KM. Histone H3. 3 lysine 9 and 27 control repressive chromatin states at cryptic cis-regulatory elements and bivalent promoters in mouse embryonic stem cells. bioRxiv. doi: https://doi.org/10.1101/2023.05.08.539859.

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• Owen B, Davidovich C. DNA binding by polycomb-group proteins: searching for the link to CpG islands. Nucleic Acids Res. 2022 Apr 30;gkac290. doi: 10.1093/nar/gkac290. PMID: 35489059.

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• Uckelmann M, Davidovich C. An added layer of repression for human genes. Nature. 2022 Mar 30. doi: 10.1038/d41586-022-00519-3. PMID: 35354969

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• Bose T, Fridkin G, Davidovich C, Krupkin M, Dinger N, Falkovich AH, Peleg Y, Agmon I, Bashan A, Yonath A. Origin of life: protoribosome forms peptide bonds and links RNA and protein dominated worlds. Nucleic Acids Res. 2022 Feb 28;50(4):1815-1828. doi: 10.1093/nar/gkac052. PMID: 35137169

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• Bravo JPK, Bartnik K, Venditti L, Acker J, Gail EH, Colyer A, Davidovich C, Lamb DC, Tuma R, Calabrese AN, Borodavka A. Structural basis of rotavirus RNA chaperone displacement and RNA annealing. Proc Natl Acad Sci U S A. 2021 Oct 12;118(41):e2100198118. doi: 10.1073/pnas.2100198118.
  PMID: 34615715.

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• Zhang Q*, Agius SC*, Flanigan SF, Uckelmann M, Levina L, Owen BM, Davidovich C. PALI1 facilitates DNA and nucleosome binding by PRC2 and triggers an allosteric activation of catalysis. Nature Comm. 2021. Jul 28;12(1):4592. doi: 10.1038/s41467-021-24866-3.

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• Uckelmann M, Davidovich C. Not just a writer: PRC2 as a chromatin reader. Biochem Soc Trans. 2021 Jun 30;49(3):1159-1170. doi: 10.1042/BST20200728. PMID: 34060617.

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• Davidovich C, Zhang Q. Allosteric regulation of histone lysine methyltransferases: from context-specific regulation to selective drugs. Biochem Soc Trans. 2021 Apr 30;49(2):591-607. doi: 10.1042/BST20200238. PMID: 33769454.

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• Gail EH, Shah AD, Schittenhelm RB, Davidovich C. crisscrosslinkeR: identification and visualization of protein-RNA and protein-protein interactions from crosslinking mass spectrometry. Bioinformatics (Oxford) 2020. btaa1043; doi: 10.1093/bioinformatics/btaa1043. PMID: 33346827

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• Scheer S, Bramhall M, Runting J, Russ B, Zhang Q, Flanigan SF, Zaini A, Ellemor J, Rodrigues G, Ng J, Davidovich C, Zaph C. The lysine methyltransferase DOT1L controls CD4+ T cell-dependent immunity and inflammation. bioRxiv 821348v2

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• Horn V*, Uckelmann M*, Zhang H, Eerland J, Aarsman I, le Paige UB, Davidovich C, Sixma TK, van Ingen H.  Structural basis of specific H2A K13/K15 ubiquitination by RNF168. Nature Comm. 2019. doi: 10.1038/s41467-019-09756-z. PMID 30988309

 

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• Zhang Q*, McKenzie NJ*, Warneford-Thomson R*, Gail EH, Flanigan FF, Owen BM, Lauman R, Levina V, Garcia BA, Schittenhelm RB, Bonasio R, Davidovich C. RNA exploits an exposed regulatory site to inhibit the enzymatic activity of PRC2. Nature Struct Mol Biol. 2019. doi: 10.1038/s41594-019-0197-y. PMID: 30833789

 

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• Wang X, Davidovich C. Targeting PRC2: RNA offers new opportunities. Oncotarget. 2017 Nov 27;8(64):107346-107347. doi: 10.18632/oncotarget.22715. PMID: 29296169

 

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• Wekselman I, Zimmerman E, Davidovich C, Belousoff M, Matzov D, Krupkin M, Rozenberg H, Bashan A, Friedlander G, Kjeldgaard J, Ingmer H, Lindahl L, Zengel JM, Yonath A. The Ribosomal Protein uL22 Modulates the Shape of the Protein Exit Tunnel. Structure. 2017 Aug 1;25(8):1233-1241.e3. doi: 10.1016/j.str.2017.06.004. PMID: 28689968

 

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• Wang X, Goodrich KJ, Gooding AR, Naeem H, Archer S, Paucek RD, Youmans DT, Cech TR, Davidovich C. Targeting of Polycomb repressive complex 2 to RNA by short repeats of consecutive guanines. Mol Cell. 2017 Mar;65(6)1056-1067; PubMed PMID: 28306504; doi: 10.1016/j.molcel.2017.02.003.

 

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• Auerbach-Nevo T, Baram D, Bashan A, Belousoff M, Breiner E, Davidovich C, Cimicata G, Eyal Z, Halfon Y, Krupkin M, Matzov D, Metz M, Rufayda M, Peretz M, Pick O, Pyetan E, Rozenberg H, Shalev-Benami M, Wekselman I, Zarivach R, Zimmerman E, Assis N, Bloch J, Israeli H, Kalaora R, Lim L, Sade-Falk O, Shapira T, Taha-Salaime L, Tang H, Yonath A.  Ribosomal antibiotics: contemporary challenges. Antibiotics (Basel). 2016 Jun 29;5(3). pii: E24. PubMed PMID: 27367739; doi: 10.3390/antibiotics5030024.

 

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• Lu Z, Zhang QC, Lee B, Flynn RA, Smith MA, Robinson JT, Davidovich C, Gooding AR, Goodrich KJ, Mattick JS, Mesirov JP, Cech TR, Chang HY. RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. Cell. 2016 May;pii: S0092-8674(16)30422-6. PubMed PMID: 27180905; doi: 10.1016/j.cell.2016.04.028.

 

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• Davidovich C, Cech TR. The recruitment of chromatin modifiers by long noncoding RNAs: lessons from PRC2. RNA. 2015 Dec;21(12):2007-22. PubMed PMID: 26574518; doi: 10.1261/rna.053918.115.

 

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• Davidovich C, Wang X, Cifuentes-Rojas C, Goodrich KJ, Gooding AR, Lee JT, Cech TR. Toward a consensus on the binding specificity and promiscuity of PRC2 for RNA. Mol Cell. 2015 Feb 5;57(3):552-8. doi: 10.1016/j.molcel.2014.12.017. Epub 2015 Jan 15. PubMed PMID: 25601759; PubMed Central PMCID: PMC4320675.

 

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• Davidovich C, Goodrich KJ, Gooding AR, Cech TR. A dimeric state for PRC2. Nucleic Acids Res. 2014 Aug;42(14):9236-48. doi: 10.1093/nar/gku540. Epub 2014 Jul 3. PubMed PMID: 24992961; PubMed Central PMCID: PMC4132707.

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• Davidovich C, Zheng L, Goodrich KJ, Cech TR. Promiscuous RNA binding by Polycomb repressive complex 2. Nature Struct Mol Biol. 2013 Nov;20(11):1250-7. doi: 10.1038/nsmb.2679. Epub 2013 Sep 29. PubMed PMID: 24077223; PubMed Central PMCID: PMC3823624.

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• Auerbach T, Mermershtain I, Davidovich C, Bashan A, Belousoff M, Wekselman I, Zimmerman E, Xiong L, Klepacki D, Arakawa K, Kinashi H, Mankin AS, Yonath A. The structure of ribosome-lankacidin complex reveals ribosomal sites for synergistic antibiotics. Proc Natl Acad Sci U S A. 2010 Feb 2;107(5):1983-8. doi: 10.1073/pnas.0914100107. Epub 2010 Jan 11. PubMed PMID: 20080686; PubMed Central PMCID: PMC2804743.

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• Davidovich C, Belousoff M, Bashan A, Yonath A. The evolving ribosome: from non-coded peptide bond formation to sophisticated translation machinery. Res Microbiol. 2009 Sep;160(7):487-92. doi: 10.1016/j.resmic.2009.07.004. Epub 2009 Jul 18. Review. PubMed PMID: 19619641.

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• Davidovich C, Bashan A, Yonath A. Structural basis for cross-resistance to ribosomal PTC antibiotics. Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):20665-70. doi: 10.1073/pnas.0810826105. Epub 2008 Dec 19. PubMed PMID: 19098107; PubMed Central PMCID: PMC2605634.

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• Davidovich C, Bashan A, Auerbach-Nevo T, Yaggie RD, Gontarek RR, Yonath A. Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity. Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4291-6. Epub 2007 Mar 8. PubMed PMID: 17360517; PubMed Central PMCID: PMC1817833.

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* equal contribution.