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Inflammatory regulatory network mediated by the joint action of NF-kB, STAT3, and AP-1 factors is involved in many human cancers.

Ji Z, He L, Regev A, Struhl K.

Proc Natl Acad Sci U S A. 2019 May 7;116(19):9453-9462. doi: 10.1073/pnas.1821068116. Epub 2019 Mar 25.


Requirements for RNA polymerase II preinitiation complex formation in vivo.

Petrenko N, Jin Y, Dong L, Wong KH, Struhl K.

Elife. 2019 Jan 25;8. pii: e43654. doi: 10.7554/eLife.43654.


Lysine methyltransferase 2D regulates pancreatic carcinogenesis through metabolic reprogramming.

Koutsioumpa M, Hatziapostolou M, Polytarchou C, Tolosa EJ, Almada LL, Mahurkar-Joshi S, Williams J, Tirado-Rodriguez AB, Huerta-Yepez S, Karavias D, Kourea H, Poultsides GA, Struhl K, Dawson DW, Donahue TR, Fernández-Zapico ME, Iliopoulos D.

Gut. 2019 Jul;68(7):1271-1286. doi: 10.1136/gutjnl-2017-315690. Epub 2018 Oct 18.


Extensive Structural Differences of Closely Related 3' mRNA Isoforms: Links to Pab1 Binding and mRNA Stability.

Moqtaderi Z, Geisberg JV, Struhl K.

Mol Cell. 2018 Dec 6;72(5):849-861.e6. doi: 10.1016/j.molcel.2018.08.044. Epub 2018 Oct 11.


Targeted profiling of RNA translation reveals mTOR-4EBP1/2-independent translation regulation of mRNAs encoding ribosomal proteins.

Li BB, Qian C, Gameiro PA, Liu CC, Jiang T, Roberts TM, Struhl K, Zhao JJ.

Proc Natl Acad Sci U S A. 2018 Oct 2;115(40):E9325-E9332. doi: 10.1073/pnas.1805782115. Epub 2018 Sep 17.


Nutrient Deprivation Elicits a Transcriptional and Translational Inflammatory Response Coupled to Decreased Protein Synthesis.

Gameiro PA, Struhl K.

Cell Rep. 2018 Aug 7;24(6):1415-1424. doi: 10.1016/j.celrep.2018.07.021.


Genome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation.

Ji Z, He L, Rotem A, Janzer A, Cheng CS, Regev A, Struhl K.

Nat Commun. 2018 May 25;9(1):2068. doi: 10.1038/s41467-018-04406-2.


Correction: Evidence that Mediator is essential for Pol II transcription, but is not a required component of the preinitiation complex in vivo.

Petrenko N, Jin Y, Wong KH, Struhl K.

Elife. 2017 Sep 18;6. pii: e32061. doi: 10.7554/eLife.32061. No abstract available.


The Ground State and Evolution of Promoter Region Directionality.

Jin Y, Eser U, Struhl K, Churchman LS.

Cell. 2017 Aug 24;170(5):889-898.e10. doi: 10.1016/j.cell.2017.07.006. Epub 2017 Aug 10.


Evidence that Mediator is essential for Pol II transcription, but is not a required component of the preinitiation complex in vivo.

Petrenko N, Jin Y, Wong KH, Struhl K.

Elife. 2017 Jul 12;6. pii: e28447. doi: 10.7554/eLife.28447. Erratum in: Elife. 2017 Sep 18;6:.


Mediator Undergoes a Compositional Change during Transcriptional Activation.

Petrenko N, Jin Y, Wong KH, Struhl K.

Mol Cell. 2016 Nov 3;64(3):443-454. doi: 10.1016/j.molcel.2016.09.015. Epub 2016 Oct 20.


LINC00520 is induced by Src, STAT3, and PI3K and plays a functional role in breast cancer.

Henry WS, Hendrickson DG, Beca F, Glass B, Lindahl-Allen M, He L, Ji Z, Struhl K, Beck AH, Rinn JL, Toker A.

Oncotarget. 2016 Dec 13;7(50):81981-81994. doi: 10.18632/oncotarget.11962.


Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers.

Miotto B, Ji Z, Struhl K.

Proc Natl Acad Sci U S A. 2016 Aug 16;113(33):E4810-9. doi: 10.1073/pnas.1609060113. Epub 2016 Jul 19.


Transcriptome-scale RNase-footprinting of RNA-protein complexes.

Ji Z, Song R, Huang H, Regev A, Struhl K.

Nat Biotechnol. 2016 Apr;34(4):410-3. doi: 10.1038/nbt.3441. Epub 2016 Feb 22.


Many lncRNAs, 5'UTRs, and pseudogenes are translated and some are likely to express functional proteins.

Ji Z, Song R, Regev A, Struhl K.

Elife. 2015 Dec 19;4:e08890. doi: 10.7554/eLife.08890.


Alternative to the soft-agar assay that permits high-throughput drug and genetic screens for cellular transformation.

Rotem A, Janzer A, Izar B, Ji Z, Doench JG, Garraway LA, Struhl K.

Proc Natl Acad Sci U S A. 2015 May 5;112(18):5708-13. doi: 10.1073/pnas.1505979112. Epub 2015 Apr 20.


Mapping 3' mRNA isoforms on a genomic scale.

Jin Y, Geisberg JV, Moqtaderi Z, Ji Z, Hoque M, Tian B, Struhl K.

Curr Protoc Mol Biol. 2015 Apr 1;110:4.23.1-17. doi: 10.1002/0471142727.mb0423s110.


STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer.

Fleming JD, Giresi PG, Lindahl-Allen M, Krall EB, Lieb JD, Struhl K.

Epigenetics Chromatin. 2015 Feb 14;8:7. doi: 10.1186/1756-8935-8-7. eCollection 2015.


Metformin and phenformin deplete tricarboxylic acid cycle and glycolytic intermediates during cell transformation and NTPs in cancer stem cells.

Janzer A, German NJ, Gonzalez-Herrera KN, Asara JM, Haigis MC, Struhl K.

Proc Natl Acad Sci U S A. 2014 Jul 22;111(29):10574-9. doi: 10.1073/pnas.1409844111. Epub 2014 Jul 7.


TFIIH phosphorylation of the Pol II CTD stimulates mediator dissociation from the preinitiation complex and promoter escape.

Wong KH, Jin Y, Struhl K.

Mol Cell. 2014 May 22;54(4):601-12. doi: 10.1016/j.molcel.2014.03.024. Epub 2014 Apr 17.


Is DNA methylation of tumour suppressor genes epigenetic?

Struhl K.

Elife. 2014 Mar 12;3:e02475. doi: 10.7554/eLife.02475.


Global analysis of mRNA isoform half-lives reveals stabilizing and destabilizing elements in yeast.

Geisberg JV, Moqtaderi Z, Fan X, Ozsolak F, Struhl K.

Cell. 2014 Feb 13;156(4):812-24. doi: 10.1016/j.cell.2013.12.026.


Species-specific factors mediate extensive heterogeneity of mRNA 3' ends in yeasts.

Moqtaderi Z, Geisberg JV, Jin Y, Fan X, Struhl K.

Proc Natl Acad Sci U S A. 2013 Jul 2;110(27):11073-8. doi: 10.1073/pnas.1309384110. Epub 2013 Jun 17.


NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors.

Fleming JD, Pavesi G, Benatti P, Imbriano C, Mantovani R, Struhl K.

Genome Res. 2013 Aug;23(8):1195-209. doi: 10.1101/gr.148080.112. Epub 2013 Apr 17.


Determinants of nucleosome positioning.

Struhl K, Segal E.

Nat Struct Mol Biol. 2013 Mar;20(3):267-73. doi: 10.1038/nsmb.2506. Review.


Metformin inhibits the inflammatory response associated with cellular transformation and cancer stem cell growth.

Hirsch HA, Iliopoulos D, Struhl K.

Proc Natl Acad Sci U S A. 2013 Jan 15;110(3):972-7. doi: 10.1073/pnas.1221055110. Epub 2012 Dec 31.


An integrated transcriptional regulatory circuit that reinforces the breast cancer stem cell state.

Polytarchou C, Iliopoulos D, Struhl K.

Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14470-5. doi: 10.1073/pnas.1212811109. Epub 2012 Aug 20.


A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern.

Hughes AL, Jin Y, Rando OJ, Struhl K.

Mol Cell. 2012 Oct 12;48(1):5-15. doi: 10.1016/j.molcel.2012.07.003. Epub 2012 Aug 9.


SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation.

Barber MF, Michishita-Kioi E, Xi Y, Tasselli L, Kioi M, Moqtaderi Z, Tennen RI, Paredes S, Young NL, Chen K, Struhl K, Garcia BA, Gozani O, Li W, Chua KF.

Nature. 2012 Jul 5;487(7405):114-8. doi: 10.1038/nature11043.


Histone H3R2 symmetric dimethylation and histone H3K4 trimethylation are tightly correlated in eukaryotic genomes.

Yuan CC, Matthews AG, Jin Y, Chen CF, Chapman BA, Ohsumi TK, Glass KC, Kutateladze TG, Borowsky ML, Struhl K, Oettinger MA.

Cell Rep. 2012 Feb 23;1(2):83-90.


The Cyc8-Tup1 complex inhibits transcription primarily by masking the activation domain of the recruiting protein.

Wong KH, Struhl K.

Genes Dev. 2011 Dec 1;25(23):2525-39. doi: 10.1101/gad.179275.111.


An HNF4α-miRNA inflammatory feedback circuit regulates hepatocellular oncogenesis.

Hatziapostolou M, Polytarchou C, Aggelidou E, Drakaki A, Poultsides GA, Jaeger SA, Ogata H, Karin M, Struhl K, Hadzopoulou-Cladaras M, Iliopoulos D.

Cell. 2011 Dec 9;147(6):1233-47. doi: 10.1016/j.cell.2011.10.043. Erratum in: Cell. 2013 Feb 28;152(5):1196.


MiR-27b targets PPARγ to inhibit growth, tumor progression and the inflammatory response in neuroblastoma cells.

Lee JJ, Drakaki A, Iliopoulos D, Struhl K.

Oncogene. 2012 Aug 16;31(33):3818-25. doi: 10.1038/onc.2011.543. Epub 2011 Nov 28.


SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers.

Krebs AR, Karmodiya K, Lindahl-Allen M, Struhl K, Tora L.

Mol Cell. 2011 Nov 4;44(3):410-423. doi: 10.1016/j.molcel.2011.08.037.


Extensive divergence of yeast stress responses through transitions between induced and constitutive activation.

Tirosh I, Wong KH, Barkai N, Struhl K.

Proc Natl Acad Sci U S A. 2011 Oct 4;108(40):16693-8. doi: 10.1073/pnas.1113718108. Epub 2011 Sep 19.


Iwr1 protein is important for preinitiation complex formation by all three nuclear RNA polymerases in Saccharomyces cerevisiae.

Esberg A, Moqtaderi Z, Fan X, Lu J, Struhl K, Byström A.

PLoS One. 2011;6(6):e20829. doi: 10.1371/journal.pone.0020829. Epub 2011 Jun 10.


Inhibition of miR-193a expression by Max and RXRα activates K-Ras and PLAU to mediate distinct aspects of cellular transformation.

Iliopoulos D, Rotem A, Struhl K.

Cancer Res. 2011 Aug 1;71(15):5144-53. doi: 10.1158/0008-5472.CAN-11-0425. Epub 2011 Jun 13.


Akt2 regulates all Akt isoforms and promotes resistance to hypoxia through induction of miR-21 upon oxygen deprivation.

Polytarchou C, Iliopoulos D, Hatziapostolou M, Kottakis F, Maroulakou I, Struhl K, Tsichlis PN.

Cancer Res. 2011 Jul 1;71(13):4720-31. doi: 10.1158/0008-5472.CAN-11-0365. Epub 2011 May 9.


Metformin decreases the dose of chemotherapy for prolonging tumor remission in mouse xenografts involving multiple cancer cell types.

Iliopoulos D, Hirsch HA, Struhl K.

Cancer Res. 2011 May 1;71(9):3196-201. doi: 10.1158/0008-5472.CAN-10-3471. Epub 2011 Mar 17.


Inducible formation of breast cancer stem cells and their dynamic equilibrium with non-stem cancer cells via IL6 secretion.

Iliopoulos D, Hirsch HA, Wang G, Struhl K.

Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1397-402. doi: 10.1073/pnas.1018898108. Epub 2011 Jan 10.


Splitting of H3-H4 tetramers at transcriptionally active genes undergoing dynamic histone exchange.

Katan-Khaykovich Y, Struhl K.

Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1296-301. doi: 10.1073/pnas.1018308108. Epub 2011 Jan 10.


High-throughput sequencing reveals a simple model of nucleosome energetics.

Locke G, Tolkunov D, Moqtaderi Z, Struhl K, Morozov AV.

Proc Natl Acad Sci U S A. 2010 Dec 7;107(49):20998-1003. doi: 10.1073/pnas.1003838107. Epub 2010 Nov 17.


Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation.

Fan X, Moqtaderi Z, Jin Y, Zhang Y, Liu XS, Struhl K.

Proc Natl Acad Sci U S A. 2010 Oct 19;107(42):17945-50. doi: 10.1073/pnas.1012674107. Epub 2010 Oct 4.


Loss of miR-200 inhibition of Suz12 leads to polycomb-mediated repression required for the formation and maintenance of cancer stem cells.

Iliopoulos D, Lindahl-Allen M, Polytarchou C, Hirsch HA, Tsichlis PN, Struhl K.

Mol Cell. 2010 Sep 10;39(5):761-72. doi: 10.1016/j.molcel.2010.08.013.


STAT3 activation of miR-21 and miR-181b-1 via PTEN and CYLD are part of the epigenetic switch linking inflammation to cancer.

Iliopoulos D, Jaeger SA, Hirsch HA, Bulyk ML, Struhl K.

Mol Cell. 2010 Aug 27;39(4):493-506. doi: 10.1016/j.molcel.2010.07.023.


Evidence against a genomic code for nucleosome positioning. Reply to "Nucleosome sequence preferences influence in vivo nucleosome organization.".

Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K.

Nat Struct Mol Biol. 2010 Aug;17(8):920-3. No abstract available.


Genome-wide mapping indicates that p73 and p63 co-occupy target sites and have similar dna-binding profiles in vivo.

Yang A, Zhu Z, Kettenbach A, Kapranov P, McKeon F, Gingeras TR, Struhl K.

PLoS One. 2010 Jul 14;5(7):e11572. doi: 10.1371/journal.pone.0011572.


Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells.

Moqtaderi Z, Wang J, Raha D, White RJ, Snyder M, Weng Z, Struhl K.

Nat Struct Mol Biol. 2010 May;17(5):635-40. doi: 10.1038/nsmb.1794. Epub 2010 Apr 25.

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