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RUNX1-ETO Depletion in t(8;21) AML Leads to C/EBPα- and AP-1-Mediated Alterations in Enhancer-Promoter Interaction.

Ptasinska A, Pickin A, Assi SA, Chin PS, Ames L, Avellino R, Gröschel S, Delwel R, Cockerill PN, Osborne CS, Bonifer C.

Cell Rep. 2019 Nov 12;29(7):2120. doi: 10.1016/j.celrep.2019.10.075. No abstract available.


RUNX1-ETO Depletion in t(8;21) AML Leads to C/EBPα- and AP-1-Mediated Alterations in Enhancer-Promoter Interaction.

Ptasinska A, Pickin A, Assi SA, Chin PS, Ames L, Avellino R, Gröschel S, Delwel R, Cockerill PN, Osborne CS, Bonifer C.

Cell Rep. 2019 Sep 17;28(12):3022-3031.e7. doi: 10.1016/j.celrep.2019.08.040. Erratum in: Cell Rep. 2019 Nov 12;29(7):2120.


Rewiring of the Transcription Factor Network in Acute Myeloid Leukemia.

Assi SA, Bonifer C, Cockerill PN.

Cancer Inform. 2019 Jun 25;18:1176935119859863. doi: 10.1177/1176935119859863. eCollection 2019.


The Oncogenic Transcription Factor RUNX1/ETO Corrupts Cell Cycle Regulation to Drive Leukemic Transformation.

Martinez-Soria N, McKenzie L, Draper J, Ptasinska A, Issa H, Potluri S, Blair HJ, Pickin A, Isa A, Chin PS, Tirtakusuma R, Coleman D, Nakjang S, Assi S, Forster V, Reza M, Law E, Berry P, Mueller D, Osborne C, Elder A, Bomken SN, Pal D, Allan JM, Veal GJ, Cockerill PN, Wichmann C, Vormoor J, Lacaud G, Bonifer C, Heidenreich O.

Cancer Cell. 2019 Apr 15;35(4):705. doi: 10.1016/j.ccell.2019.03.012. No abstract available.


Global long terminal repeat activation participates in establishing the unique gene expression programme of classical Hodgkin lymphoma.

Edginton-White B, Cauchy P, Assi SA, Hartmann S, Riggs AG, Mathas S, Cockerill PN, Bonifer C.

Leukemia. 2019 Jun;33(6):1463-1474. doi: 10.1038/s41375-018-0311-x. Epub 2018 Dec 13.


Subtype-specific regulatory network rewiring in acute myeloid leukemia.

Assi SA, Imperato MR, Coleman DJL, Pickin A, Potluri S, Ptasinska A, Chin PS, Blair H, Cauchy P, James SR, Zacarias-Cabeza J, Gilding LN, Beggs A, Clokie S, Loke JC, Jenkin P, Uddin A, Delwel R, Richards SJ, Raghavan M, Griffiths MJ, Heidenreich O, Cockerill PN, Bonifer C.

Nat Genet. 2019 Jan;51(1):151-162. doi: 10.1038/s41588-018-0270-1. Epub 2018 Nov 12.


The Oncogenic Transcription Factor RUNX1/ETO Corrupts Cell Cycle Regulation to Drive Leukemic Transformation.

Martinez-Soria N, McKenzie L, Draper J, Ptasinska A, Issa H, Potluri S, Blair HJ, Pickin A, Isa A, Chin PS, Tirtakusuma R, Coleman D, Nakjang S, Assi S, Forster V, Reza M, Law E, Berry P, Mueller D, Osborne C, Elder A, Bomken SN, Pal D, Allan JM, Veal GJ, Cockerill PN, Wichmann C, Vormoor J, Lacaud G, Bonifer C, Heidenreich O.

Cancer Cell. 2018 Oct 8;34(4):626-642.e8. doi: 10.1016/j.ccell.2018.08.015. Erratum in: Cancer Cell. 2019 Apr 15;35(4):705.


Prospective Isolation and Characterization of Genetically and Functionally Distinct AML Subclones.

de Boer B, Prick J, Pruis MG, Keane P, Imperato MR, Jaques J, Brouwers-Vos AZ, Hogeling SM, Woolthuis CM, Nijk MT, Diepstra A, Wandinger S, Versele M, Attar RM, Cockerill PN, Huls G, Vellenga E, Mulder AB, Bonifer C, Schuringa JJ.

Cancer Cell. 2018 Oct 8;34(4):674-689.e8. doi: 10.1016/j.ccell.2018.08.014. Epub 2018 Sep 20.


C/EBPα overrides epigenetic reprogramming by oncogenic transcription factors in acute myeloid leukemia.

Loke J, Chin PS, Keane P, Pickin A, Assi SA, Ptasinska A, Imperato MR, Cockerill PN, Bonifer C.

Blood Adv. 2018 Feb 13;2(3):271-284. doi: 10.1182/bloodadvances.2017012781.


Integration of Kinase and Calcium Signaling at the Level of Chromatin Underlies Inducible Gene Activation in T Cells.

Brignall R, Cauchy P, Bevington SL, Gorman B, Pisco AO, Bagnall J, Boddington C, Rowe W, England H, Rich K, Schmidt L, Dyer NP, Travis MA, Ott S, Jackson DA, Cockerill PN, Paszek P.

J Immunol. 2017 Oct 15;199(8):2652-2667. doi: 10.4049/jimmunol.1602033. Epub 2017 Sep 13.


Prognostic significance of high GFI1 expression in AML of normal karyotype and its association with a FLT3-ITD signature.

Volpe G, Walton DS, Grainger DE, Ward C, Cauchy P, Blakemore D, Coleman DJL, Cockerill PN, Garcia P, Frampton J.

Sci Rep. 2017 Sep 11;7(1):11148. doi: 10.1038/s41598-017-11718-8.


RUNX1-ETO and RUNX1-EVI1 Differentially Reprogram the Chromatin Landscape in t(8;21) and t(3;21) AML.

Loke J, Assi SA, Imperato MR, Ptasinska A, Cauchy P, Grabovska Y, Soria NM, Raghavan M, Delwel HR, Cockerill PN, Heidenreich O, Bonifer C.

Cell Rep. 2017 May 23;19(8):1654-1668. doi: 10.1016/j.celrep.2017.05.005.


T Cell Receptor and Cytokine Signaling Can Function at Different Stages to Establish and Maintain Transcriptional Memory and Enable T Helper Cell Differentiation.

Bevington SL, Cauchy P, Withers DR, Lane PJ, Cockerill PN.

Front Immunol. 2017 Mar 3;8:204. doi: 10.3389/fimmu.2017.00204. eCollection 2017. Review.


Chromatin priming of genes in development: Concepts, mechanisms and consequences.

Bonifer C, Cockerill PN.

Exp Hematol. 2017 May;49:1-8. doi: 10.1016/j.exphem.2017.01.003. Epub 2017 Feb 7. Review.


Receptor Signaling Directs Global Recruitment of Pre-existing Transcription Factors to Inducible Elements.

Cockerill PN.

Yale J Biol Med. 2016 Dec 23;89(4):591-596. eCollection 2016 Dec. Review.


Cooperative binding of AP-1 and TEAD4 modulates the balance between vascular smooth muscle and hemogenic cell fate.

Obier N, Cauchy P, Assi SA, Gilmour J, Lie-A-Ling M, Lichtinger M, Hoogenkamp M, Noailles L, Cockerill PN, Lacaud G, Kouskoff V, Bonifer C.

Development. 2016 Dec 1;143(23):4324-4340. Epub 2016 Oct 17.


Inducible chromatin priming is associated with the establishment of immunological memory in T cells.

Bevington SL, Cauchy P, Piper J, Bertrand E, Lalli N, Jarvis RC, Gilding LN, Ott S, Bonifer C, Cockerill PN.

EMBO J. 2016 Mar 1;35(5):515-35. doi: 10.15252/embj.201592534. Epub 2016 Jan 21.


Wellington-bootstrap: differential DNase-seq footprinting identifies cell-type determining transcription factors.

Piper J, Assi SA, Cauchy P, Ladroue C, Cockerill PN, Bonifer C, Ott S.

BMC Genomics. 2015 Nov 25;16:1000. doi: 10.1186/s12864-015-2081-4.


Chromatin Structure Profiling Identifies Crucial Regulators of Tumor Maintenance.

Bonifer C, Cockerill PN.

Trends Cancer. 2015 Nov;1(3):157-160. doi: 10.1016/j.trecan.2015.10.003. Epub 2015 Nov 5.


Chronic FLT3-ITD Signaling in Acute Myeloid Leukemia Is Connected to a Specific Chromatin Signature.

Cauchy P, James SR, Zacarias-Cabeza J, Ptasinska A, Imperato MR, Assi SA, Piper J, Canestraro M, Hoogenkamp M, Raghavan M, Loke J, Akiki S, Clokie SJ, Richards SJ, Westhead DR, Griffiths MJ, Ott S, Bonifer C, Cockerill PN.

Cell Rep. 2015 Aug 4;12(5):821-36. doi: 10.1016/j.celrep.2015.06.069. Epub 2015 Jul 23.


Mapping of transcription factor motifs in active chromatin identifies IRF5 as key regulator in classical Hodgkin lymphoma.

Kreher S, Bouhlel MA, Cauchy P, Lamprecht B, Li S, Grau M, Hummel F, Köchert K, Anagnostopoulos I, Jöhrens K, Hummel M, Hiscott J, Wenzel SS, Lenz P, Schneider M, Küppers R, Scheidereit C, Giefing M, Siebert R, Rajewsky K, Lenz G, Cockerill PN, Janz M, Dörken B, Bonifer C, Mathas S.

Proc Natl Acad Sci U S A. 2014 Oct 21;111(42):E4513-22. doi: 10.1073/pnas.1406985111. Epub 2014 Oct 6.


Identification of a dynamic core transcriptional network in t(8;21) AML that regulates differentiation block and self-renewal.

Ptasinska A, Assi SA, Martinez-Soria N, Imperato MR, Piper J, Cauchy P, Pickin A, James SR, Hoogenkamp M, Williamson D, Wu M, Tenen DG, Ott S, Westhead DR, Cockerill PN, Heidenreich O, Bonifer C.

Cell Rep. 2014 Sep 25;8(6):1974-1988. doi: 10.1016/j.celrep.2014.08.024. Epub 2014 Sep 18.


A multi-centre phase 2 study of azacitidine in chronic myelomonocytic leukaemia.

Drummond MW, Pocock C, Boissinot M, Mills J, Brown J, Cauchy P, Cross NC, Hartley S, Kell J, Szubert A, Cockerill PN, Bowen DT.

Leukemia. 2014 Jul;28(7):1570-2. doi: 10.1038/leu.2014.85. Epub 2014 Feb 26. No abstract available.


Delineating MEIS1 cis-regulatory elements active in hematopoietic cells.

Xiang P, Wei W, Lo C, Rosten P, Hou J, Hoodless PA, Bilenky M, Bonifer C, Cockerill PN, Kirkpatrick A, Gottgens B, Hirst M, Humphries KR.

Leukemia. 2014 Feb;28(2):433-6. doi: 10.1038/leu.2013.287. Epub 2013 Oct 7. No abstract available.


Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data.

Piper J, Elze MC, Cauchy P, Cockerill PN, Bonifer C, Ott S.

Nucleic Acids Res. 2013 Nov;41(21):e201. doi: 10.1093/nar/gkt850. Epub 2013 Sep 25. Erratum in: Nucleic Acids Res. 2014;42(17):11272.


The inducible tissue-specific expression of the human IL-3/GM-CSF locus is controlled by a complex array of developmentally regulated enhancers.

Baxter EW, Mirabella F, Bowers SR, James SR, Bonavita AM, Bertrand E, Strogantsev R, Hawwari A, Bert AG, Gonzalez de Arce A, West AG, Bonifer C, Cockerill PN.

J Immunol. 2012 Nov 1;189(9):4459-69. doi: 10.4049/jimmunol.1201915. Epub 2012 Sep 28.


Induction of differentiation and apoptosis in leukaemic cell lines by the novel benzamide family histone deacetylase 2 and 3 inhibitor MI-192.

Boissinot M, Inman M, Hempshall A, James SR, Gill JH, Selby P, Bowen DT, Grigg R, Cockerill PN.

Leuk Res. 2012 Oct;36(10):1304-10. doi: 10.1016/j.leukres.2012.07.002. Epub 2012 Jul 20.


Depletion of RUNX1/ETO in t(8;21) AML cells leads to genome-wide changes in chromatin structure and transcription factor binding.

Ptasinska A, Assi SA, Mannari D, James SR, Williamson D, Dunne J, Hoogenkamp M, Wu M, Care M, McNeill H, Cauchy P, Cullen M, Tooze RM, Tenen DG, Young BD, Cockerill PN, Westhead DR, Heidenreich O, Bonifer C.

Leukemia. 2012 Aug;26(8):1829-41. doi: 10.1038/leu.2012.49. Epub 2012 Feb 20.


Chromatin mechanisms regulating gene expression in health and disease.

Bonifer C, Cockerill PN.

Adv Exp Med Biol. 2011;711:12-25. Review.


Structure and function of active chromatin and DNase I hypersensitive sites.

Cockerill PN.

FEBS J. 2011 Jul;278(13):2182-210. doi: 10.1111/j.1742-4658.2011.08128.x. Epub 2011 May 26. Review.


Runx1 binds as a dimeric complex to overlapping Runx1 sites within a palindromic element in the human GM-CSF enhancer.

Bowers SR, Calero-Nieto FJ, Valeaux S, Fernandez-Fuentes N, Cockerill PN.

Nucleic Acids Res. 2010 Oct;38(18):6124-34. doi: 10.1093/nar/gkq356. Epub 2010 May 18.


Transcriptional and epigenetic regulation of the GM-CSF promoter by RUNX1.

Oakford PC, James SR, Qadi A, West AC, Ray SN, Bert AG, Cockerill PN, Holloway AF.

Leuk Res. 2010 Sep;34(9):1203-13. doi: 10.1016/j.leukres.2010.03.029. Epub 2010 May 1.


Derepression of an endogenous long terminal repeat activates the CSF1R proto-oncogene in human lymphoma.

Lamprecht B, Walter K, Kreher S, Kumar R, Hummel M, Lenze D, Köchert K, Bouhlel MA, Richter J, Soler E, Stadhouders R, Jöhrens K, Wurster KD, Callen DF, Harte MF, Giefing M, Barlow R, Stein H, Anagnostopoulos I, Janz M, Cockerill PN, Siebert R, Dörken B, Bonifer C, Mathas S.

Nat Med. 2010 May;16(5):571-9, 1p following 579. doi: 10.1038/nm.2129. Epub 2010 May 2.


Aberrant expression of CD19 in AML with t(8;21) involves a poised chromatin structure and PAX5.

Walter K, Cockerill PN, Barlow R, Clarke D, Hoogenkamp M, Follows GA, Richards SJ, Cullen MJ, Bonifer C, Tagoh H.

Oncogene. 2010 May 20;29(20):2927-37. doi: 10.1038/onc.2010.56. Epub 2010 Mar 8.


Transcription-dependent silencing of inducible convergent transgenes in transgenic mice.

Calero-Nieto FJ, Bert AG, Cockerill PN.

Epigenetics Chromatin. 2010 Jan 19;3(1):3. doi: 10.1186/1756-8935-3-3.


The human IL-3/granulocyte-macrophage colony-stimulating factor locus is epigenetically silent in immature thymocytes and is progressively activated during T cell development.

Mirabella F, Baxter EW, Boissinot M, James SR, Cockerill PN.

J Immunol. 2010 Mar 15;184(6):3043-54. doi: 10.4049/jimmunol.0901364. Epub 2010 Feb 10.


A conserved insulator that recruits CTCF and cohesin exists between the closely related but divergently regulated interleukin-3 and granulocyte-macrophage colony-stimulating factor genes.

Bowers SR, Mirabella F, Calero-Nieto FJ, Valeaux S, Hadjur S, Baxter EW, Merkenschlager M, Cockerill PN.

Mol Cell Biol. 2009 Apr;29(7):1682-93. doi: 10.1128/MCB.01411-08. Epub 2009 Jan 21.


The LPS-induced transcriptional upregulation of the chicken lysozyme locus involves CTCF eviction and noncoding RNA transcription.

Lefevre P, Witham J, Lacroix CE, Cockerill PN, Bonifer C.

Mol Cell. 2008 Oct 10;32(1):129-39. doi: 10.1016/j.molcel.2008.07.023.


NFAT is well placed to direct both enhancer looping and domain-wide models of enhancer function.

Cockerill PN.

Sci Signal. 2008 Apr 1;1(13):pe15. doi: 10.1126/stke.113pe15.


The Pu.1 locus is differentially regulated at the level of chromatin structure and noncoding transcription by alternate mechanisms at distinct developmental stages of hematopoiesis.

Hoogenkamp M, Krysinska H, Ingram R, Huang G, Barlow R, Clarke D, Ebralidze A, Zhang P, Tagoh H, Cockerill PN, Tenen DG, Bonifer C.

Mol Cell Biol. 2007 Nov;27(21):7425-38. Epub 2007 Sep 4.


In vivo genomic footprinting using LM-PCR methods.

Tagoh H, Cockerill PN, Bonifer C.

Methods Mol Biol. 2006;325:285-314.


Role of a 5'-enhancer in the transcriptional regulation of the human endothelial cell protein C receptor gene.

Mollica LR, Crawley JT, Liu K, Rance JB, Cockerill PN, Follows GA, Landry JR, Wells DJ, Lane DA.

Blood. 2006 Aug 15;108(4):1251-9. Epub 2006 Apr 20.


Transcriptional regulation of human CD5: important role of Ets transcription factors in CD5 expression in T cells.

Arman M, Calvo J, Trojanowska ME, Cockerill PN, Santana M, López-Cabrera M, Vives J, Lozano F.

J Immunol. 2004 Jun 15;172(12):7519-29.


Regulation of the human endothelial cell protein C receptor gene promoter by multiple Sp1 binding sites.

Rance JB, Follows GA, Cockerill PN, Bonifer C, Lane DA, Simmonds RE.

Blood. 2003 Jun 1;101(11):4393-401. Epub 2003 Jan 30.


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