Centre for Epigenetics Publications

2011

Williams K, Christensen J, Pedersen MT, Johansen JV, Cloos PA, Rappsilber J, Helin K (2011). TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 473(7347):343-8. Epub 2011 Apr 13.

Schmitz SU, Albert M, Malatesta M, Morey L, Johansen JV, Bak M, Tommerup N, Abarrategui I, Helin K (2011). Jarid1b targets genes regulating development and is involved in neural differentiation. EMBO J. 30(22) doi: 10.1038/emboj.2011.383. [Epub ahead of print]

Schepeler T, Holm A, Halvey P, Nordentoft I, Lamy P, Riising EM, Christensen LL, Thorsen K, Liebler DC, Helin K, Orntoft TF, Andersen CL (2011). Attenuation of the beta-catenin/TCF4 complex in colorectal cancer cells induces several growth-suppressive microRNAs that target cancer promoting genes. Oncogene doi: 10.1038/onc.2011.453. [Epub ahead of print]

Stojic L, Jasencakova Z, Prezioso C, Stützer A, Bodega B, Pasini D, Klingberg R, Mozzetta C, Margueron R, Puri PL, Schwarzer D, Helin K, Fischle W, Orlando V (2011). Chromatin regulated interchange between polycomb repressive complex 2 (PRC2)-Ezh2 and PRC2-Ezh1 complexes controls myogenin activation in skeletal muscle cells. Epigenetics Chromatin 4:16.

Lohse B, Kristensen JL, Kristensen LH, Agger K, Helin K, Gajhede M, Clausen RP (2011). Inhibitors of histone demethylases. Bioorg Med Chem. 19(12):3625-36. Epub 2011 Feb 1.

Hudlebusch HR, Skotte J, Santoni-Rugiu E, Zimling ZG, Lees MJ, Simon R, Sauter G, Rota R, De Ioris MA, Quarto M, Johansen JV, Jørgensen M, Rechnitzer C, Maroun LL, Schrøder H, Petersen BL, Helin K (2011). MMSET is highly expressed and associated with aggressiveness in neuroblastoma. Cancer Res. 71(12):4226-35. Epub 2011 Apr 28.

Hudlebusch HR, Santoni-Rugiu E, Simon R, Ralfkiær E, Rossing HH, Johansen JV, Jørgensen M, Sauter G, Helin K (2011). The histone methyltransferase and putative oncoprotein MMSET is overexpressed in a large variety of human tumors. Clin Cancer Res 17(9):2919-33. Epub 2011 Mar 8.

Anderton JA, Bose S, Vockerodt M, Vrzalikova K, Wei W, Kuo M, Helin K, Christensen J, Rowe M, Murray PG, Woodman CB (2011). The H3K27me3 demethylase, KDM6B, is induced by Epstein-Barr virus and over-expressed in Hodgkin's Lymphoma. Oncogene 30(17):2037-43. Epub 2011 Jan 17.

Jørgensen S, Eskildsen M, Fugger K, Hansen L, Larsen MS, Kousholt AN, Syljuåsen RG, Trelle MB, Jensen ON, Helin K, Sørensen CS (2011). SET8 is degraded via PCNA-coupled CRL4(CDT2) ubiquitylation in S phase and after UV irradiation. J Cell Biol. 192(1):43-54.

2010

Agrawal-Singh S, Koschmieder S, Gelsing S, Stocking C, Stehling M, Thiede C, Thoennissen NH, Köhler G, Valk PJ, Delwel R, Mills K, Bäumer N, Tickenbrock L, Hansen K, Berdel WE, Müller-Tidow C, Serve H (2010). Pim2 cooperates with PML-RARalpha to induce acute myeloid leukemia in a bone marrow transplantation model. Blood 115(22):4507-16. 

Albert M and Helin K (2010). Histone methyl transferases in cancer. Seminars in Cell and Develop. Biol. 21(2):209-20. 

BouKheir T, Lund AH (2010). Epigenetic dynamics across the cell cycle. Essays Biochem 48(1):107-20. 

Christophersen NS and Helin K (2010). Epigenetic control of embryonic stem cell fate. J Exp Med. 207(11):2287-95.

Foltyn VN, Zehl M, Dikopoltsev E, Jensen ON, Wolosker H (2010). Phosphorylation of mouse serine racemase regulates D-serine synthesis. FEBS letters 584(13):2937-41. 

von Freyend SJ, Rosenqvist H, Fink A, Melzer IM, Clos J, Jensen ON, Wiese M (2010). LmxMPK4, an essential mitogen-activated protein kinase of Leishmania mexicana is phosphorylated and activated by the STE7-like protein kinase LmxMKK5. Int J Parasitol. 40(8):969-78. 

Gehani SS, Agrawal-Singh S, Dietrich N, Christophersen NS, Helin K, Hansen K (2010). Polycomb group protein displacement and gene activation through MSK-dependent H3K27me3S28 phosphorylation. Mol Cell, 39(6):886-900.

Gregersen LH, Jacobsen AB, Frankel LB, Wen J, Krogh A, Lund AH (2010). MicroRNA-145 targets YES and STAT1 in colon cancer cells. PLoS One 5(1):e8836. 

Jung HR, Pasini D, Helin K, Jensen ON (2010) Quantitative mass spectrometry of histone H3.2 and H3.3 in Suz12 deficient mouse ES cells reveals distinct, dynamic post-translational modifications at K27 and K36. Mol Cell Proteomics 9:838-50. 

Kleine-Kohlbrecher D, Christensen J, Vandamme J, Abarrategui I, Bak M, Tommerup N, Shi X, Gozani O, Rappsilber J, Salcini AE and Helin K (2010). A functional link between the histone demethylase PHF8 and the transcription factor ZNF711 in X-linked mental retardation. Mol Cell 38(2):165-78. 

Kondo A, Thaysen-Andersen M, Hjernø K, Jensen ON (2010). Characterization of sialylated and fucosylated glycopeptides of beta2-glycoprotein I by a combination of HILIC LC and MALDI MS/MS. J Sep Sci 33(6-7):891-902. 

Kool J, Uren AG, Martins CP, Sie D, de Ridder J, Turner G, van Uitert M, Matentzoglu K, Lagcher W, Krimpenfort P, Gadiot J, Pritchard C, Lenz J, Lund AH, Jonkers J, Rogers J, Adams DJ, Wessels L, Berns A, van Lohuizen M (2010). Insertional mutagenesis in mice deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 reveals cancer gene interactions and correlations with tumor phenotypes. Cancer Res 70(2):520-31. 

Leeb M, Pasini D, Novatchkova M, Jaritz M, Helin K, Wutz A (2010). Polycomb complexes act redundantly to repress genomic repeats and genes. Genes Dev 24(3):265-76. 

Lund AH (2010). miR-10 in development and cancer. Cell Death Differ 17(2):209-14. 

Manteca A, Jung HR, Schwämmle V, Jensen ON, Sanchez J (2010). Quantitative Proteome Analysis of Streptomyces coelicolor Nonsporulating Liquid Cultures Demonstrates a Complex Differentiation Process Comparable to That Occurring in Sporulating Solid Cultures. J Proteome Res. 9(9):4801-11.

Manteca A, Sanchez J, Jung HR, Schwämmle V, Jensen ON (2010). Quantitative proteomic analysis of Streptomyces coelicolor development demonstrates that onset of secondary metabolism coincides with hyphae differentiation. Mol Cell Proteomics 9(7):1423-36. 

Morey L, Helin K (2010). Polycomb group protein-mediated transcriptional repression. Trends Biochem 35:323-32. 

Negishi M, Saraya A, Mochizuki S, Helin K, Koseki H, and Iwama A (2010). A novel zinc finger protein Zfp277 mediates transcriptional repression of the Ink4a/Arf locus through polycomb repressive complex 1. PlosOne, 5, el 2373. 

Pasini D, Cloos PA, Walfridsson J, Olsson L, Bukowski JP, Johansen JV, Bak M, Tommerup N, Rappsilber J, Helin K (2010). JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells. Nature 464:306-10. 

Pasini D, Malatesta M, Jung HR, Walfridsson J, Willer A, Olsson L, Skotte J, Wutz A, Porse B, Jensen ON, Helin K (2010). Characterization of an antagonistic switch between Histone H3 lysine 27 methylation and acetylation in the transcriptional regulation of Polycomb group target genes. Nucleic Acids Res 38:4958-69. 

Pedersen MT, Helin K (2010). Histone demethylases in development and disease. Trends Cell Biol. 20(11):662-71. 

Roepstorff P, Jensen ON (2010). Analysis of post-translationally modified proteins in proteomics. Functional Proteomics: Principles and practical applications. Edit. P. Ping, Humana Press.

Schubert S, Knoch K-P, Ouwendijk J, Mohammed S, Bodrov Y, Jäger M, Altkrüger A, Wegbrod C, Adams ME, Kim Y, Froehner SC, Jensen ON, Kalaidzidis Y, Solimena M (2010). b2-Syntrophin is a Cdk5 Substrate that Restrains the Motility of Insulin Secretory Granules. PLOS One 5(9):e12929.

Sprenger RR, Jensen ON. Proteomics and the dynamic plasma membrane: Quo Vadis? Proteomics, in press.

Sørensen CS, Melixetian M, Klein DK, Helin K (2010). NEK11: linking CHK1 and CDC25A in DNA damage checkpoint signaling. Cell Cycle 9(3):450-5.

Ye J, Zhang X, Young C, Zhao X, Hao Q, Cheng L, Jensen ON (2010). Optimized IMAC-IMAC protocol for phosphopeptide recovery from complex biological samples. J Proteome Res. 2;9(7):3561-73.

Ytterberg AJ, Jensen ON (2010). Modification-specific proteomics in plant biology. Journal of proteomics 2010-Jun-10. 0 s.

Zhao X, Leon IR, Bak S, Mogensen M, Wrzesinski K, Hojlund K, Jensen ON (2010). Phosphoproteome analysis of functional mitochondria isolated from resting human muscle reveals extensive phosphory¬lation of inner membrane protein complexes and enzymes. Mol Cell Proteomics, in press.

Ørom UA, Lund AH (2010). Experimental identification of microRNA targets. Gene 451(1-2):1-5.

2009

Agger K, Cloos  PAC, Rudkjaer L, Williams K, Andersen G, Christensen J, Helin K (2009). The H3K27me3 demethylase JMJD3 contributes to the activation of the INK4A-ARF locus in response to oncogene- and stress-induced senescence. Genes Dev 23(10):1171-6.

Balan L, Foltyn VN, Zehl M, Dumin E, Dikopoltsev E, Knoh D, Ohno Y, Kihara A, Jensen ON, Radzishevsky IS, Wolosker H (2009). Feedback inactivation of D-serine synthesis by NMDA receptor-elicited translocation of serine racemase to the membrane. Proceedings of the National Academy of Science of the United States of America 106(18):7589-94.

Ballabeni A, Zamponi R, Caprara G, Melixetian M, Bossi S, Masiero L, Helin K (2009). Human CDT1 associates with CDC7 and recruits CDC45 to chromatin during S phase. J Biol Chem 284(5):3028-36.

Barends S, Zehl M, Bialek S, de Waal E, Traag BA, Willemse J, Jensen ON, Vijgenboom E, van Wezel GP (2009). Transfer-messenger RNA controls the translation of cell-cycle and stress proteins in Streptomyces. EMBO Rep. 11(2):119-25.

Boccalatte FE, Voena C, Riganti C, Bosia A, D’Amico L, Riera L, Cheng M, Ruggeri B, Jensen ON, Goss VL, Lee K, Nardone J, Rush J, Polakiewicz RD, Comb MJ, Chiarle R, Inghirami G (2009). The enzymatic activity of 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (ATIC) is enhanced by NPM-ALK: new insights in ALK-mediated pathogenesis and the treatment of ALCL. Blood 8(3):2776-90. 

Bracken AP, Helin K (2009). Polycomb group proteins: navigators of lineage pathways led astray in cancer. Nat Rev Cancer 9(11):773-84. 

Callesen AK, Madsen JS, Vach W, Kruse TA, Mogensen O, Jensen ON (2009). Serum protein profiling by solid phase extraction and mass spectrometry: A future diagnostics tool? Proteomics 9(6):1428-41. 

Callesen AK, Madsen JS, Iachina M, Vach W, Kruse TA, Jensen ON, Mogensen O (2009). Serum peptin/protein profiling by mass spectrometry provides diagnostic information independently of CA125 in women with an ovarian tumor. Cancer Biomark. 6(2):73-82. 

Calvano C, Jensen ON, Zambonin C (2009). Selective extraction of phospholipids from dairy products by micro-solid phase extraction based on titanium dioxide microcolumns followed by MALDI-TOF-MS analysis. Analytical and Bioanalytical Chemistry 394(5):1453-61. 

Caprara G, Zamponi R, Melixetian M, Helin K (2009). Isolation and characterization of DUSP11, a novel p53 target gene. J Cell Mol Med 13(8B):2158-70. 

Ciró M, Prosperini E, Quarto M, Grazini U, Walfridsson J, McBlane F, Nucifero P, Pacchiana G, Capra M, Christensen J, Helin K (2009). ATAD2 is a novel cofactor for MYC, overexpressed and amplified in aggressive tumors. Cancer Res 69(21): 8491-8. 

Christoffersen NR, Shalgi R, Frankel LB, Leucci E, Lees M, Klausen M, Pilpel Y, Nielsen FC, Oren M, Lund AH (2009). p53-independent upregulation of miR-34a during oncogene-induced senescence represses MYC. Cell Death and Differ 17(2):235-45. 

Dettori R, Sonzogni S, Meyer  L, Lopez-Garcia LA, Morrice NA, Zeuzem S, Engel M, Piiper A, Neimanis S, Frödin M, Biondi RM (2009). Regulation of the interaction between protein kinase C-related protein kinase 2 (PRK2) and its upstream kinase, 3-phosphoinositide-dependent protein kinase 1 (PDK1). J Biol Chem 284(44)30318-27. 

Doehn U, Hauge C, Frank SR, Jensen CAJ, Duda K, Nielsen JV, Cohen MS, Johansen JV, Winther BR, Lund LR, Winther O, Taunton J, Hansen SH, Frödin M (2009). RSK is a principal effector of the RAS-ERK pathway for eliciting a coordinate promotile/invasive gene program and phenotype in epithelial cells. Mol Cell 35(4):511-22. 

Hansen K, Helin K (2009). Epigenetic inheritance through self-recruitment of the polycomb repressive complex 2. Epigenetics 4(3):133-8. 

Hulleman E, Quarto M, Vernell R, Masserdotti G, Colli E, Kros JM, Levi D, Gaetani P, Tunici P, Finocchiaro G, Baena RR, Capra M, Helin K (2009). A role for the transcription factor HEY1 in glioblastoma. J Cell Mol Med 13(1):136-46. 

Hynek R, Svensson B, Jensen ON, Barkholt V, Finnie C (2009). The plasma membrane proteome of germinating barley embryos. Proteomics 9(14):3787-94. 

Jenal M, Trinh E, Britschgi C, Britschgi A, Roh V, Vorburger SA, Tobler A, Leprince D, Fey MF, Helin K, Tschan MP (2009). The tumor suppressor gene hypermethylated in cancer 1 is transcriptionally regulated by E2F1. Mol Cancer Res 7(6):916-22. 

Kondo A, Miyamoto T, Yonekawa O, Giessing A, Østerlund EC, Jensen ON (2009). Glycopeptide profiling of beta-2-glycoprotein I by mass spectrometry reveals attenuated sialylation in patients with antiphospholipid syndrome. Journal of Proteomics 73(1):123-33. 

Leth-Larsen R, Lund R, Hansen HV, Laenkholm A, Tarin D, Jensen ON, Ditzel H (2009). Metastasis-related plasma membrane proteins of human breast cancer cells identified by comparative quantitative mass spectrometry. Molecular and Cellular Proteomics 8(6):1436-49. 

Lund R, Leth-Larsen R, Jensen ON, Ditzel HJ (2009). Efficient Isolation and Quantitative Proteomic Analysis of Cancer Cell Plasma Membrane Proteins for Identification of Metastasis-Associated Cell Surface Markers. Journal of Proteome Research 8(6):3078–90. 

Melixetian M, Klein DK, Sørensen CS, Helin K (2009). NEK11 regulates CDC25A degradation and the IR-induced G2/M checkpoint. Nat Cell Biol 11(10):1247-53. 

Nienhuijs MEL, Poulsen K, van der Zande M, Briest A, Merkx MAW, Stoelinga PJW, Jensen ON, Jansen JA, Walboomers XF (2009). Analytical assessment of the osteoinductive material COL-LOSSE. Journal of Biomedical Materials Research. Part B: Applied Biomaterials 89B(2):300-5. 

Rand KD, Zehl M, Jensen ON, Jørgensen TJD (2009). Protein hydrogen exchange measured at single-residue resolution by electron transfer dissociation mass spectrometry. Analytical Chemistry 81(14):5577-84. 

Salcedo-Amaya AM, van Driel MA, Alako BT, Trelle MB, van den Elzen AMG, Cohen AM, Janssen-Megens EM, van de Vegte-Bolmer M, Selzer RR, Iniguez AL, Green RD, Sauerwein RW, Jensen ON, Stunnenberg HG (2009). ‘Dynamic histone H3 epigenome marking during the intraerythrocytic cycle of Plasmodium falciparum’. Proceedings of the National Academy of Science of the United States of America 106(24):9655-60. 

Stulemeijer IJE, Joosten MHAJ, Jensen ON (2009). Quantitative Phosphoproteomics of Tomato Mounting a Hypersensitive Response Reveals a Swift Suppression of Photosynthetic Activity and a Differential Role for Hsp90 Isoforms. Journal of Proteome Research 8(3):1168-82. 

Svenningsen P, Bistrup C, Friis UG, Bertog M, Haerteis S, Krueger B, Stubbe J, Jensen ON, Thiesson HC, Uhrenholt TR, Jespersen B, Jensen BL, Korbmacher C, Skøtt O (2009). Plasmin in Nephrotic Urine Activates the Epithelial Sodium Channel. Journal of the American Society of Nephrology 20(2):299-310. 

Thingholm TE, Jensen ON, Larsen MR (2009). Analytical strategies for phosphoproteomics. Proteomics 9(6):1451-68.   

Thingholm TE, Jensen ON, Larsen MR (2009). Enrichment and characterization of phosphopeptides by immobilized metal affinity chromatography (IMAC) and mass spectrometry. Methods Mol Biol. 527:47-56 xi. 

Thingholm TE, Jensen ON, Larsen MR (2009). Enrichment and separation of mono- and multiply phosphorylated peptides using sequential elution from IMAC prior to mass spectrometric analysis. Methods Mol Biol. 527:67-78, xi. 

Trelle MB, Salcedo-Amaya AM, Cohen A, Stunnenberg HG, Jensen ON (2009). Global histone analysis by mass spectrometry reveals a high content of acetylated lysine residues in the malaria parasite Plasmodium falciparum. Journal of Proteome Research 8(7):3439-50. 

Uren AG, Mikkers H, Kool J, van der Weyden L, Lund AH, Wilson CH, Rance R, Jonkers J, van Lohuizen M, Berns A, Adams DJ (2009). A high-throughput splinkerette-PCR method for the isolation and sequencing of retroviral insertion sites. Nat Protoc. 4(5):789-98. 

Zhao Y, Jensen ON (2009). Modification-specific proteomics: strategies for characterization of post-translational modifications using enrichment techniques. Proteomics 9(20):4632-41. 

2008

Agger K, Christensen J, Cloos PA, Helin K (2008). The emerging functions of histone demethylases. Curr Opin Genet Dev. 18(2):159-68. 

Britschgi A, Trinh E, Rizzi M, Jenal M, Ress A, Tobler A, Fey MF, Helin K, Tschan MP (2008). DAPK2 is a novel E2F1/KLF6 target gene involved in their proapoptotic function. Oncogene 27(43):5706-16. 

Cloos PA, Christensen J, Agger K, Helin K (2008). Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease. Genes Dev. 22(9):1115-40. 

Hansen KH, Bracken AP, Pasini D, Dietrich N, Gehani SS, Monrad A, Rappsilber J, Lerdrup M, Helin K (2008). A model for transmission of the H3K27me3 epigenetic mark. Nat Cell Biol. 10(11):1291-300. 

Herranz N, Pasini D, Díaz VM, Francí C, Gutierrez A, Dave N, Escrivà M, Hernandez-Muñoz I, Di Croce L, Helin K, García de Herreros A, Peiró S (2008). Polycomb complex 2 is required for E-cadherin repression by the Snail1 transcription factor. Mol Cell Biol. 28(15):4772-81. 

Hørning OB, Kjeldsen F, Theodorsen S, Vorm O, Jensen ON (2008). Isocratic Solid Phase Extraction-Liquid Chromatography (SPE-LC) Interfaced to High-Performance Tandem Mass Spectrometry for Rapid Protein Identification. J Proteome Res. 7(8):3159-67. 

Kjeldsen F, Hørning OB, Jensen SS, Giessing AM, Jensen ON (2008). Towards Liquid Chromatography Time-Scale Peptide Sequencing and Characterization of Post-Translational Modifications in the Negative-Ion Mode Using Electron Detachment Dissociation Tandem Mass Spectrometry. J Am Soc Mass Spectrom. 19(8):1156-62. 

Lindroth AM, Park YJ, McLean CM, Dokshin GA, Persson JM, Herman H, Pasini D, Miró X, Donohoe ME, Lee JT, Helin K, Soloway PD (2008). Antagonism between DNA and H3K27 methylation at the imprinted Rasgrf1 locus. PLoS Genet. 4(8):e1000145. 

Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL, Björling E, Blagoev B, Bose R, Brahmachari SK, Burlingame AS, Bustelo XR, Cagney G, Cantin GT, Cardasis HL, Celis JE, Chaerkady R, Chu F, Cole PA, Costello CE, Cotter RJ, Crockett D, DeLany JP, De Marzo AM, DeSouza LV, Deutsch EW, Dransfield E, Drewes G, Droit A, Dunn MJ, Elenitoba-Johnson K, Ewing RM, Van Eyk J, Faca V, Falkner J, Fang X, Fenselau C, Figeys D, Gagné P, Gelfi C, Gevaert K, Gimble JM, Gnad F, Goel R, Gromov P, Hanash SM, Hancock WS, Harsha HC, Hart G, Hays F, He F, Hebbar P, Helsens K, Herme¬king H, Hide W, Hjernø K, Hochstrasser DF, Hofmann O, Horn DM, Hruban RH, Ibarrola N, James P, Jensen ON, Jensen PH, Jung P, Kandasamy K, Kheterpal I, Kikuno RF, Korf U, Körner R, Kuster B, Kwon MS, Lee HJ, Lee YJ, Lefevre M, Lehvaslaiho M, Lescuyer P, Levander F, Lim MS, Löbke C, Loo JA, Mann M, Martens L, Martinez-Heredia J, McComb M, McRed¬mond J, Mehrle A, Menon R, Miller CA, Mischak H, Mohan SS, Mohmood R, Molina H, Moran MF, Morgan JD, Moritz R, Morzel M, Muddiman DC, Nalli A, Navarro JD, Neubert TA, Ohara O, Oliva R, Omenn GS, Oyama M, Paik YK, Pennington K, Pepperkok R, Periaswamy B, Petricoin EF, Poirier GG, Prasad TS, Purvine SO, Rahiman BA, Ramachan¬dran P, Ramachandra YL, Rice RH, Rick J, Ronnholm RH, Salonen J, Sanchez JC, Sayd T, Seshi B, Shankari K, Sheng SJ, Shetty V, Shivakumar K, Simpson RJ, Sirdesh¬mukh R, Siu KW, Smith JC, Smith RD, States DJ, Sugano S, Sullivan M, Superti-Furga G, Takatalo M, Thongboonkerd V, Trinidad JC, Uhlen M, Vandekerckhove J, Vasilescu J, Veenstra TD, Vidal-Taboada JM, Vihinen M, Wait R, Wang X, Wiemann S, Wu B, Xu T, Yates JR, Zhong J, Zhou M, Zhu Y, Zurbig P, Pandey A (2008). Human Proteinpedia enables sharing of human protein data. Nat Biotechnol. 26(2):164-167. 

Pasini D, Bracken AP, Agger K, Christensen J, Hansen K, Cloos PA, Helin K (2008). Regulation of Stem Cell Differentiation by Histone Methyltransferases and Demethylases. Cold Spring Harb Symp Quant Biol. 73:253-63. 

Pasini D, Hansen KH, Christensen J, Agger K, Cloos PA, Helin K (2008). Coordinated regulation of transcriptional repression by the RBP2 H3K4 demethylase and Polycomb-Repressive Complex 2. Genes Dev. 22(10):1345-55. 

Riising EM, Boggio R, Chiocca S, Helin K, Pasini D (2008). The polycomb repressive complex 2 is a potential target of SUMO modifications. PLoS ONE. 3(7):e2704. 

Thingholm TE, Jensen ON, Robinson P, Larsen MR (2008). SIMAC (sequential elution from IMAC), a phosphoproteomics strategy for the rapid separation of monophosphorylated from multiply phosphorylated peptides. Mol Cell Proteomics. 7(4):661-71. 

Thingholm TE, Larsen MR, Ingrell CR, Kassem M, Jensen ON (2008). TiO2-Based Phosphoproteomic Analysis of the Plasma Membrane and the Effects of Phosphatase Inhibitor Treatment. J Proteome Res. 7(8):3304-13. 

Trelle MB, Jensen ON (2008). Utility of immonium ions for assignment of epsilon-N-acetyllysine-containing peptides by tandem mass spectrometry. Anal Chem. 80(9):3422-30. 

Ørom UA, Nielsen FC, Lund AH (2008). MicroRNA-10a binds the 5’UTR of ribosomal protein mRNAs and enhances their translation. Mol Cell 30(4):460-71. 

2007

Agger K, Christensen J, Cloos PA, Pasini D, Rose S, Rappsilber J, Issaeva I, Canaani E, Salsini AE and Helin K (2007). UTX and JMJD3 are H3K27 demethylases involved in HOX gene regulation and development. Nature 449(7163):731-4. 

Albar JP, Corthals GL, Gil C, James P, Jensen ON, Palagi PM, Penque D (2007). Promoting Proteomics Knowledge on Europe:report on the Activities of the EuPA Education Committee 2006-2007. Proteomics Suppl 1:90-4. 

Banuelos S, Omaetxebarria MJ, Ramos I, Laesen MR, Arregi I, Jensen ON, Arizmendi JM, Prado A, Muga A (2007). Phosphorylation of both nucleaoplasmin domains is required for activity. J Biol Chem 282(29):21213-21. 

Basu U, Gyrd-Hansen M, Baby SM, Lozynska O, Krag TOB, Jensen CJ, Frodin M, Khurena TS (2007). Heregulin-induced epigenetic regulation of the Utrophin-A promoter. FEBS Letters 581(22)4153-8. 

Bracken AP, Kleine-Kohlbrecher D, Dietrich N, Pasini D, Gargiulo G, Beekman C, Theilgaard- Monch K, Minucci S, Porse BT, Marine JC, Hansen KH and Helin K (2007). The Polycomb group proteins bind thoughout the INK4A-ARF locus and are dissociated in senescent cells. Genes Dev 21(5):535-40. 

Christoffersen NR, Silahtaroglu A, Orom UA, Kauppinen S, Lund AH (2007). miR-200b mediates post-transcriptional repression of ZFHX1B. RNA 13:1172-8. 

Christensen J, Agger K, Cloos P, Pasini D, Sennels L, Rappsilber J, Hansen KH, Salcini AE and Helin K (2007). RBP2 belongs to family of demethylases specific for tri- and di-methylated lysine 4 on Histone 3. Cell 128(6):1063-76. 

Chuankhayan P, Rimlumduan T, Tantanuch W, Mothong N, Kongsaeree PT, Metheenukul P, Svasti J, Jensen ON, Cairns JR (2007). Functional and structural differences between isoflavonoid beta-glycosidases from Dalbergia sp. Arch Biochem Biophys. 468(2) 205-16. 

Del Arroyo AG, Messaoudi SE, Clark PA, James M, Stott F, Bracken A, Helin K, and Peters G (2007). E2F-dependent induction of p14ARF during cell cycle re-entry in human T cells. Cell Cycle 6(21):2697-2705. 

Dietrich N, Bracken AP, Trinh E, Schjerling CK, Koseki H, Rappsilber J, Helin K, and Hansen KH (2007). Bypass of senescence by the Polycomb group protein CBX8 throuh direct binding to the INK4A-ARF locus. EMBO Journal 26(6):1637-48.  .

Duran MC, Boeri-Erba E, Mohammed S, Martin-Ventura JL, Egido J, Vivanco F, Jensen ON (2007). Characterization of HSP27 phosphorylation sites in human atherosclerotic plaque secretome. Metods Mol Biol 357:151-63. 

Duran MC, Martin-Ventura JL, Mas S, Barderas MG, Darde VM, Jensen ON, Egido J, Vivanco F (2007). Characterization of the human atheroma plaque secretome by proteomic analysis. Methods Mol Biol. 357: 141-50. 

Duran MC, Martin-Ventura Jl, Mohammed S, Barderas MG, Blanco-Colio LM, Mas S, Moral V, Otega L, Tunon J, Jensen ON, Vivanco F, Egido J (2007). Atorvastatin modulates the profile of proteins released by human atherosclerotic plaques. Eur J Pharmacol. 562(1-2): 119-29. 

Erba EB, Matthiesen R, Bunkenborg J, Schulze WX, Stefano PD, Cabodi S, Tarone G, Delfilippi P, Jensen ON (2007). Quantitation of Multisite EGF Receptor Phosphorylation Using Mass Spectrometry and a Novel Normalization Approach. J Proteome Res 6(7): 2768-85. 

Fog CK, Jensen KT, Lund AH, Kunder S, Quintanilla-Martinez L, Schmidt J, Wang B, Wabl M, Pedersen FS (2007). Impairment of alternative splice sites defining a novel gammaretroviral exon within gag modifies the oncogenic properties of Akv murine leukemia virus. Retrovirology. 2007 Jul 6;4:46. 

Frankel LB, Christoffersen NR, Jacobsen A, Lindow M, Krogh A, Lund AH (2007). Programmed cell death 4 (PDCD4) is an important functional target of the microRNA miR in breast cancer cells. J Biol Chem.283: 1026-33. 

Hagen L, Kavli B, Sousa MM, Torseth K, Liabakk NB, Sundheim O, Pena-diaz J, Otterlei M, Hørning O, Jensen ON, Krokan HE, Slupphaugh G(2007). Cell cycle-specific UNG2 phosphorylations regulate protein turnover, activity and association with RPA. EMBO J. 27(1) 51-61. 

Hagglund P, Matthiesen R, Elortza F, Hojrup P, Roepstorff P, Jensen ON, Bunkenborg J(2007). An enzymatic deglycosylation scheme enabling indentification of core fucosylated N-glycans and O-glycosylation site mapping of human plasma proteins. J Proteome Res. 6(8) 3021-31. 

Hauge C, Antal TL, Hirschberg D, Doehn U, Thorup K, Idrissova L, Hansen K, Jensen ON, Jørgensen TJD, Biondi RM and Frodin M(2007). Mechanism for activation of the growth factor-activated AGC kinases by turn motif phosphorylation. EMBO J. 26(9)2251-61. 

Hørning O, Theodorsen S, Vorm, O, Jensen ON (2007). Solid phase extraction-liquid chromatography (SPE-LC) interface for automated peptide separation and identification by tandem mass spectrometry. Int J Mass Spectrom. 268(2-3) 147-57.

Jensen ON, Heck AJR, Hillenkamp F (2007). Peter Roepstorff, a brief biography. Int J Mass Spectrom. 268, 2-3.

Jørgensen S, Elvers I, Trelle MB, Menzel T, Eskildsen M, Jensen ON, Helleday T, Helin K, Sørensen CS (2007). The histone methyltransferase SET8 is required for S-phase progression. Journal of Cell Biol 179(7):1337-45. 

Kedde M, Strasser MJ, Boldajiipour B, Vrielink JA, Slanchev K, le Sage C, Nagel R, Voorhoeve PM, van Duijse J, Ørom UA, Lund AH, Perrakis A, Raz E, Agami R (2007). RNA-Binding Protein Dnd 1 Inhibits MicroRNA Access to Target mRNA. Cell 131:1273-86. 

Kjeldsen F, Giessing AM, Ingrell CR, Jensen ON (2007). Peptide Sequincing and Characterization of Post-Translational Modifications by Enhanced ion-Charging and Liquid Cromatography Electron-Transfer Dissociation Tandem Mass Spectrometry. Anal Chem. 79(24)9243-52. 

Kleinnijenhuis AJ, Kjeldsen F, Kallipolitis B, Haselmann KF, Jensen ON (2007). Analysis of Histidine Phosphorylation Using Tandem MS and Ion-Electron Reactions. Anal Chem. 79(19)7450-6. 

Omaetxebarria MJ, Elortza F, Rodriguez-Suarez E, Aloria K, Arizmendi JM, Jensen ON, Matthiesen R(2007). Computional approach for identification and characterization of GPI-anchored peptides in proteomics experiments. Proteomics. 7(12):1951-60. 

Pasini D, Bracken AP, Hansen JB, Capillo M and Helin K (2007). The Polycomb group protein Suz12 is required for embryonic stem cell differentiation. Mol Cel Biol 27(10):3769-79. 

Qiao H, Di Stefano L, Tian C, Li Y-Y, Qian X-P, Pang X-W, Li Y, McNutt MA, Helin K, Zhang Y, Chen W-F (2007). Human TFDP3, a novel DP protein inhibits DNA binding and transactivation by E2F. J Biol Chem 282(1):454-66. 

Sachon, E, Nielsen, PF, Jensen ON (2007). Characterization of N-palmitoylated human growth homone by in situ liquid extraction and MALDI tandem mass spectrometry. J Mass Spectrom 42(6):724-34. 

Sorensen AB, Lund AH, Kunder S, Quintanilla-Martinez L, Schmidt J, Wang B, Wabl M, Pedersen FS (2007). Impairment of alternative splice sites defining a novel gammaretroviral exon within gag modifies the oncogenic properties of Akv murine leukemia virua. Retrovirology 4:46. 

Trelle, M.B, and Jensen, ON (2007). Proteomics in histone research and epigenetics. Expert Rev. Proteomics 4(4)491-503. 

Villa R, Pasini D, Gutierrez A, Morey L, Occhionorelli M, Vire E, Nomdedeu JF, Jenuwein T, Pelicci PG, Minucci S, Fuks F, Helin K, Di Croce L (2007). Role of the Polycomb repressive complex 2 in acute promyelocytic leukemia. Cancer Cell 11(6):513-25. 

Voena C, Conte C, Ambrogio C, Boeri Erba E, Boccalatte F, Mohammed S, Jensen ON, Palestro G, Inghirami G, Chiarle R (2007). The tysine phosphatase Shp2 interacts with NPM-ALK and regulates anaplastic lymphoma cell growth and migration. Cancer Res. 67(9):4278-86. 

Yang J, Valineva T, Hong J, Bu T, Yao Z, Jensen ON, Frilander MJ, Silvennoinen O (2007). Transcriptional co-activator protein p100 interacts with snRNP proteins and facilitates the assembly of the spliceosome. Nucleic Acids Res. 35(13):4485-94. 

Zhang X, Ye J, Jensen ON, Roepstorff P (2007). Highly efficient phosphopeptide enrichment by calcium phosphate precipitation combined with subsequent serial immobilized metal ion affinity chromatography (IMAC) enrichment. Mol Cell Proteomics. 6 (11) 2032-42. 

Ørum, UA, Lund AH (2007). Isolation of microRNA targets using biotinylated synthetic microRNAs. Methods 43:162-5. 

PhD theses

Characterization of histone proteins using mass spectrometry. Hye R Jung 2010.

Characterization of the MMSET gene involved in multiple myeloma. Heidi Hudlebusch 2010.

Regulation of RSK and other AGC kinases. Claus Juel Jensen 2010.

Identification and characterization of the novel tumor suppressor PRDM11. Tonnesen CKF 2009.

Mechanisms for regulation of the kinase activity of the AGC kinases RSK and MSK. Hauge C 2009.

Identification and characterization of miRNA target interactions. Ørom ULA 2008.

Identification and quantitation of multisite histone modifications by MS. Trelle MB 2008.

miRNA and cancer. Christoffersen NR 2008.

Regulation of cell proliferation and target gene repression by the polycomb group protein CBX8. Dietrich N 2008.