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Items: 1 to 50 of 130

1.

Dot1 promotes H2B ubiquitination by a methyltransferase-independent mechanism.

van Welsem T, Korthout T, Ekkebus R, Morais D, Molenaar TM, van Harten K, Poramba-Liyanage DW, Sun SM, Lenstra TL, Srivas R, Ideker T, Holstege FCP, van Attikum H, El Oualid F, Ovaa H, Stulemeijer IJE, Vlaming H, van Leeuwen F.

Nucleic Acids Res. 2018 Sep 8. doi: 10.1093/nar/gky801. [Epub ahead of print]

PMID:
30203048
2.

Sequence-Directed Action of RSC Remodeler and General Regulatory Factors Modulates +1 Nucleosome Position to Facilitate Transcription.

Kubik S, O'Duibhir E, de Jonge WJ, Mattarocci S, Albert B, Falcone JL, Bruzzone MJ, Holstege FCP, Shore D.

Mol Cell. 2018 Jul 5;71(1):89-102.e5. doi: 10.1016/j.molcel.2018.05.030.

PMID:
29979971
3.

FOXO Transcription Factors Both Suppress and Support Breast Cancer Progression.

Hornsveld M, Smits LMM, Meerlo M, van Amersfoort M, Groot Koerkamp MJA, van Leenen D, Kloet DEA, Holstege FCP, Derksen PWB, Burgering BMT, Dansen TB.

Cancer Res. 2018 May 1;78(9):2356-2369. doi: 10.1158/0008-5472.CAN-17-2511. Epub 2018 Feb 12.

PMID:
29440168
4.

The ribosome assembly gene network is controlled by the feedback regulation of transcription elongation.

Gómez-Herreros F, Margaritis T, Rodríguez-Galán O, Pelechano V, Begley V, Millán-Zambrano G, Morillo-Huesca M, Muñoz-Centeno MC, Pérez-Ortín JE, de la Cruz J, Holstege FCP, Chávez S.

Nucleic Acids Res. 2017 Sep 19;45(16):9302-9318. doi: 10.1093/nar/gkx529.

5.

EBV MicroRNA BART16 Suppresses Type I IFN Signaling.

Hooykaas MJG, van Gent M, Soppe JA, Kruse E, Boer IGJ, van Leenen D, Groot Koerkamp MJA, Holstege FCP, Ressing ME, Wiertz EJHJ, Lebbink RJ.

J Immunol. 2017 May 15;198(10):4062-4073. doi: 10.4049/jimmunol.1501605. Epub 2017 Apr 17.

6.

Growth condition dependency is the major cause of non-responsiveness upon genetic perturbation.

Amini S, Holstege FC, Kemmeren P.

PLoS One. 2017 Mar 3;12(3):e0173432. doi: 10.1371/journal.pone.0173432. eCollection 2017.

7.

Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters.

de Jonge WJ, O'Duibhir E, Lijnzaad P, van Leenen D, Groot Koerkamp MJ, Kemmeren P, Holstege FC.

EMBO J. 2017 Feb 1;36(3):274-290. doi: 10.15252/embj.201695621. Epub 2016 Dec 15.

8.

Mapping of a FEB3 homologous febrile seizure locus on mouse chromosome 2 containing candidate genes Scn1a and Scn3a.

Hessel EV, van Lith HA, Wolterink-Donselaar IG, de Wit M, Groot Koerkamp MJ, Holstege FC, Kas MJ, Fernandes C, de Graan PN.

Eur J Neurosci. 2016 Dec;44(11):2950-2957. doi: 10.1111/ejn.13420.

PMID:
27690330
9.

An endometrial gene expression signature accurately predicts recurrent implantation failure after IVF.

Koot YE, van Hooff SR, Boomsma CM, van Leenen D, Groot Koerkamp MJ, Goddijn M, Eijkemans MJ, Fauser BC, Holstege FC, Macklon NS.

Sci Rep. 2016 Jan 22;6:19411. doi: 10.1038/srep19411.

10.

A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions.

Sameith K, Amini S, Groot Koerkamp MJ, van Leenen D, Brok M, Brabers N, Lijnzaad P, van Hooff SR, Benschop JJ, Lenstra TL, Apweiler E, van Wageningen S, Snel B, Holstege FC, Kemmeren P.

BMC Biol. 2015 Dec 23;13:112. doi: 10.1186/s12915-015-0222-5.

11.

Expression Profiling after Prolonged Experimental Febrile Seizures in Mice Suggests Structural Remodeling in the Hippocampus.

Jongbloets BC, van Gassen KL, Kan AA, Olde Engberink AH, de Wit M, Wolterink-Donselaar IG, Groot Koerkamp MJ, van Nieuwenhuizen O, Holstege FC, de Graan PN.

PLoS One. 2015 Dec 18;10(12):e0145247. doi: 10.1371/journal.pone.0145247. eCollection 2015.

12.

Genome-wide analysis reveals NRP1 as a direct HIF1α-E2F7 target in the regulation of motorneuron guidance in vivo.

de Bruin A, A Cornelissen PW, Kirchmaier BC, Mokry M, Iich E, Nirmala E, Liang KH, D Végh AM, Scholman KT, Groot Koerkamp MJ, Holstege FC, Cuppen E, Schulte-Merker S, Bakker WJ.

Nucleic Acids Res. 2016 May 5;44(8):3549-66. doi: 10.1093/nar/gkv1471. Epub 2015 Dec 17.

13.

FOXO target gene CTDSP2 regulates cell cycle progression through Ras and p21(Cip1/Waf1).

Kloet DE, Polderman PE, Eijkelenboom A, Smits LM, van Triest MH, van den Berg MC, Groot Koerkamp MJ, van Leenen D, Lijnzaad P, Holstege FC, Burgering BM.

Biochem J. 2015 Jul 15;469(2):289-98. doi: 10.1042/BJ20140831. Epub 2015 May 20.

14.

Identification of Srp9 as a febrile seizure susceptibility gene.

Hessel EV, de Wit M, Wolterink-Donselaar IG, Karst H, de Graaff E, van Lith HA, de Bruijn E, de Sonnaville S, Verbeek NE, Lindhout D, de Kovel CG, Koeleman BP, van Kempen M, Brilstra E, Cuppen E, Loos M, Spijker SS, Kan AA, Baars SE, van Rijen PC, Gosselaar PH, Groot Koerkamp MJ, Holstege FC, van Duijn C, Vergeer J, Moll HA, Taubøll E, Heuser K, Ramakers GM, Pasterkamp RJ, van Nieuwenhuizen O, Hoogenraad CC, Kas MJ, de Graan PN.

Ann Clin Transl Neurol. 2014 Apr;1(4):239-50. doi: 10.1002/acn3.48. Epub 2014 Mar 12.

15.

The genomic landscape of compensatory evolution.

Szamecz B, Boross G, Kalapis D, Kovács K, Fekete G, Farkas Z, Lázár V, Hrtyan M, Kemmeren P, Groot Koerkamp MJ, Rutkai E, Holstege FC, Papp B, Pál C.

PLoS Biol. 2014 Aug 26;12(8):e1001935. doi: 10.1371/journal.pbio.1001935. eCollection 2014 Aug.

16.

Cell cycle population effects in perturbation studies.

O'Duibhir E, Lijnzaad P, Benschop JJ, Lenstra TL, van Leenen D, Groot Koerkamp MJ, Margaritis T, Brok MO, Kemmeren P, Holstege FC.

Mol Syst Biol. 2014 Jun 21;10:732. doi: 10.15252/msb.20145172.

17.

Aberrant expression and distribution of enzymes of the urea cycle and other ammonia metabolizing pathways in dogs with congenital portosystemic shunts.

van Straten G, van Steenbeek FG, Grinwis GC, Favier RP, Kummeling A, van Gils IH, Fieten H, Groot Koerkamp MJ, Holstege FC, Rothuizen J, Spee B.

PLoS One. 2014 Jun 19;9(6):e100077. doi: 10.1371/journal.pone.0100077. eCollection 2014.

18.

Insulin-FOXO3 signaling modulates circadian rhythms via regulation of clock transcription.

Chaves I, van der Horst GT, Schellevis R, Nijman RM, Koerkamp MG, Holstege FC, Smidt MP, Hoekman MF.

Curr Biol. 2014 Jun 2;24(11):1248-55. doi: 10.1016/j.cub.2014.04.018. Epub 2014 May 22.

19.

Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors.

Kemmeren P, Sameith K, van de Pasch LA, Benschop JJ, Lenstra TL, Margaritis T, O'Duibhir E, Apweiler E, van Wageningen S, Ko CW, van Heesch S, Kashani MM, Ampatziadis-Michailidis G, Brok MO, Brabers NA, Miles AJ, Bouwmeester D, van Hooff SR, van Bakel H, Sluiters E, Bakker LV, Snel B, Lijnzaad P, van Leenen D, Groot Koerkamp MJ, Holstege FC.

Cell. 2014 Apr 24;157(3):740-52. doi: 10.1016/j.cell.2014.02.054.

20.

Suppression of Mediator is regulated by Cdk8-dependent Grr1 turnover of the Med3 coactivator.

Gonzalez D, Hamidi N, Del Sol R, Benschop JJ, Nancy T, Li C, Francis L, Tzouros M, Krijgsveld J, Holstege FC, Conlan RS.

Proc Natl Acad Sci U S A. 2014 Feb 18;111(7):2500-5. doi: 10.1073/pnas.1307525111. Epub 2014 Feb 3.

21.

Uterine selection of human embryos at implantation.

Brosens JJ, Salker MS, Teklenburg G, Nautiyal J, Salter S, Lucas ES, Steel JH, Christian M, Chan YW, Boomsma CM, Moore JD, Hartshorne GM, Sućurović S, Mulac-Jericevic B, Heijnen CJ, Quenby S, Koerkamp MJ, Holstege FC, Shmygol A, Macklon NS.

Sci Rep. 2014 Feb 6;4:3894. doi: 10.1038/srep03894.

22.

Translation of branched-chain aminotransferase-1 transcripts is impaired in cells haploinsufficient for ribosomal protein genes.

Pereboom TC, Bondt A, Pallaki P, Klasson TD, Goos YJ, Essers PB, Groot Koerkamp MJ, Gazda HT, Holstege FC, Costa LD, MacInnes AW.

Exp Hematol. 2014 May;42(5):394-403.e4. doi: 10.1016/j.exphem.2013.12.010. Epub 2014 Jan 23.

PMID:
24463277
23.

Suppression of intragenic transcription requires the MOT1 and NC2 regulators of TATA-binding protein.

Koster MJ, Yildirim AD, Weil PA, Holstege FC, Timmers HT.

Nucleic Acids Res. 2014 Apr;42(7):4220-9. doi: 10.1093/nar/gkt1398. Epub 2014 Jan 22.

24.

The role of Ctk1 kinase in termination of small non-coding RNAs.

Lenstra TL, Tudek A, Clauder S, Xu Z, Pachis ST, van Leenen D, Kemmeren P, Steinmetz LM, Libri D, Holstege FC.

PLoS One. 2013 Dec 4;8(12):e80495. doi: 10.1371/journal.pone.0080495. eCollection 2013.

25.

Recruitment of TREX to the transcription machinery by its direct binding to the phospho-CTD of RNA polymerase II.

Meinel DM, Burkert-Kautzsch C, Kieser A, O'Duibhir E, Siebert M, Mayer A, Cramer P, Söding J, Holstege FC, Sträßer K.

PLoS Genet. 2013 Nov;9(11):e1003914. doi: 10.1371/journal.pgen.1003914. Epub 2013 Nov 14.

26.

Early adipogenesis is regulated through USP7-mediated deubiquitination of the histone acetyltransferase TIP60.

Gao Y, Koppen A, Rakhshandehroo M, Tasdelen I, van de Graaf SF, van Loosdregt J, van Beekum O, Hamers N, van Leenen D, Berkers CR, Berger R, Holstege FC, Coffer PJ, Brenkman AB, Ovaa H, Kalkhoven E.

Nat Commun. 2013;4:2656. doi: 10.1038/ncomms3656.

PMID:
24141283
27.

Elucidation of the distal convoluted tubule transcriptome identifies new candidate genes involved in renal Mg(2+) handling.

de Baaij JH, Groot Koerkamp MJ, Lavrijsen M, van Zeeland F, Meijer H, Holstege FC, Bindels RJ, Hoenderop JG.

Am J Physiol Renal Physiol. 2013 Dec 1;305(11):F1563-73. doi: 10.1152/ajprenal.00322.2013. Epub 2013 Oct 2.

28.

Lmx1a encodes a rostral set of mesodiencephalic dopaminergic neurons marked by the Wnt/B-catenin signaling activator R-spondin 2.

Hoekstra EJ, von Oerthel L, van der Heide LP, Kouwenhoven WM, Veenvliet JV, Wever I, Jin YR, Yoon JK, van der Linden AJ, Holstege FC, Groot Koerkamp MJ, Smidt MP.

PLoS One. 2013 Sep 16;8(9):e74049. doi: 10.1371/journal.pone.0074049. eCollection 2013.

29.

Kinetochore function and chromosome segregation rely on critical residues in histones H3 and H4 in budding yeast.

Ng TM, Lenstra TL, Duggan N, Jiang S, Ceto S, Holstege FC, Dai J, Boeke JD, Biggins S.

Genetics. 2013 Nov;195(3):795-807. doi: 10.1534/genetics.113.152082. Epub 2013 Sep 13.

30.

High-throughput genetic and gene expression analysis of the RNAPII-CTD reveals unexpected connections to SRB10/CDK8.

Aristizabal MJ, Negri GL, Benschop JJ, Holstege FC, Krogan NJ, Kobor MS.

PLoS Genet. 2013 Aug;9(8):e1003758. doi: 10.1371/journal.pgen.1003758. Epub 2013 Aug 29.

31.

Maspin is a marker for early recurrence in primary stage III and IV colorectal cancer.

Snoeren N, Emmink BL, Koerkamp MJ, van Hooff SR, Goos JA, van Houdt WJ, de Wit M, Prins AM, Piersma SR, Pham TV, Belt EJ, Bril H, Stockmann HB, Meijer GA, van Hillegersberg R, Holstege FC, Jimenez CR, Fijneman RJ, Kranenburg OW, Rinkes IH.

Br J Cancer. 2013 Sep 17;109(6):1636-47. doi: 10.1038/bjc.2013.489. Epub 2013 Sep 3.

32.

Canonical Wnt signaling negatively modulates regulatory T cell function.

van Loosdregt J, Fleskens V, Tiemessen MM, Mokry M, van Boxtel R, Meerding J, Pals CE, Kurek D, Baert MR, Delemarre EM, Gröne A, Koerkamp MJ, Sijts AJ, Nieuwenhuis EE, Maurice MM, van Es JH, Ten Berge D, Holstege FC, Staal FJ, Zaiss DM, Prakken BJ, Coffer PJ.

Immunity. 2013 Aug 22;39(2):298-310. doi: 10.1016/j.immuni.2013.07.019. Epub 2013 Aug 15.

33.

From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II.

Braberg H, Jin H, Moehle EA, Chan YA, Wang S, Shales M, Benschop JJ, Morris JH, Qiu C, Hu F, Tang LK, Fraser JS, Holstege FC, Hieter P, Guthrie C, Kaplan CD, Krogan NJ.

Cell. 2013 Aug 15;154(4):775-88. doi: 10.1016/j.cell.2013.07.033. Epub 2013 Aug 8.

34.

Specification of dopaminergic subsets involves interplay of En1 and Pitx3.

Veenvliet JV, Dos Santos MT, Kouwenhoven WM, von Oerthel L, Lim JL, van der Linden AJ, Koerkamp MJ, Holstege FC, Smidt MP.

Development. 2013 Aug;140(16):3373-84. doi: 10.1242/dev.094565. Epub 2013 Jul 17. Erratum in: Development. 2013 Oct;140(19):4116.

35.

Centromere binding and a conserved role in chromosome stability for SUMO-dependent ubiquitin ligases.

van de Pasch LA, Miles AJ, Nijenhuis W, Brabers NA, van Leenen D, Lijnzaad P, Brown MK, Ouellet J, Barral Y, Kops GJ, Holstege FC.

PLoS One. 2013 Jun 13;8(6):e65628. doi: 10.1371/journal.pone.0065628. Print 2013.

36.

Systematic triple-mutant analysis uncovers functional connectivity between pathways involved in chromosome regulation.

Haber JE, Braberg H, Wu Q, Alexander R, Haase J, Ryan C, Lipkin-Moore Z, Franks-Skiba KE, Johnson T, Shales M, Lenstra TL, Holstege FC, Johnson JR, Bloom K, Krogan NJ.

Cell Rep. 2013 Jun 27;3(6):2168-78. doi: 10.1016/j.celrep.2013.05.007. Epub 2013 Jun 6.

37.

A novel role for Sem1 and TREX-2 in transcription involves their impact on recruitment and H2B deubiquitylation activity of SAGA.

García-Oliver E, Pascual-García P, García-Molinero V, Lenstra TL, Holstege FC, Rodríguez-Navarro S.

Nucleic Acids Res. 2013 Jun;41(11):5655-68. doi: 10.1093/nar/gkt272. Epub 2013 Apr 17.

38.

Balancing of histone H3K4 methylation states by the Kdm5c/SMCX histone demethylase modulates promoter and enhancer function.

Outchkourov NS, Muiño JM, Kaufmann K, van Ijcken WF, Groot Koerkamp MJ, van Leenen D, de Graaf P, Holstege FC, Grosveld FG, Timmers HT.

Cell Rep. 2013 Apr 25;3(4):1071-9. doi: 10.1016/j.celrep.2013.02.030. Epub 2013 Mar 28.

39.

PP035. Genome-wide expression profile of first and second trimester human uterine natural killer cells.

Post Uiterweer ED, Eijkelkamp N, Groot Koerkamp MJ, Peeters LL, Holstege FC, Heijnen CJ, Franx A.

Pregnancy Hypertens. 2013 Apr;3(2):79. doi: 10.1016/j.preghy.2013.04.062. Epub 2013 Jun 6.

PMID:
26105890
40.

A central role for TFIID in the pluripotent transcription circuitry.

Pijnappel WW, Esch D, Baltissen MP, Wu G, Mischerikow N, Bergsma AJ, van der Wal E, Han DW, Bruch Hv, Moritz S, Lijnzaad P, Altelaar AF, Sameith K, Zaehres H, Heck AJ, Holstege FC, Schöler HR, Timmers HT.

Nature. 2013 Mar 28;495(7442):516-9. doi: 10.1038/nature11970. Epub 2013 Mar 17.

PMID:
23503660
41.

Altered subcellular localization of heat shock protein 90 is associated with impaired expression of the aryl hydrocarbon receptor pathway in dogs.

van Steenbeek FG, Spee B, Penning LC, Kummeling A, van Gils IH, Grinwis GC, Van Leenen D, Holstege FC, Vos-Loohuis M, Rothuizen J, Leegwater PA.

PLoS One. 2013;8(3):e57973. doi: 10.1371/journal.pone.0057973. Epub 2013 Mar 5.

42.

Aberrant gene expression in dogs with portosystemic shunts.

van Steenbeek FG, Van den Bossche L, Grinwis GC, Kummeling A, van Gils IH, Koerkamp MJ, van Leenen D, Holstege FC, Penning LC, Rothuizen J, Leegwater PA, Spee B.

PLoS One. 2013;8(2):e57662. doi: 10.1371/journal.pone.0057662. Epub 2013 Feb 25. Erratum in: PLoS One. 2013;8(10). doi:10.1371/annotation/5cccaae3-f06c-413f-857e-46546e87fce1.

43.

PDGFRB promotes liver metastasis formation of mesenchymal-like colorectal tumor cells.

Steller EJ, Raats DA, Koster J, Rutten B, Govaert KM, Emmink BL, Snoeren N, van Hooff SR, Holstege FC, Maas C, Borel Rinkes IH, Kranenburg O.

Neoplasia. 2013 Feb;15(2):204-17.

44.

Gene expression profiling of early intervertebral disc degeneration reveals a down-regulation of canonical Wnt signaling and caveolin-1 expression: implications for development of regenerative strategies.

Smolders LA, Meij BP, Onis D, Riemers FM, Bergknut N, Wubbolts R, Grinwis GC, Houweling M, Groot Koerkamp MJ, van Leenen D, Holstege FC, Hazewinkel HA, Creemers LB, Penning LC, Tryfonidou MA.

Arthritis Res Ther. 2013 Jan 29;15(1):R23. doi: 10.1186/ar4157.

45.

Genome wide expression profiling of the mesodiencephalic region identifies novel factors involved in early and late dopaminergic development.

Chakrabarty K, Von Oerthel L, Hellemons A, Clotman F, Espana A, Groot Koerkamp M, Holstege FC, Pasterkamp RJ, Smidt MP.

Biol Open. 2012 Aug 15;1(8):693-704. doi: 10.1242/bio.20121230. Epub 2012 May 17.

46.

Exploring gene expression signatures for predicting disease free survival after resection of colorectal cancer liver metastases.

Snoeren N, van Hooff SR, Adam R, van Hillegersberg R, Voest EE, Guettier C, van Diest PJ, Nijkamp MW, Brok MO, van Leenen D, Koerkamp MJ, Holstege FC, Rinkes IH.

PLoS One. 2012;7(11):e49442. doi: 10.1371/journal.pone.0049442. Epub 2012 Nov 21.

47.

Novel diagnostic modalities for assessment of the clinically node-negative neck in oral squamous-cell carcinoma.

Leusink FK, van Es RJ, de Bree R, Baatenburg de Jong RJ, van Hooff SR, Holstege FC, Slootweg PJ, Brakenhoff RH, Takes RP.

Lancet Oncol. 2012 Dec;13(12):e554-61. doi: 10.1016/S1470-2045(12)70395-9.

PMID:
23182196
48.

Lmx1a is an activator of Rgs4 and Grb10 and is responsible for the correct specification of rostral and medial mdDA neurons.

Hoekstra EJ, von Oerthel L, van der Linden AJ, Schellevis RD, Scheppink G, Holstege FC, Groot-Koerkamp MJ, van der Heide LP, Smidt MP.

Eur J Neurosci. 2013 Jan;37(1):23-32. doi: 10.1111/ejn.12022. Epub 2012 Oct 29.

PMID:
23106268
49.

Validation of a gene expression signature for assessment of lymph node metastasis in oral squamous cell carcinoma.

van Hooff SR, Leusink FK, Roepman P, Baatenburg de Jong RJ, Speel EJ, van den Brekel MW, van Velthuysen ML, van Diest PJ, van Es RJ, Merkx MA, Kummer JA, Leemans CR, Schuuring E, Langendijk JA, Lacko M, De Herdt MJ, Jansen JC, Brakenhoff RH, Slootweg PJ, Takes RP, Holstege FC.

J Clin Oncol. 2012 Nov 20;30(33):4104-10. doi: 10.1200/JCO.2011.40.4509. Epub 2012 Oct 8.

PMID:
23045589
50.

Two distinct repressive mechanisms for histone 3 lysine 4 methylation through promoting 3'-end antisense transcription.

Margaritis T, Oreal V, Brabers N, Maestroni L, Vitaliano-Prunier A, Benschop JJ, van Hooff S, van Leenen D, Dargemont C, Géli V, Holstege FC.

PLoS Genet. 2012 Sep;8(9):e1002952. doi: 10.1371/journal.pgen.1002952. Epub 2012 Sep 20.

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