Original publications by members of the Ekwall Epigenetics group


2014
Deneberg S, Kanduri M, Ali D, Bengtzen S, Karimi M, Qu Y, Kimby E, Mansouri L, Rosenquist R, Lennartsson A#, Sören Lehmann#. MicroRNA-34b/c on chromosome 11q23 is aberrantly methylated in chronic lymphocytic leukemi. Epigenetics in press.

Forrest ARR, Kawaji H, Rehli M, Baillie JK, de Hoon MJL, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M et al. (Ekwall K. number 61 and Lennartsson A. number 136 out of 250 authors) (2014): A promoter level mammalian expression atlas. Nature. doi: 10.1038/nature13182. Epub 2014 Mar 27.

Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Boyd M, Bornholdt J, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Otzen Bagger F, Jørgensen M, Andersen P, Bertin N, Rackham O, Burroughs A.M, Baillie J.K, Ishizu Y, Shimizu Y, Furhata E, Maeda S, Negishi Y, Mungall C, Meehan T.F, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub C.O, Heutink P, Hume D.A, Jensen T., Suzuki H, Hayashizaki Y, Müller F, Forrest A., Carninci P., Rehli M*, Sandelin A.* An atlas of active enhancers across human cell types and tissues. Nature doi: 10.1038/nature12787. Epub 2014 Mar 27.

Rönnerblad M, Andersson R, Olofsson T, Douagi I, Karimi M, Lehmann S, Hoof I, de Hoon M, Itoh M, Nago-Sato S, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Sandelin A, the FANTOM consortium, Ekwall K*, Arner E*, Lennartsson A* Analysis of the DNA methylome and transcriptome in granulopoiesis reveal timed changes and dynamic enhancer methylation. Blood. Epub 2014 Mar 27

Prasad P#, Rönnerblad M#, Arner E, Itoh M, Kawaji H, Lassmann T, Daub C, Forrest A.R.R, the FANTOM consortium, Lennartsson A*, Ekwall K*. High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesi. Blood. Epub 2014 Mar 27

Sadeghi L*, Siggens L*, Svensson JP#, Ekwall K#. Centromeric H2B monoubiquitination promotes non-coding transcription and chromatin integrity. Nat Struct Mol Biol. 21, 236–243 doi:10.1038/nsmb.2776.

Smialowska A, Djupedal I, Wang J, Kylsten P, Swoboda P, Ekwall K. RNAi mediates post-transcriptional repression of gene expression in fission yeast Schizosaccharomyces pombe. Biochem Biophys Res Commun. 2014 Jan 23. pii: S0006-291X(14)00081-3. doi: 10.1016/j.bbrc.2014.01.057.

Reviews and book chapters:
Siggens L, Ekwall K. Epigenetics, chromatin and genome organization: recent advances from the ENCODE project.
J Intern Med. 2014 Mar 8. doi: 10.1111/joim.122A31.

Allshire RC, Ekwall K. Epigenetics Regulation of Chromatin States in Schizosaccharomyces pombe. Cold Spring Harb Perspect Biol 2014;7:a018770 doi:10.1101/cshperspect.a018770

2013
Sandén C, Ageberg M, Petersson J, Lennartsson A, Gullberg U. Forced expression of the DEK-NUP214 fusion protein promotes proliferation dependent on upregulation of mTOR. BMC Cancer. 2013 Sep 27;13(1):440.

Vidovic K, Ullmark T, Rosberg B, Lennartsson A, Olofsson T, Nilsson B, Gullberg U. Leukemia associated mutant Wilms' tumor gene 1 protein promotes expansion of human hematopoietic progenitor cells. Leuk Res. 2013 Oct;37(10):1341-9.

Grövdal M, Karimi M, Tobiasson M, Reinius L, Jansson M, Ekwall K, Ungerstedt J, Kere J, Greco D, Hellström-Lindberg E. Azacitidine induces profound genome-wide hypomethylation in primary myelodysplastic bone marrow cultures but may also reduce histone acetylation. Leukemia. 2013 Sep 12. doi: 10.1038/leu.2013.265

Castillo AG, Pidoux AL, Catania S, Durand-Dubief M, Choi ES, Hamilton G, Ekwall K, Allshire RC. Telomeric repeats facilitate CENP-A(Cnp1) incorporation via telomere binding proteins. PLoS One. 2013 Jul 31;8(7):e69673. PMID: 23936074. Link

Melas PA, Lennartsson A, Vakifahmetoglu-Norberg H, Wei Y, Aberg E, Werme M, Rogdaki M, Mannervik M, Wegener G, Brené S, Mathé AA, Lavebratt C. Allele-specific programming of Npy and epigenetic effects of physical activity in a genetic model of depression. Transl Psychiatry. 2013 May 7;3:e255. PMID: 23652932. Link

Norman-Axelsson U, Durand-Dubief M, Prasad P, Ekwall K. DNA topoisomerase III localizes to centromeres and affects centromeric CENP-A levels in fission yeast. PLoS Genet. 2013 Mar;9(3):e1003371. PMID: 23516381. Link

Svensson JP, Quirós Pesudo L, McRee SK, Adeleye Y, Carmichael P, Samson LD. Genomic Phenotyping by Barcode Sequencing Broadly Distinguishes between Alkylating Agents, Oxidizing Agents, and Non-Genotoxic Agents, and Reveals a Role for Aromatic Amino Acids in Cellular Recovery after Quinone Exposure. PLoS One. 2013 Sep 9;8(9):e73736.

Vahey MD, Quiros Pesudo L, Svensson JP, Samson LD, Voldman J. Microfluidic genome-wide profiling of intrinsic electrical properties in Saccharomyces cerevisiae.Lab Chip. 2013 May 9. PMID: 23661198. Link

Reviews and book chapters:
Prasad P, Ekwall K. A snapshot of Snf2 enzymes in fission yeast. Biochem Soc Trans. 2013 Dec;41(6):1640-7. doi: 10.1042/BST20130145.

Steglich B, Sazer S, Ekwall K.Transcriptional regulation at the yeast nuclear envelope. Nucleus. 2013 Sep 6;4(5). Full text

2012
Pointner J*, Persson J*, Prasad P*, Norman-Axelsson U, Strålfors A, Khorosjutina O, Krietenstein N, Svensson JP, Ekwall K#, Korber P#. CHD1 remodelers space nucleosomes in vitro and link regular arrays to 5’ ends of genes in S. pombe. EMBO J. 31(23):4388-403. Link

Choi ES, Strålfors A, Castillo AG, Svensson JP, Pidoux AL, Ekwall K and Allshire RC. Factors which promote integrity of H3 chromatin during transcription prevent promiscuous deposition of CENP-ACnp1 in fission yeast. PLoS Genetics 8(9): e1002985. Link

Carlsten JO, Szilagyi Z, Liu B, Davila Lopez M, Szászi E, Djupedal I, Nyström T, Ekwall K, Gustafsson CM, Zhu X. Mediator Promotes CENP-A Incorporation at Fission Yeast Centromeres. Mol Cell Biol. 2012 Jul 30. Pubmed

Steglich B, Filion G, van Steensel B, Ekwall K. The inner nuclear membrane proteins Man1 and Ima1 link to two different types of chromatin at the nuclear periphery in S. pombe. Nucleus. 2012 Jan 1;3(1). Abstract

Ryan CJ*, Roguev A*, Patrick K, Xu J, Jahari H, Tong Z, Beltrao P, Shales M, Qu H, Collins SR, Kliegman JI, Jiang L, Kuo D, Tosti E, Kim HS, Edelmann W, Keogh MC, Greene D, Tang C, Cunningham P, Shokat KM, Cagney G, Svensson JP, Guthrie C, Espenshade PJ, Ideker T, Krogan NJ. Hierarchical modularity and the evolution of genetic interactomes across species. Molecular Cell 46(5): 691. Link

Svensson JP, Fry RC, Wang E, Somoza LA, Samson LD (2012) Identification of novel human damage response proteins targeted through yeast orthology. PLoS ONE 7(5): e37368. Link

2011

Svensson JP, Pesudo LQ, Fry RC, Adeleye YA, Carmichael P, Samson LD. Genomic phenotyping of the essential and non-essential yeast genome detects novel pathways for alkylation resistance. BMC Syst Biol. 2011 Oct 6;5:157. Full text

Deneberg S, Guardiola P, Lennartsson A, Qu Y, Gaidzik VI, Blanchet O, Karimi M, Bengtzen S, Nahi H, Uggla B, Tidefelt U, Höglund M, Paul C, Ekwall K, Doehner K, Lehmann S. "Prognostic DNA methylation patterns in cytogenetically normal acute myeloid leukemia are predefined by stem cell chromatin marks." Blood. Blood. 2011 Nov 17;118(20):5573-82. Full text

Sadeghi L, Bonilla C, Strålfors A, Ekwall K, Svensson JP. "Podbat: A Novel Genomic Tool Reveals Swr1-independent H2A.Z Incorporation at Gene Coding Sequences Through Epigenetic Meta Analysis". PLoS Comput Biol 7(8): e1002163. doi:10.1371/journal.pcbi.1002163. Full text.

Melas P.A., Rogdaki M., Lennartsson A., Björk K., Qi H., Witasp A., Werme M., Wegener G., Greengard P., Mathé A.A., Svenningsson P., Lavebratt C. "Antidepressant Treatment is Associated with Epigenetic Alterations in the Promoter of P11 in a Genetic Model of Depression". Int J Neuropsychopharmacol. 2011 Jun 20:1-11. Pubmed.

Choi ES, Stralfors A, Castillo AG, Durand-Dubief M, Ekwall K, Allshire RC. "Identification of non-coding transcripts from within CENP-A chromatin at fission yeast centromeres." J Biol Chem. 2011 Apr 28. Pubmed

Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF, Heiman DI, Young SK, Furuya K, Guo Y, Pidoux A, Chen HM, Robbertse B, Goldberg JM, Aoki K, Bayne EH, Berlin AM, Desjardins CA, Dobbs E, Dukaj L, Fan L, Fitzgerald MG, French C, Gujja S, Hansen K, Keifenheim D, Levin JZ, Mosher RA, Müller CA, Pfiffner J, Priest M, Russ C, Smialowska A, Swoboda P, Sykes SM, Vaughn M, Vengrova S, Yoder R, Zeng Q, Allshire R, Baulcombe D, Birren BW, Brown W, Ekwall K, Kellis M, Leatherwood J, Levin H, Margalit H, Martienssen R, Nieduszynski CA, Spatafora JW, Friedman N, Dalgaard JZ, Baumann P, Niki H, Regev A, Nusbaum C (2011) "Comparative Functional Genomics of the Fission Yeasts" Science.May 20;332(6032):930-6. Epub 2011 Apr 21. Full text

Strålfors A., J. Walfridsson, H. Bhuiyan, and K. Ekwall  (2011) ‘The FUN30 Chromatin Remodeler, Fft3, Insulates Centromeric and Subtelomeric Chromatin Domains from Euchromatin’ PLoS Genetics, Mar 17;7(3): e1001334.

Durand-Dubief, M, Svensson, JP, Persson, J and Ekwall, K (2011) "Topoisomerases, chromatin and transcription termination" Transcription 2(2):66-70.

Chang DY, Shi G, Durand-Dubief M, Ekwall K, Lu AL. (2011) ”The Role of MutY Homolog (Myh1) in Controlling the Histone Deacetylase Hst4 in the Fission Yeast Schizosaccharomyces pombe” J Mol Biol. Jan 21;405(3):653-65.

Reviews and book chapters:
Strålfors A, Ekwall K. (2011) "Heterochromatin andEuchromatin –Organization, Boundaries, and Gene Regulation" in Meyers: Encyclopedia of Molecular Cell Biology and Molecular Medicine: Epigenetic Regulation and Epigenomics, Second Edition. Edited by Robert A. Meyers. Wiley-VCH Verlag GmbH & Co. KGaA.

Prasad P, Ekwall K. (2011) New insights into how chromatin remodellers direct CENP-A to centromeres. EMBO J. 2011 May 18;30(10):1875-6. Full text

2010

Hogan C. , S. Aligianni, M. Durand-Dubief, J. Persson , W. Will, L. Wheeler, C.  Mathews, S. Elderkin, D. Oxley, K. Ekwall,  and P. Varga-Weisz  (2010) ”Fission yeast Iec1-Ino80 mediated nucleosome eviction regulates nucleotide and phosphate metabolism” Mol Cell Biol Feb;30(3):657-74

Lantermann, A., T. Straub, A. Stralfors, G-C Yuan, P. Korber*, K. Ekwall* (2010) ”Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae” Nature Structural & Molecular Biology Feb;17(2):251-7. *shared last authorship

Sinha, I, L.Buchanan, M. Rönnerblad, C. Bonilla, M. Durand-Dubief, A. Shevchenko, M. Grunstein, A. F. Stewart and K. Ekwall (2010) Genome wide mapping of histone modifications and mass spectrometry reveal an H4 acetylation bias in coding regions and a role for H3K36 methylation at gene promoters in fission yeast’ Epigenomics 2(3), 377–393

Mickaël Durand-Dubief, Jenna Persson, Ulrika Norman, Edgar Hartsuiker, Karl Ekwall (2010) ‘Topoisomerase I regulates open chromatin and controls gene expression in vivo’ EMBO journal, Jul 7;29(13):2126-34. Epub  Jun 4

Khorosjutina O, Wanrooij PH, Walfridsson J, Szilagyi Z, Zhu X, Baraznenok V, Ekwall K, Gustafsson CM (2010) A chromatin remodeling protein is a component of fission yeast mediator. J Biol Chem. 2010 Sep 24;285(39):29729-37

Karina Vidovic1, Emelie Svensson1, Björn Nilsson2, Britt Thuresson1, Andreas Lennartsson3 and Urban Gullberg1 The Wilms´ tumour gene 1 protein represses expression of the tumour suppressor Interferon Response Factor 8 in human hematopoietic and leukemic cells
Leukemia. 2010 May;24(5):992-1000

Reviews and book chapters:
Persson, J., K. Ekwall (2010). "CHD1 Remodelers Maintain Open Chromatin and Regulate the Epigenetics of Differentiation." Exp Cell Res. Mar 5. Full text

2009

Durand-Dubief, M. and K. Ekwall (2009). "Chromatin immunoprecipitation using microarrays." Methods Mol Biol 529: 279-95.

Johnsson, A., M. Durand-Dubief, Y. Xue-Franzen, M. Ronnerblad, K. Ekwall and A. Wright (2009). "HAT-HDAC interplay modulates global histone H3K14 acetylation in gene-coding regions during stress." EMBO Rep 10(9): 1009-14.

Lantermann, A., A. Stralfors, F. Fagerstrom-Billai, P. Korber and K. Ekwall (2009). "Genome-wide mapping of nucleosome positions in Schizosaccharomyces pombe." Methods 48(3): 218-25.

Buchanan, L., M. Durand-Dubief, A.,Roguev, C. Sakalar, B. Wilhelm, A. Stralfors, A.  Shevchenko, R. Aasland, A. Shevchenko, K. Ekwall and A. F. Stewart. (2009) The JmjC-protein Msc1 ensures that H2A.Z is not found in the wrong chromatin domains.  PLoS Genetics Nov;5(11):e1000726. Epub 2009 Nov 13.

Djupedal, I. Kos-Braun, R. Mosher, N. Soderholm, F. Simmer, T. Hardcastle, A. Fender, N. Heidrich, A. Kagansky, E. Bayne, E. Wagner, D. Baulcombe, R. Allshire, K. Ekwall  (2009) ”Analysis of small RNA in Fission yeast; centromeric siRNAs are potentially generated via a structured RNA” EMBO journal, Dec 16;28(24):3832-44.

Harukazu Suzuki, Alistair R. R. Forrest, Erik van Nimwegen, Carsten O.Daub, Timo Lassmann Timothy Ravasi, Yuki Hasegawa, Michiel J. L. de Hoon, Shintaro Katayama, Katharine M. Irvine, Kate Schroder, Piero Carninci, Altuna Akalin, Yoshinari Ando, Erik Arner, Maki Asada, Hiroshi Asahara,Timothy Bailey, Vladimir B. Bajic, Piotr Balwierz, Denis Bauer, Anthony G. Beckhouse, Nicolas Bertin, Johan Björkegren, Frank Brombacher, Erika Bulger, Alistair M. Chalk, Joe Chiba, Nicole Cloonan, Adam Dawe, Josee Dostie, Pär G. Engström, Magbubah Essack, Geoffrey Faulkner, J Lynn Fink, David Fredman, Isao Fujimori, Masaaki Furuno, Takashi Gojobori, Julian Gough, Sean M. Grimmond, Mika Gustafsson, Megumi Hashimoto, Takehiro Hashimoto, Mariko Hatakeyama, Susanne Heinzel, Winston Hide, Oliver Hofmann, Michael Hörnquist, Lukasz Huminiecki, Kazuho Ikeo, Naoko Imamoto, Satoshi Inoue, Yusuke Inoue, Ryoko Ishihara, Takao Iwayanagi, Anders Jacobsen, Mutsumi Kanamori-Katayama, Mandeep Kaur, Hideya Kawaji, Markus C. Kerr, Ryuichiro Kimura, Syuhei Kimura, Yasumasa Kimura, Hiroaki Kitano, Hisashi Koga,Toshio Kojima, Shinji Kondo, Takeshi Konno, Anders Krogh, Adele Kruger, Atsutaka Kubosaki, Ajit Kumar, Boris Lenhard, Andreas Lennartsson, Morten Lindow, Marina Lizio, Cameron MacPherson, Norihiro Maeda, Christopher A. Maher, Monique Maqungo, Jessica Mar, Nicholas A. Matigian, Hideo Matsuda, John S. Mattick, Stuart Meier, Sei Miyamoto, Etsuko Miyamoto-Sato, Kazuhiko Nakabayashi, Yutaka Nakachi, Sanne Nygaard, Toshitsugu Okayama, Yasushi Okazaki, Haruka Okuda-Yabukami, Valerio Orlando, Mikhail Pachkov, Nikolai Petrovsky, Charles Plessy, John Quackenbush, Aleksandar Radovanovic, Michael Rehli, Rintaro Saitoh, Albin Sandelin, Sebastian Schmeier, Christian Schönbach, Ariel S. Schwartz, Colin A. Semple, Miho Sera, Jessica Severin, Katsuhiko Shirahige, Cas Simons, George St. Laurent, Masanori Suzuki, Takahiro Suzuki, Ryan J. Taft, Yoichi Takenaka, Kai Tan, Martin S. Taylor, Rohan D. Teasdale, Jesper Tegnér, Sarah Teichmann, Yasuhiro Tomaru, Eivind Valen, Claes Wahlestedt, Kazunori Waki, Andrew Waterhouse, Christine A. Wells, Ole Winther, Linda Wu, Kazumi Yamaguchi, Hiroshi Yanagawa, Jun Yasuda, Mihaela Zavolan, David A. Hume. A complex transcriptional network controls growth arrest and differentiation in a human myeloid leukemia cell line. The FANTOM consortium and RIKEN Genome Exploration Research Group (Genome Network Project Expression Cluster Workshop). The FANTOM Consortium (Genome Network Project, Expression Cluster Workshop) Nat Genet. 2009 May;41(5):553-62

Reviews and book chapters:
Djupedal, I. and K. Ekwall (2009). "Epigenetics: heterochromatin meets RNAi." Cell Res 19(3): 282-95.

Lennartsson, A. and Ekwall, K. (2009) "Histone modifications and epigenetic codes." Biochim Biophys Acta. Sep;1790(9):863-8. Full text

2008

Dunleavy E, Pidoux A, Monet M, Bonilla C, Richardson W, Hamilton G, Ekwall K, McLaughlin P, Allshire R: A NASP (N1/N2)-related protein Sim3, binds CENP-A and is required for its deposition at fission yeast centromeres. Molecular Cell 2008 Dec 28;28(6):1029-44

Pascal Bernard, Christine Schmidt, Sabine Vaur, Sonia Dheur, Julie Drogat, Sylvie Genier, Karl Ekwall, Frank Uhlman and Jean-Paul Javerzat: Cohesin turn-over on fission yeast G1 chromosomes is down-regulated during S phase independently of DNA replication. EMBO journal, 2008 Jan 9;27(1):111-21. Epub 2007 Dec 13

Bayne EH, Portoso M, Kagansky A, Kos-Braun IC, Urano T, Ekwall K, Alves F, Rappsilber J, Allshire RC: Splicing factors facilitate RNAi-directed silencing in fission yeast. Science. 2008 Oct 24;322(5901):602-6.56.'

Fry RC*, Svensson JP*, Valiathan C*, Wang E, Hogan BJ, Bhattacharya S, Bugni J, Whittaker C and Samson LD. Genomic predictors of interindividual differences in response to DNA damaging agents. Genes Dev. 2008 22(19):*shared first authors

 

2007

Fagerström-Billai, F., Durand-Dubief, M., Ekwall, K. and A.P.H. Wright (2007) ’Individual subunits of the Ssn6-Tup11/12 co-repressor are selectively required for repression of different target genes.’ Mol Cell Biol, 27(3):1069-82.

Sara Isaac, Julian Walfridsson, Tal Zohar, David Lazar, Tamar Kahan, Karl Ekwall and Amikam Cohen (2007) ‘Interaction of Epe1 with the Heterochromatin Assembly Pathway in Schizosaccharomyces pombe.’ Genetics Apr;175(4):1549-60.

Durand-Dubief, M., Sinha, I., Fagerström-Billai, F., Bonilla, C. , Wright, A. , Grunstein, M. and Ekwall, K. (2007) Specific functions for the fission yeast Sirtuins Hst2 and Hst4 in gene regulation and retrotransposon silencing. EMBO journal, May 16;26(10):2477-88. Epub 2007 Apr 19.

Opel, M., Lando, D.Bonilla, C., Trewick, S., Boubaka, A., Walfridsson, J., Cauwood, J., Werler, P., Carr, A., Kouzarides, T., Murzina, N., Allsire, R. , Ekwall, K. , Laue, E. (2007) Genome-Wide Studies of Histone Demethylation Catalysed by the Fission Yeast Homologues of Mammalian LSD1. PLOS One, Issue 4: (April 18) e 386

Walfridsson, J., Khorosjutina, O., Matikainen, P., Gustafsson, C.M. and Ekwall, K. (2007). A genome-wide role for CHD remodelling factors and Nap1 in nucleosome disassembly. EMBO journal, May 17; [Epub ahead of print]

Lejeune E, Bortfeld M, White SA, Pidoux AL, Ekwall K, Allshire RC, Ladurner AG. The chromatin-remodeling factor FACT contributes to centromeric heterochromatin independently of RNAi. Curr Biol. 2007 Jul 17;17(14):1219-24. Epub 2007 Jul 5.

van Bezooijen RL, Svensson JP, Eefting D, Visser A, van der Horst G, Karperien M, Quax PH, Vrieling H, Papapoulos SE, ten Dijke P, Lowik CW. Wnt but not BMP signaling is involved in the inhibitory action of sclerostin on BMP-stimulated bone formation. J Bone Miner Res. 2007 22(1):19-28.

Kruse JJ*, Svensson JP*, Huigsloot M*, Giphart-Gassler M, Schoonen WG, Polman JE, Horbach GJ, van de Water B, Vrieling H. A portrait of cisplatin-induced transcriptional changes in mouse embryonic stem cells reveals a dominant p53-like response. Mutat Res. 2007 617(1-2):58-70.

Fry RC, Navasumrit P, Valiathan C, Hogan BJ, Luo M, Bhattacharya S, Svensson JP, Kandjanapa K, Soontararuks S,  Nookabkaew S, Mahidol C, Ruchirawat M and Samson LD.  Activation of inflammation/NF-κB signaling in infants born to arsenic exposed mothers. PLoS Genetics 2007 3(11): e207.

Rusyn I, Fry RC, Begley TJ, Klapacz J, Ambrose M, Hogan BJ, Svensson JP, Samson LD. Transcriptional networks in S. cerevisiae linked to an accumulation of base excision repair intermediates. PLoS ONE 2007 2(11):e1252.

 

2006
Sinha, I., Wiren, M., and K. Ekwall (2006) ’Histone modification patterns in fission yeast’ Chromosome Research: 14:95-105.

Zhu, X., Wiren, M., Sinha, I., Rasmussen, N., Linder, T., Holmberg, S., Ekwall, K. and C., Gustafsson (2006) ‘Genome wide occupancy profile of Mediator and the Srb8-11 module reveals interactions with coding regions’. Molecular Cell 22: 179-192.

Lennartsson A., Vidovic K., Gullberg U (2006) All-Trans Retinoic Acid-Induced Expression of Bactericidal/Permeability-Increasing Protein (BPI) in Myeloid Cells Correlates to Binding of C/EBPbeta and C/EBPepsilon to the BPI Promoter. J Leukoc Biol. Jul;80(1):196-203

Svensson JP, Stalpers LJ, Esveldt-van Lange RE, Franken NA, Haveman J, Klein B, Turesson I, Vrieling H, Giphart-Gassler M. Analysis of gene expression using gene sets discriminates cancer patients with and without late radiation toxicity. PLoS Med. 2006 Oct;3(10):e422.

 

2005

Walfridsson, J. Bjerling, P. Thalen, M., Yoo, E-J., Park, S-D. and K Ekwall (2005) ’The CHD remodelling factor Hrp1 stimulates CENP-A loading to centromeres ’ Nucleic Acids Res. 33: 2868-79.

Wirén, M:,  R. A. Silverstein, I. Sinha, J. Walfridsson, H. Lee, P. Laurenson, L. Pillus, D. Robyr, M. Grunstein, and K. Ekwall. (2005) ‘Genome wide analysis of nucleosome density histone acetylation and HDAC function in fission yeast ‘ EMBO J 24:2906-18

Djupedal, I., Portoso, M., Spåhr, H., Bonilla, C., Gustafsson, C., Allshire, R., Ekwall, K. (2005) ‘RNA pol II subunit Rpb7 promotes centromeric transcription and RNAi-directed chromatin silencing’. Genes & Development 19:2301-2306

Geraldine Canny1, Ciara Brennan1, Andreas Lennartsson2, Urban Gullberg2, Elke Cario3, Ofer Levy4, Charles N. Serhan1 and Sean P. Colgan1 (2005) Functional and Biochemical Characterization of EpithelialBactericidal / Permeability-Increasing Protein (BPI) Am J Physiol Gastrointest Liver Physiol.

Boerma M, van der Wees CG, Vrieling H, Svensson JP, Wondergem J, van der Laarse A, Mullenders LH, van Zeeland AA. Microarray analysis of gene expression profiles of cardiac myocytes and fibroblasts after mechanical stress, ionising or ultraviolet radiation. BMC Genomics. 2005 6(1):6.

Svensson JP, de Menezes RX, Turesson I, Giphart-Gassler M, Vrieling H. Dissecting systems-wide data using mixture models: application to identify affected cellular processes. BMC Bioinformatics. 2005 6:177.

Jahangir Tafrechi RS, Svensson PJ, Janssen GM, Szuhai K, Maassen JA, Raap3AK. Distinct nuclear gene expression profiles in cells with mtDNA depletion and homoplasmic A3243G mutation. Mutat Res. 2005 Oct 15;578(1-2):43-52.

Lennartsson A., Garwicz D., Lindmark A. and Gullberg U (2005) The Proximal Promoter of Human Cathepsin G Conferring Myeloid-Specific Expression includes C/EBP, c-myb and PU.1 Binding Sites Gene. Aug 15;356:193-202

Lennartsson A.,Pieters K., Vidovic K. and Gullberg U (2005) A murine antibacterial orthologue to human Bactericidal/Permeability Increasing protein (BPI) is expressed in testis, epididymis and bone marrow J Leukoc Biol. Mar;77(3):369-77

Garwicz D, Lennartsson A, Jacobsen SEW*, Gullberg U, Lindmark A, (2005) Biosynthetic profiles of neutrophil serine proteases in a human bone marrow-derived cellular myeloid differentiation model Haematologica, Jan; 90 (1):38-44

 

2004

Xue, Y., Haas, S, Brino, L., Gusnanto, A., Reimers, M., Talibi, D., Vingron, M., Ekwall, K. and A. Wright (2004) ‘A DNA microarray for genome-wide gene expression analysis in fission yeast’. Yeast. 21:25-39.

Carmichael JB, Provost P, Ekwall K, Hobman TC (2004) ” Ago1 and Dcr1, Two Core Components of the RNA Interference Pathway, Functionally Diverge from Rdp1 in Regulating Cell Cycle Events in Schizosaccharomyces pombe” Mol. Biol. of the Cell 15: 1425-35.

Bjerling PB. K. Ekwall, R. Egel and G. Thon (2004) ‘ A novel silencing factor, Clr2, is necessary for transcriptional silencing at various locations in the fission yeast Schizosaccharomyces pombe.’ Nucleic Acids Res. 32: 4421-28.

 

2003

Silverstein, R. A., Richardson W., Levin H., Allshire, R., and Ekwall, K (2003) ’A New Role for the Transcriptional Corepressor SIN3; Regulation of Centromeres’. Current Biology 13, 68-72.

Nakayama, J., Xiao G., Noma K., Malikzay A., Bjerling P., Ekwall K., Kobayashi R. and S. I Grewal (2003) ’Alp13, an MRG family protein, is a component of fission yeast Clr6 histone deacetylase required for genomic integrity’ EMBO J. 22, 2776-2787.

Okorokova-Facanha AL, Okorokov LA, Ekwall K. (2003) An inventory of the P-type ATPases in the fission yeast Schizosaccharomyces pombe. Curr Genet. 43:273-80.

Appelgren, H., Kniola, B., and Ekwall K. (2003) ’Distinct centromere domain structures with separate functions demonstrated in live fission yeast cells’. J. Cell Science. 116:4035-
42.

Lennartsson A, Pieters K, Ullmark T, Vidovic K, Gullberg U (2003) AML-1, PU.1, and Sp3 regulate expression of human bactericidal/permeability increasing protein. Biochem Biophys Res Commun. Nov 28;311(4):853-63

 

2002

Bjerling, P, Silverstein, R., Thon, G., Caudy, A., Grewal, S. and K . Ekwall (2002) "Functional divergence of histone deacetylases by distinct localisation and specificity in fission yeast" Mol Cell Biol 22:2170-2181.

Okorokova Façanha A, Appelgren H, Tabish M, Okorokov L and K. Ekwall (2002) ‘The endoplasmic reticulum cation P-type ATPase Cta4p is required for control of cell shape and microtubule dynamics’ Journal of Cell Biology 157:1029-1039.

Yoo, Y. J., Jang, K., Lee, M., Bjerling, P., Kim, J., Ekwall, K., Seong, R., and S. D. Park (2002) “Hrp3, a chromodomain helicase/ATPase DNA binding protein, is required for heterochromatin silencing in fission yeast” Bioch. And Biophys. Res. Comm. 295:970-974.

Provost, P., Silverstein, R. A., Walfridsson, J., Djupedal, I., Kniola, B., Wright, A., Samuelsson, B., Rådmark, O., and Ekwall, K. (2002) ’Dicer is Required for Chromosome Segregation and Gene Silencing in Fission Yeast Cells’. PNAS 99, 16648-53.

 

2001

Kniola, B., O’Toole, E., McIntosh, J. R., Mellone, B., Allshire, R., Mengarelli, S., Hultenby, K., and K. Ekwall (2001) ”The domain structure of centromeres is conserved from fission yeast to humans.” Mol. Biol. of the Cell 12: 2767-2775.

 

Highlights before 2000

Ekwall, K., T. Olsson, B. M. Turner, G. Cranston and R. C. Allshire (1997). “Transient inhibition of histone deacetylation alters the structural and functional imprint at fission yeast centromeres.” Cell 91(7): 1021-32.

Ekwall, K., J. P. Javerzat, A. Lorentz, H. Schmidt, G. Cranston and R. Allshire (1995). “The chromodomain protein Swi6: a key component at fission yeast centromeres.” Science 269(5229): 1429-31.

 

Previous review articles and book chapters

2008
Djupedal, I., and Ekwall, K. (2008) "The paradox of silent heterochromatin." Science, May 2;320(5876):624-5.65.

Durand-Dubief, M. and Ekwall K (2008) "Heterochromatin tells CENP-A where to go." BioEssays 30: 526-529.64.

2007
Ekwall K. (2007) "Epigenetic control of centromere behavior". Annual Reviews in Genetics, 41:63-81.

Ekwall, K (2007) "ARC escorts siRNAs in heterochromatin assembly." Nature Struct & Mol. Biol. 14:178-179.

2005
Ekwall, K (2005) ’Genome wide analysis of HDAC function." Trends in Genetics 21:608- 614.

Silverstein, R. A. and Ekwall, K (2005) "Sin3: A flexible regulator of global gene expression and genome stability." Current Genetics 47:1-17.