Research library: Transcription/Chromatin
2008:
| December
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Other Years: 2002 | 2003 | 2004 | 2005 | 2006 | 2007
December
letter
Activation of TGF-β/activin signalling resets the circadian clock through rapid induction of Dec1 transcripts
Naohiro Kon et al.
Nature Cell Biology 10, 1463–1469
(December 2008); doi:10.1038/ncb1806
| Summary | Full Text (HTML / PDF) |
review
Transcriptional regulation by AIRE: molecular mechanisms of central tolerance
Pärt Peterson, Tõnis Org & Ana Rebane
Nature Reviews Immunology 8, 948–957
(December 2008); doi:10.1038/nri2450
| Summary | Full Text (HTML / PDF) |
review
Epigenetic regulation of centromeric chromatin: old dogs, new tricks?
Robin C. Allshire & Gary H. Karpen
Nature Reviews Genetics 9, 923–937
(December 2008); doi:10.1038/nrg2466
| Summary | Full Text (HTML / PDF) |
article
Single-RNA counting reveals alternative modes of gene expression in yeast
Daniel Zenklusen, Daniel R Larson & Robert H Singer
Nature Structural & Molecular Biology 15, 1263–1271
(December 2008); doi:10.1038/nsmb.1514
| Summary | Full Text (HTML / PDF) |
article
Bach1 inhibits oxidative stress–induced cellular senescence by impeding p53 function on chromatin
Yoshihiro Dohi et al.
Nature Structural & Molecular Biology 15, 1246–1254
(December 2008); doi:10.1038/nsmb.1516
| Summary | Full Text (HTML / PDF) |
letter
Regulation of ERBB2 by oestrogen receptor–PAX2 determines response to tamoxifen
Antoni Hurtado et al.
Nature 456, 663–666
(04 December 2008); doi:10.1038/nature07483
| Summary | Full Text (HTML / PDF) |
review
Transcription-coupled DNA repair: two decades of progress and surprises
Philip C. Hanawalt & Graciela Spivak
Nature Reviews Molecular Cell Biology 9, 958–970
(December 2008); doi:10.1038/nrm2549
| Summary | Full Text (HTML / PDF) |
November
letter
A fast, robust and tunable synthetic gene oscillator
Jesse Stricker et al.
Nature 456, 516–519
(27 November 2008); doi:10.1038/nature07389
| Summary | Full Text (HTML / PDF) |
letter
53BP1 promotes non-homologous end joining of telomeres by increasing chromatin mobility
Nadya Dimitrova, Yi-Chun M. Chen, David L. Spector & Titia de Lange
Nature 456, 524–528
(27 November 2008); doi:10.1038/nature07433
| Summary | Full Text (HTML / PDF) |
letter
53BP1 facilitates long-range DNA end-joining during V(D)J recombination
Simone Difilippantonio et al.
Nature 456, 529–533
(27 November 2008); doi:10.1038/nature07476
| Summary | Full Text (HTML / PDF) |
review
Biological principles of microRNA-mediated regulation: shared themes amid diversity
Alex S. Flynt & Eric C. Lai
Nature Reviews Genetics 9, 831–842
(November 2008); doi:10.1038/nrg2455
| Summary | Full Text (HTML / PDF) |
article
A quantitative model of transcription factor–activated gene expression
Harold D Kim & Erin K O'Shea
Nature Structural & Molecular Biology 15, 1192–1198
(November 2008); doi:10.1038/nsmb.1500
| Summary | Full Text (HTML / PDF) |
article
Insights into interferon regulatory factor activation from the crystal structure of dimeric IRF5
Weijun Chen et al.
Nature Structural & Molecular Biology 15, 1213–1220
(November 2008); doi:10.1038/nsmb.1496
| Summary | Full Text (HTML / PDF) |
article
Structure of the intact PPAR-γ–RXR-α nuclear receptor complex on DNA
Vikas Chandra et al.
Nature 456, 350–356
doi:10.1038/nature07413
| Summary | Full Text (HTML / PDF) |
letter
A fasting inducible switch modulates gluconeogenesis via activator/coactivator exchange
Yi Liu et al.
Nature 456, 269–273
(13 November 2008); doi:10.1038/nature07349
| Summary | Full Text (HTML / PDF) |
article
Suppressed NFAT-dependent VEGFR1 expression and constitutive VEGFR2 signaling in infantile hemangioma
Masatoshi Jinnin et al.
Nature Medicine 14, 1236–1246
(November 2008); doi:10.1038/nm.1877
| Summary | Full Text (HTML / PDF) |
news and views
Healing hemangiomas
Lena Claesson-Welsh
Nature Medicine 14, 1147–1148
(November 2008); doi:10.1038/nm1108-1147
| Full Text (HTML / PDF) |
review
The von Hippel–Lindau tumour suppressor protein: O2 sensing and cancer
William G. Kaelin Jr
Nature Reviews Cancer 8, 865–873
(November 2008); doi:10.1038/nrc2502
| Summary | Full Text (HTML / PDF) |
article
Functional organization of the transcriptome in human brain
Michael C Oldham et al.
Nature Neuroscience 11, 1271–1282
(November 2008); doi:10.1038/nn.2207
| Summary | Full Text (HTML / PDF) |
news and views
What is in the brain soup?
Károly Mirnics
Nature Neuroscience 11, 1237–1238
(November 2008); doi:10.1038/nn1108-1237
| Full Text (HTML / PDF) |
article
FANCI phosphorylation functions as a molecular switch to turn on the Fanconi anemia pathway
Masamichi Ishiai et al.
Nature Structural & Molecular Biology 15, 1138–1146
(November 2008); doi:10.1038/nsmb.1504
| Summary | Full Text (HTML / PDF) |
news and views
A major switch for the Fanconi anemia DNA damage–response pathway
Weidong Wang
Nature Structural & Molecular Biology 15, 1128–1130
(November 2008); doi:10.1038/nsmb1108-1128
| Full Text (HTML / PDF) |
article
The H3K36 demethylase Jhdm1b/Kdm2b regulates cell proliferation and senescence through p15Ink4b
Jin He, Eric M Kallin, Yu-ichi Tsukada & Yi Zhang
Nature Structural & Molecular Biology 15, 1169–1175
(November 2008); doi:10.1038/nsmb.1499
| Summary | Full Text (HTML / PDF) |
news and views
An INKlination for epigenetic control of senescence
Gordon Peters
Nature Structural & Molecular Biology 15, 1133–1134
(November 2008); doi:10.1038/nsmb1108-1133
| Full Text (HTML / PDF) |
letter
Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases
Pilar Redondo et al.
Nature 456, 107–111
(6 November 2008); doi:10.1038/nature07343
| Summary | Full Text (HTML / PDF) |
letter
Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks
Daniel Zilberman, Devin Coleman-Derr, Tracy Ballinger & Steven Henikoff
Nature 456, 125–129
(6 November 2008); doi:10.1038/nature07324
| Summary | Full Text (HTML / PDF) |
letter
Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs
Kouji Hirota, Tomoichiro Miyoshi, Kazuto Kugou, Charles S. Hoffman, Takehiko Shibata & Kunihiro Ohta
Nature 456, 130–134
(6 November 2008); doi:10.1038/nature07348
| Summary | Full Text (HTML / PDF) |
article
Priming for T helper type 2 differentiation by interleukin 2—mediated induction of interleukin 4 receptor α-chain expression
Wei Liao et al.
Nature Immunology 9, 1288–1296
(November 2008); doi:10.1038/ni.1656
| Summary | Full Text (HTML / PDF) |
article
Interactions among the transcription factors Runx1, RORγt and Foxp3 regulate the differentiation of interleukin 17–producing T cells
Fuping Zhang, Guangxun Meng & Warren Strober
Nature Immunology 9, 1297–1306
(November 2008); doi:10.1038/ni.1663
| Summary | Full Text (HTML / PDF) |
October
article
Activity-dependent regulation of inhibitory synapse development by Npas4
Yingxi Lin et al.
Nature 455, 1198–1204
(30 October 2008); doi:10.1038/nature07319
| Summary | Full Text (HTML / PDF) |
letter
ROS3 is an RNA-binding protein required for DNA demethylation in Arabidopsis
Xianwu Zheng et al.
Nature 455, 1259–1262
(30 October 2008); doi:10.1038/nature07305
| Summary | Full Text (HTML / PDF) |
article
Proof-by-synthesis of the transcriptional logic of mammalian circadian clocks
Maki Ukai-Tadenuma, Takeya Kasukawa & Hiroki R. Ueda
Nature Cell Biology 10, 1154–1163
(October 2008); doi:10.1038/ncb1775
| Summary | Full Text (HTML / PDF) |
perspective
Replication licensing and cancer — a fatal entanglement?
J. Julian Blow & Peter J. Gillespie
Nature Reviews Cancer 8, 799–806
(October 2008); doi:10.1038/nrc2500
| Summary | Full Text (HTML / PDF) |
analysis
MicroRNAs in the Hox network: an apparent link to posterior prevalence
Soraya Yekta, Clifford J. Tabin & David P. Bartel
Nature Reviews Genetics 9, 789–796
(October 2008); doi:10.1038/nrg2400
| Summary | Full Text (HTML / PDF) |
article
Autonomous onset of the circadian clock in the zebrafish embryo
Marcus P S Dekens and David Whitmore
The EMBO Journal 27, 2757–2765
(October 2008); doi:10.1038/emboj.2008.183
| Summary | Full Text (HTML / PDF) |
perspective
Transcription-independent functions of MYC: regulation of translation and DNA replication
Michael D. Cole & Victoria H. Cowling
Nature Reviews Molecular Cell Biology 9, 810–815
(October 2008); doi:10.1038/nrm2467
| Summary | Full Text (HTML / PDF) |
article
Notch2 integrates signaling by the transcription factors RBP-J and CREB1 to promote T cell cytotoxicity
Yoichi Maekawa et al.
Nature Immunology 9, 1140–1147
(October 2008); doi:10.1038/ni.1649
| Summary | Full Text (HTML / PDF) |
letter
The Creb1 coactivator Crtc1 is required for energy balance and fertility
Judith Y Altarejos et al.
Nature Medicine 14, 1112–1117
(October 2008); doi:10.1038/nm.1866
| Summary | Full Text (HTML / PDF) |
review
The genetics of mammalian circadian order and disorder: implications for physiology and disease
Joseph S. Takahashi, Hee-Kyung Hong, Caroline H. Ko & Erin L. McDearmon
Nature Reviews Genetics 9, 764–775
(October 2008); doi:10.1038/nrg2430
| Summary | Full Text (HTML / PDF) |
article
Sae2, Exo1 and Sgs1 collaborate in DNA double-strand break processing
Eleni P. Mimitou & Lorraine S. Symington
Nature 455, 770–774
(9 October 2008); doi:10.1038/nature07312
| Summary | Full Text (HTML / PDF) |
news and views
Molecular biology: DNA endgames
Hannah L. Klein
Nature 455, 740–741
(9 October 2008); doi:10.1038/455740a
| Full Text (HTML / PDF) |
perspective
Is there a code embedded in proteins that is based on post-translational modifications?
Robert J. Sims 3rd & Danny Reinberg
Nature Reviews Molecular Cell Biology 9, 815–820
(October 2008); doi:10.1038/nrm2502
| Summary | Full Text (HTML / PDF) |
review
Chemical probes for histone-modifying enzymes
Philip A Cole
Nature Chemical Biology 4, 590–597
(October 2008); doi:10.1038/nchembio.111
| Summary | Full Text (HTML / PDF) |
article
In vivo reprogramming of adult pancreatic exocrine cells to β-cells
Qiao Zhou, Juliana Brown, Andrew Kanarek, Jayaraj Rajagopal & Douglas A. Melton
Nature 455, 627–632
(2 October 2008); doi:10.1038/nature07314
| Summary | Full Text (HTML / PDF) |
news and views
Regenerative medicine: Short cut to cell replacement
Robert Blelloch
Nature 455, 604–605
(2 October 2008); doi:10.1038/455604a;
| Full Text (HTML / PDF) |
letter
Modelling Myc inhibition as a cancer therapy
Laura Soucek et al.
Nature 455, 679–683
(2 October 2008); doi:10.1038/nature07260
| Summary | Full Text (HTML / PDF) |
letter
CDK targets Sae2 to control DNA-end resection and homologous recombination
Pablo Huertas, Felipe Cortés-Ledesma, Alessandro A. Sartori, Andrés Aguilera & Stephen P. Jackson
Nature 455, 689–692
(2 October 2008); doi:10.1038/nature07215
| Summary | Full Text (HTML / PDF) |
article
Cascading suppression of transcriptional silencers by ThPOK seals helper T cell fate
Sawako Muroi et al.
Nature Immunology 9, 1113–1121
(October 2008); doi:10.1038/ni.1650
| Summary | Full Text (HTML / PDF) |
article
Distinct functions for the transcription factors GATA-3 and ThPOK during intrathymic differentiation of CD4+ T cells
Lie Wang et al.
Nature Immunology 9, 1122–1130
(October 2008); doi:10.1038/ni.1647
| Summary | Full Text (HTML / PDF) |
article
ThPOK acts late in specification of the helper T cell lineage and suppresses Runx-mediated commitment to the cytotoxic T cell lineage
Takeshi Egawa & Dan R Littman
Nature Immunology 9, 1131–1139
(October 2008); doi:10.1038/ni.1652
| Summary | Full Text (HTML / PDF) |
news and views
Putting ThPOK in place
J Jeremiah Bell & Avinash Bhandoola
Nature Immunology 9, 1095–1096
(October 2008); doi:10.1038/ni1008-1095;
| Full Text (HTML / PDF) |
September
letter
CDK8 is a colorectal cancer oncogene that regulates β-catenin activity
Ron Firestein et al.
Nature 455, 547–551
(25 September 2008); doi:10.1038/nature07179
| Summary | Full Text (HTML / PDF) |
letter
E2F1 represses β-catenin transcription and is antagonized by both pRB and CDK8
Erick J. Morris et al.
Nature 455, 552–556
(25 September 2008); doi:10.1038/nature07310
| Summary | Full Text (HTML / PDF) |
news and views
Cancer: Entangled pathways
René Bernards
Nature 455, 479–480
(September 2008); doi:10.1038/455479a;
| Full Text (HTML / PDF) |
article
A ribosomal protein L23-nucleophosmin circuit coordinates Miz1 function with cell growth
Michael Wanzel et al.
Nature Cell Biology 10, 1051–1061
(25 September 2008); doi:10.1038/ncb1764
| Summary | Full Text (HTML / PDF) |
letter
Plk1-dependent phosphorylation of FoxM1 regulates a transcriptional programme required for mitotic progression
Zheng Fu et al.
Nature Cell Biology 10, 1076–1082
(25 September 2008); doi:10.1038/ncb1767
| Summary | Full Text (HTML / PDF) |
review
A complex barcode underlies the heterogeneous response of p53 to stress
Fiona Murray-Zmijewski, Elizabeth A. Slee & Xin Lu
Nature Reviews Molecular Cell Biology 9, 702–712
(September 2008); doi:10.1038/nrm2451
| Summary | Full Text (HTML / PDF) |
article
The HP1–p150/CAF-1 interaction is required for pericentric heterochromatin replication and S-phase progression in mouse cells
Jean-Pierre Quivy, Annabelle Gérard, Adam J L Cook, Danièle Roche & Geneviève Almouzni
Nature Structural & Molecular Biology 15, 972–979
(September 2008) doi:10.1038/nsmb.1470
| Summary | Full Text (HTML / PDF) |
letter
Regulatory networks define phenotypic classes of human stem cell lines
Franz-Josef Müller et al.
Nature 455, 401–405
(18 September 2008); doi:10.1038/nature07213
| Summary | Full Text (HTML / PDF) |
letter
S-nitrosylation of histone deacetylase 2 induces chromatin remodelling in neurons
Alexi Nott, P. Marc Watson, James D. Robinson, Luca Crepaldi & Antonella Riccio
Nature 455, 411–415
(18 September 2008); doi:10.1038/nature07238
| Summary | Full Text (HTML / PDF) |
letter
Ripples from neighbouring transcription
Miki Ebisuya, Takuya Yamamoto, May Nakajima & Eisuke Nishida
Nature Cell Biology 10, 1106–1113
(September 2008); doi:10.1038/ncb1771
| Summary | Full Text (HTML / PDF) |
news and views
Non-coding RNA transcription: turning on neighbours
Piero Carninci
Nature Cell Biology 10, 1023–1024
(September 2008); doi:10.1038/ncb0908-1023
| Full Text (HTML / PDF) |
review
Conserved functions of the pRB and E2F families
Sander van den Heuvel & Nicholas J. Dyson
Nature Reviews Molecular Cell Biology 9, 713–724
(September 2008); doi:10.1038/nrm2469
| Summary | Full Text (HTML / PDF) |
perspective
Hypoxia, HIF1 and glucose metabolism in the solid tumour
Nicholas C. Denko
Nature Reviews Cancer 8, 705–713
(September 2008); doi:10.1038/nrc2468
| Summary | Full Text (HTML / PDF) |
review
The multiple lives of NMD factors: balancing roles in gene and genome regulation
Olaf Isken & Lynne E. Maquat
Nature Reviews Genetics 9, 699–712
(September 2008); doi:10.1038/nrg2402
| Summary | Full Text (HTML / PDF) |
review
The genetics of early telencephalon patterning: some assembly required
Jean M. Hébert & Gord Fishell
Nature Reviews Neuroscience 9, 678–685
(September 2008); doi:10.1038/nrn2463
| Summary | Full Text (HTML / PDF) |
letter
Heterochromatin links to centromeric protection by recruiting shugoshin
Yuya Yamagishi, Takeshi Sakuno, Mari Shimura & Yoshinori Watanabe
Nature 455, 251–255
(11 September 2008); doi:10.1038/nature07217
| Summary | Full Text (HTML / PDF) |
review
A new MAFia in cancer
Alain Eychène, Nathalie Rocques & Celio Pouponnot
Nature Reviews Cancer 8, 683–693
(September 2008); doi:10.1038/nrc2460
| Summary | Full Text (HTML / PDF) |
article
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
Anton Valouev et al.
Nature Methods 5, 829–834
(September 2008); doi:10.1038/nmeth.1246
| Summary | Full Text (HTML / PDF) |
article
Widespread changes in protein synthesis induced by microRNAs
Matthias Selbach et al.
Nature 455, 58–63
(04 September 2008); doi:10.1038/nature07228
| Summary | Full Text (HTML / PDF) |
article
The impact of microRNAs on protein output
Daehyun Baek et al.
Nature 455, 64–71
(04 September 2008); doi:10.1038/nature07242
| Summary | Full Text (HTML / PDF) |
news and views
Small RNAs: The seeds of silence
Zissimos Mourelatos
Nature 455, 44–45
(04 September 2008); doi:10.1038/455044a
| Full Text (HTML / PDF) |
article
Max-independent functions of Myc in Drosophila melanogaster
Dominik Steiger, Michael Furrer, Daniela Schwinkendorf & Peter Gallant
Nature Genetics 40, 1084–1091
(September 2008); doi:10.1038/ng.178
| Summary | Full Text (HTML / PDF) |
August
letter
Critical function of Prdm14 for the establishment of the germ cell lineage in mice
Masashi Yamaji et al.
Nature Genetics 40, 1016–1022
(August 2008); doi:10.1038/ng.186
| Summary | Full Text (HTML / PDF) |
news and views
One PRDM is not enough for germ cell development
Elizabeth K Bikoff & Elizabeth J Robertson
Nature Genetics 40, 934–935
(August 2008); doi:10.1038/ng0808-934
| Full Text (HTML / PDF) |
article
PRDM16 controls a brown fat/skeletal muscle switch
Patrick Seale et al.
Nature 454, 961–967
(21 August 2008); doi:10.1038/nature07182
| Summary | Full Text (HTML / PDF) |
letter
New role of bone morphogenetic protein 7 in brown adipogenesis and energy expenditure
Yu-Hua Tseng et al.
Nature 454, 1000–1004
(21 August 2008); doi:10.1038/nature07221
| Summary | Full Text (HTML / PDF) |
news and views
Developmental biology: Neither fat nor flesh
Barbara Cannon & Jan Nedergaard
Nature 454, 947–948
(21 August 2008); doi:10.1038/454947a
| Full Text (HTML / PDF) |
article
Hepatocyte-specific ablation of Foxa2 alters bile acid homeostasis and results in endoplasmic reticulum stress
Irina M Bochkis et al.
Nature Medicine 14, 828–836
(August 2008); doi:10.1038/nm.1853
| Summary | Full Text (HTML / PDF) |
review
DNA polymerases and human disease
Lawrence A. Loeb & Raymond J. Monnat, Jr
Nature Reviews Genetics 9, 594–604
(August 2008); doi:10.1038/nrg2345
| Summary | Full Text (HTML / PDF) |
article
A comprehensive strategy enabling high-resolution functional analysis of the yeast genome
David K Breslow et al.
Nature Methods 5, 711–718
(August 2008); doi:10.1038/nmeth.1234
| Summary | Full Text (HTML / PDF) |
review
Single-strand break repair and genetic disease
Keith W. Caldecott
Nature Reviews Genetics 9, 619–631
(August 2008); doi:10.1038/nrg2380
| Summary | Full Text (HTML / PDF) |
article
Phosphorylation of the RNA polymerase II C-terminal domain dictates transcription termination choice
Rajani Kanth Gudipati, Tommaso Villa, Jocelyne Boulay & Domenico Libri
Nature Structural & Molecular Biology 15, 786–794
doi:10.1038/nsmb.1460
| Summary | Full Text (HTML / PDF) |
article
The Nrd1–Nab3–Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain
Lidia Vasiljeva, Minkyu Kim, Hannes Mutschler, Stephen Buratowski & Anton Meinhart
Nature Structural & Molecular Biology 15, 795–804
doi:10.1038/nsmb.1468
| Summary | Full Text (HTML / PDF) |
news and views
Terminating transcription in yeast: whether to be a 'nerd' or a 'rat'
Ana G Rondon, Hannah E Mischo & Nick J Proudfoot
Nature Structural & Molecular Biology 15, 775–776
(August 2008); doi:10.1038/nsmb0808-775
| Full Text (HTML / PDF) |
article
Secreted transcription factor controls Mycobacterium tuberculosis virulence
Sridharan Raghavan, Paolo Manzanillo, Kaman Chan, Cole Dovey & Jeffery S. Cox
Nature 454, 717–721
(7 August 2008); doi:10.1038/nature07219
| Summary | Full Text (HTML / PDF) |
news and views
Tuberculosis: Shrewd survival strategy
Steven A. Porcelli
Nature 454, 702–703
(7 August 2008); doi:10.1038/454702a
| Full Text (HTML / PDF) |
review
Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation
Luis López-Maury, Samuel Marguerat & Jürg Bähler
Nature Reviews Genetics 9, 583–593
(August 2008); doi:10.1038/nrg2398
| Summary | Full Text (HTML / PDF) |
perspective
Cooperativity in macromolecular assembly
James R Williamson
Nature Chemical Biology 4, 458–465
(August 2008); doi:10.1038/nchembio.102
| Summary | Full Text (HTML / PDF) |
review
ATR: an essential regulator of genome integrity
Karlene A. Cimprich & David Cortez
Nature Reviews Molecular Cell Biology 9, 616–627
(August 2008); doi:10.1038/nrm2450
| Summary | Full Text (HTML / PDF) |
July
letter
Imbalance between pSmad3 and Notch induces CDK inhibitors in old muscle stem cells
Morgan E. Carlson, Michael Hsu & Irina M. Conboy
Nature 454, 528–532
(24 July 2008); doi:10.1038/nature07034
| Summary | Full Text (HTML / PDF) |
letter
Saccharomyces cerevisiae ATM orthologue suppresses break-induced chromosome translocations
Kihoon Lee, Yu Zhang & Sang Eun Lee
Nature 454, 543–546
(24 July 2008); doi:10.1038/nature07054
| Summary | Full Text (HTML / PDF) |
article
TAZ controls Smad nucleocytoplasmic shuttling and regulates human embryonic stem-cell self-renewal
Xaralabos Varelas et al.
Nature Cell Biology 10, 837–848
(July 2008); doi:10.1038/ncb1748
| Summary | Full Text (HTML / PDF) |
review
Mediators of reprogramming: transcription factors and transitions through mitosis
Dieter Egli, Garrett Birkhoff & Kevin Eggan
Nature Reviews Molecular Cell Biology 9, 505–516
(July 2008); doi:10.1038/nrm2439
| Summary | Full Text (HTML / PDF) |
article
Stem cell transcriptome profiling via massive-scale mRNA sequencing
Nicole Cloonan et al.
Nature Methods 5, 613–619
(July 2008); doi:10.1038/nmeth.1223
| Summary | Full Text (HTML / PDF) |
research
Treatment of arthritis with a selective inhibitor of c-Fos/activator protein-1
Yukihiko Aikawa et al.
Nature Biotechnology 26, 817–823
(July 2008); doi:10.1038/nbt1412
| Summary | Full Text (HTML / PDF) |
review
Advances in bacterial promoter recognition and its control by factors that do not bind DNA
Shanil P. Haugen, Wilma Ross & Richard L. Gourse
Nature Reviews Microbiology 6, 507–519
(July 2008); doi:10.1038/nrmicro1912
| Summary | Full Text (HTML / PDF) |
letter
Osteoclast size is controlled by Fra-2 through LIF/LIF-receptor signalling and hypoxia
Aline Bozec et al.
Nature 454, 221–225
(10 July 2008); doi:10.1038/nature07019
| Summary | Full Text (HTML / PDF) |
letter
IRF4 addiction in multiple myeloma
Arthur L. Shaffer et al.
Nature 454, 226–231
(10 July 2008); doi:10.1038/nature07064
| Summary | Full Text (HTML / PDF) |
article
The transcription factor Erg is essential for definitive hematopoiesis and the function of adult hematopoietic stem cells
Stephen J Loughran et al.
Nature Immunology 9, 810–819
(July 2008); doi:10.1038/ni.1617
| Summary | Full Text (HTML / PDF) |
news and views
Erg in stem cells: a function emerges
Ellen V Rothenberg
Nature Immunology 9, 714–716
(July 2008); doi:10.1038/ni0708-714
| Full Text (HTML / PDF) |
review
MYB function in normal and cancer cells
Robert G. Ramsay & Thomas J. Gonda
Nature Reviews Cancer 8, 523–534
(July 2008); doi:10.1038/nrc2439
| Summary | Full Text (HTML / PDF) |
article
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer & Barbara Wold
Nature Methods 5, 621–628
(July 2008); doi:10.1038/nmeth.1226
| Summary | Full Text (HTML / PDF) |
news and views
The beginning of the end for microarrays?
Jay Shendure
Nature Methods 5, 585–587
(July 2008); doi:10.1038/nmeth0708-585
| Full Text (HTML / PDF) |
June
article
The type I TGF-β receptor is covalently modified and regulated by sumoylation
Jong Seok Kang, Elise F. Saunier, Rosemary J. Akhurst & Rik Derynck
Nature Cell Biology 10, 654–664
(June 2008); doi:10.1038/ncb1728
| Summary | Full Text (HTML / PDF) |
news and views
SUMO amplifies TGF-β signalling
Kohei Miyazono, Yuto Kamiya & Keiji Miyazawa
Nature Cell Biology 10, 635–637
(June 2008); doi:10.1038/ncb0608-635
| Full Text (HTML / PDF) |
letter
Global control of cell-cycle transcription by coupled CDK and network oscillators
David A. Orlando et al.
Nature 453, 944–947
(12 June 2008); doi:10.1038/nature06955
| Summary | Full Text (HTML / PDF) |
article
Foxo1 directly regulates the transcription of recombination-activating genes during B cell development
Rupesh H Amin & Mark S Schlissel
Nature Immunology 9, 613–622
(June 2008); doi:10.1038/ni.1612
| Summary | Full Text (HTML / PDF) |
article
SLP-65 regulates immunoglobulin light chain gene recombination through the PI(3)K–PKB–Foxo pathway
Sebastian Herzog et al.
Nature Immunology 9, 623–631
(June 2008); doi:10.1038/ni.1616
| Summary | Full Text (HTML / PDF) |
news and views
Foxos around make B cells tolerable
Marta A W Rowh & Craig H Bassing
Nature Immunology 9, 586–588
(June 2008); doi:10.1038/ni0608-586
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article
Transcription factor Mef2c is required for B cell proliferation and survival after antigen receptor stimulation
Peter R Wilker et al.
Nature Immunology 9, 603–612
(June 2008); doi:10.1038/ni.1609
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article
SUMOylation of Krüppel-like transcription factor 5 acts as a molecular switch in transcriptional programs of lipid metabolism involving PPAR-δ
Yumiko Oishi et al.
Nature Medicine 14, 656–666
(June 2008); doi:10.1038/nm1756
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news and views
Multiple layers of metabolism
Mukesh K Jain
Nature Medicine 14, 603–604
(June 2008); doi:10.1038/nm0608-603
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NF-κB links innate immunity to the hypoxic response through transcriptional regulation of HIF-1α
Jordi Rius et al.
Nature 453, 807–811
(5 June 2008); doi:10.1038/nature06905
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Chemically ubiquitylated histone H2B stimulates hDot1L-mediated intranucleosomal methylation
Robert K. McGinty, Jaehoon Kim, Champak Chatterjee, Robert G. Roeder & Tom W. Muir
Nature 453, 812–816
(5 June 2008); doi:10.1038/nature06906
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Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells
Jiancong Liang et al.
Nature Cell Biology 10, 731–739
(June 2008); doi:10.1038/ncb1736
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May
letter
Single-stranded DNA-binding protein hSSB1 is critical for genomic stability
Derek J. Richard et al.
Nature 453, 677–681
(29 May 2008); doi:10.1038/nature06883
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HP1-β mobilization promotes chromatin changes that initiate the DNA damage response
Nabieh Ayoub, Anand D. Jeyasekharan, Juan A. Bernal & Ashok R. Venkitaraman
Nature 453, 682–686
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article
The HSA domain binds nuclear actin-related proteins to regulate chromatin-remodeling ATPases
Heather Szerlong et al.
Nature Structural & Molecular Biology 15, 469–476
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New clues to actin function in chromatin regulation
Aaron J Gottschalk, Ronald C Conaway & Joan Weliky Conaway
Nature Structural & Molecular Biology 15, 432–433
(May 2008); doi:10.1038/nsmb0508-432
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The ground state of embryonic stem cell self-renewal
Qi-Long Ying et al.
Nature 453, 519–523
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A crucial role of a high mobility group protein HMGA2 in cardiogenesis
Koshiro Monzen et al.
Nature Cell Biology 10, 567–574
(May 2008); doi:10.1038/ncb1719
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Nucleosome organization in the Drosophila genome
Travis N. Mavrich et al.
Nature 453, 358–362
(15 May 2008); doi:10.1038/nature06929
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review
Coordination of gene expression between organellar and nuclear genomes
Jesse D. Woodson & Joanne Chory
Nature Reviews Genetics 9, 383–395
(May 2008); doi:10.1038/nrg2348
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TGF-β-induced Foxp3 inhibits TH17 cell differentiation by antagonizing ROR γt function
Liang Zhou et al.
Nature 453, 236–240
(8 May 2008); doi:10.1038/nature06878
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Chromatin decouples promoter threshold from dynamic range
Felix H. Lam, David J. Steger & Erin K. O'Shea
Nature 453, 246–250
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analysis
Transcriptional control of human p53-regulated genes
Todd Riley, Eduardo Sontag, Patricia Chen & Arnold Levine
Nature Reviews Molecular Cell Biology 9, 402–412
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Control of Treg and TH17 cell differentiation by the aryl hydrocarbon receptor
Francisco J. Quintana et al.
Nature 453, 65–71
(1 May 2008); doi:10.1038/nature06880
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The aryl hydrocarbon receptor links TH17-cell-mediated autoimmunity to environmental toxins
Marc Veldhoen et al.
Nature 453, 106–109
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Immunology: T cells hang in the balance
Emily A. Stevens & Christopher A. Bradfield
Nature 453, 46–47
(1 May 2008); doi:10.1038/453046a
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Jund is a determinant of macrophage activation and is associated with glomerulonephritis susceptibility
Jacques Behmoaras et al.
Nature Genetics 40, 553–559
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April
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Gene transcription: Two worlds merged
David M. Lonard & Bert W. O'Malley
Nature 452, 946–947
(24 April 2008); doi:10.1038/452946a
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A bistable Rb–E2F switch underlies the restriction point
Guang Yao, Tae Jun Lee, Seiichi Mori, Joseph R. Nevins & Lingchong You
Nature Cell Biology 10, 476–482
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GATA1-related leukaemias
Ritsuko Shimizu, James Douglas Engel & Masayuki Yamamoto
Nature Reviews Cancer 8, 279–287
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Isolation of an active step I spliceosome and composition of its RNP core
Sergey Bessonov, Maria Anokhina, Cindy L. Will, Henning Urlaub & Reinhard Lührmann
Nature 452, 846–850
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LNA-mediated microRNA silencing in non-human primates
Joacim Elmén et al.
Nature 452, 896–899
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Drosophila STAT is required for directly maintaining HP1 localization and heterochromatin stability
Song Shi et al.
Nature Cell Biology 10, 489–496
(April 2008); doi:10.1038/ncb1713
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TNF activates an IRF1-dependent autocrine loop leading to sustained expression of chemokines and STAT1-dependent type I interferon–response genes
Anna Yarilina et al.
Nature Immunology 9, 378–387
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Compartment-specific transcription factors orchestrate angiogenesis gradients in the embryonic brain
Anju Vasudevan, Jason E Long, James E Crandall, John L R Rubenstein & Pradeep G Bhide
Nature Neuroscience 11, 429–439
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Newly identified prion linked to the chromatin-remodeling factor Swi1 in Saccharomyces cerevisiae
Zhiqiang Du, Kyung-Won Park, Haijing Yu, Qing Fan & Liming Li
Nature Genetics 40, 460–465
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GW182 interaction with Argonaute is essential for miRNA-mediated translational repression and mRNA decay
Ana Eulalio, Eric Huntzinger & Elisa Izaurralde
Nature Structural & Molecular Biology 15, 346–353
(April 2008); doi:10.1038/nsmb.1405
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news and views
Think you know how miRNAs work? Think again.
Joel D Richter
Nature Structural & Molecular Biology 15, 334–336
(April 2008); doi:10.1038/nsmb0408-334
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Drosophila short neuropeptide F signalling regulates growth by ERK-mediated insulin signalling
Kyu-Sun Lee et al.
Nature Cell Biology 10, 468–475
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March
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Genetics of gene expression and its effect on disease
Valur Emilsson et al.
Nature 452, 423–428
(27 March 2008); doi:10.1038/nature06758
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Variations in DNA elucidate molecular networks that cause disease
Yanqing Chen et al.
Nature 452, 429–435
(27 March 2008); doi:10.1038/nature06757
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The E3 ubiquitin ligase Itch regulates expression of transcription factor Foxp3 and airway inflammation by enhancing the function of transcription factor TIEG1
K Venuprasad et al.
Nature Immunology 9, 245–253
(March 2008); doi:10.1038/ni1564
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The E3 ligase Itch negatively regulates inflammatory signaling pathways by controlling the function of the ubiquitin-editing enzyme A20
Noula Shembade et al.
Nature Immunology 9, 254–262
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Itching to end NF-κB
Vigo Heissmeyer & Anjana Rao
Nature Immunology 9, 227–229
(March 2008); doi:10.1038/ni0308-227
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Transcription factor FOXO3a controls the persistence of memory CD4+ T cells during HIV infection
Julien van Grevenynghe et al.
Nature Medicine 14, 266–274
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review
Hypoxia and metabolism: Hypoxia, DNA repair and genetic instability
Robert G. Bristow & Richard P. Hill
Nature Reviews Cancer 8, 180–192
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Homogeneous reporter system enables quantitative functional assessment of multiple transcription factors
Sergei Romanov et al.
Nature Methods 5, 253–260
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Control of chromosome stability by the β-TrCP–REST–Mad2 axis
Daniele Guardavaccaro et al.
Nature 452, 365–369
(20 March 2008); doi:10.1038/nature06641
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SCFβ-TRCP controls oncogenic transformation and neural differentiation through REST degradation
Thomas F. Westbrook et al.
Nature 452, 370–374
(20 March 2008); doi:10.1038/nature06780
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The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men
Xiang-Jiao Yang & Edward Seto
Nature Reviews Molecular Cell Biology 9, 206–218
(March 2008); doi:10.1038/nrm2346
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SATB1 reprogrammes gene expression to promote breast tumour growth and metastasis
Hye-Jung Han, Jose Russo, Yoshinori Kohwi & Terumi Kohwi-Shigematsu
Nature 452, 187–193
(13 March 2008); doi:10.1038/nature06781
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Transcriptional repression mediated by repositioning of genes to the nuclear lamina
K. L. Reddy, J. M. Zullo, E. Bertolino & H. Singh
Nature 452, 243–247
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Direct regulation of TWIST by HIF-1α promotes metastasis
Muh-Hwa Yang et al.
Nature Cell Biology 10, 295–305
(March 2008); doi:10.1038/ncb1691
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news and views
A hypoxic twist in metastasis
Héctor Peinado & Amparo Cano
Nature Cell Biology 10, 253–254
(March 2008); doi:10.1038/ncb0308-253
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T cell antigen receptor stimulation induces MALT1 paracaspase-mediated cleavage of the NF-κB inhibitor A20
Beatrice Coornaert et al.
Nature Immunology 9, 263–271
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The proteolytic activity of the paracaspase MALT1 is key in T cell activation
Fabien Rebeaud et al.
Nature Immunology 9, 272–281
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Finally, MALT1 is a protease!
Linda M McAllister-Lucas & Peter C Lucas
Nature Immunology 9, 231–233
(March 2008); doi:10.1038/ni0308-231
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DNA repair pathways as targets for cancer therapy
Thomas Helleday, Eva Petermann, Cecilia Lundin, Ben Hodgson & Ricky A. Sharma
Nature Reviews Cancer 8, 193–204
(March 2008); doi:10.1038/nrc2342
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A core Klf circuitry regulates self-renewal of embryonic stem cells
Jianming Jiang et al.
Nature Cell Biology 10, 353–360
(March 2008); doi:10.1038/ncb1698
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Dimorphic effects of Notch signaling in bone homeostasis
Feyza Engin et al.
Nature Medicine 14, 299–305
(March 2008); doi:10.1038/nm1712
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Notch signaling maintains bone marrow mesenchymal progenitors by suppressing osteoblast differentiation
Matthew J Hilton et al.
Nature Medicine 14, 306–314
(March 2008); doi:10.1038/nm1716
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February
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Regulation of progenitor cell proliferation and granulocyte function by microRNA-223
Jonathan B. Johnnidis et al.
Nature 451, 1125–1129
(28 February 2008); doi:10.1038/nature06607
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TBL1–TBLR1 and β-catenin recruit each other to Wnt target-gene promoter for transcription activation and oncogenesis
Jiong Li & Cun-Yu Wang
Nature Cell Biology 10, 160–169
(February 2008); doi:10.1038/ncb1684
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Smad3 and NFAT cooperate to induce Foxp3 expression through its enhancer
Yukiko Tone, Keiji Furuuchi, Yoshitsugu Kojima, Mark L Tykocinski, Mark I Greene & Masahide Tone
Nature Immunology 9, 194–202
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news and views
What turns on Foxp3?
Harald von Boehmer & Jens Nolting
Nature Immunology 9, 121–122
(February 2008); doi:10.1038/ni0208-121
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The functional response of upstream DNA to dynamic supercoiling in vivo
Fedor Kouzine, Suzanne Sanford, Zichrini Elisha-Feil & David Levens
Nature Structural & Molecular Biology 15, 146–154
(February 2008); doi:10.1038/nsmb.1372
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DNA torsional stress propagates through chromatin fiber and participates in transcriptional regulation
Christophe Lavelle
Nature Structural & Molecular Biology 15, 123–125
(February 2008); doi:10.1038/nsmb0208-123
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HIF-independent regulation of VEGF and angiogenesis by the transcriptional coactivator PGC-1α
Zoltan Arany et al.
Nature 451, 1008–1012
(21 February 2008); doi:10.1038/nature06613
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A PtdIns4,5P2-regulated nuclear poly(A) polymerase controls expression of select mRNAs
David L. Mellman et al.
Nature 451, 1013–1017
(21 February 2008); doi:10.1038/nature06666
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Nanog maintains pluripotency of mouse embryonic stem cells by inhibiting NFκB and cooperating with Stat3
Josema Torres & Fiona M. Watt
Nature Cell Biology 10, 194–201
(February 2008); doi:10.1038/ncb1680
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brief communication
Epitope tagging of endogenous proteins for genome-wide ChIP-chip studies
Xiaodong Zhang et al.
Nature Methods 5, 163–165
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Dual control of nuclear EIN3 by bifurcate MAPK cascades in C2H4 signalling
Sang-Dong Yoo, Young-Hee Cho, Guillaume Tena, Yan Xiong & Jen Sheen
Nature 451, 789–795
(14 February 2008); doi:10.1038/nature06543
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The structural basis of protein acetylation by the p300/CBP transcriptional coactivator
Xin Liu et al.
Nature 451, 846–850
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Transcription factor EBF restricts alternative lineage options and promotes B cell fate commitment independently of Pax5
Jagan M R Pongubala et al.
Nature Immunology 9, 203–215
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Drosophila Pgc protein inhibits P-TEFb recruitment to chromatin in primordial germ cells
Kazuko Hanyu-Nakamura, Hiroko Sonobe-Nojima, Akie Tanigawa, Paul Lasko & Akira Nakamura
Nature 451, 730–733
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Cell cycle control of centromeric repeat transcription and heterochromatin assembly
Ee Sin Chen, Ke Zhang, Estelle Nicolas, Hugh P. Cam, Martin Zofall & Shiv I. S. Grewal
Nature 451, 734–737
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Mutations in pericentrin cause Seckel syndrome with defective ATR-dependent DNA damage signaling
Elen Griffith et al.
Nature Genetics 40, 232–236
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Epigenetic events in mammalian germ-cell development: reprogramming and beyond
Hiroyuki Sasaki & Yasuhisa Matsui
Nature Reviews Genetics 9, 129–140
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scientific report
CARM1 promotes adipocyte differentiation by coactivating PPARγ
Neelu Yadav et al.
EMBO Reports 9, 193–198
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January
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Molecular Biology: The expanding world of small RNAs
Helge Großhans & Witold Filipowicz
Nature 451, 414–416
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Akirins are highly conserved nuclear proteins required for NF-κB-dependent gene expression in drosophila and mice
Akira Goto et al.
Nature Immunology 9, 97–104
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Akirins versus infection
Bruce Beutler & Eva Marie Y Moresco
Nature Immunology 9, 7–9
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Widespread microRNA repression by Myc contributes to tumorigenesis
Tsung-Cheng Chang et al.
Nature Genetics 40, 43–50
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Peptide-conjugated antisense oligonucleotides for targeted inhibition of a transcriptional regulator in vivo
Erik Henke et al.
Nature Biotechnology 26, 91–100
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The contribution of transcription factor IRF1 to the interferon-γ–interleukin 12 signaling axis and TH1 versus TH-17 differentiation of CD4+ T cells
Shin-ichi Kano et al.
Nature Immunology 9, 34–41
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IRF1: a deus ex machina in TH1 differentiation
Derya Unutmaz & Jan Vilcek
Nature Immunology 9, 9–10
(January 2008); doi:10.1038/ni0108-9
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perspective
The interplay between MYC and HIF in cancer
Chi V. Dang, Jung-whan Kim, Ping Gao & Jason Yustein
Nature Reviews Cancer 8, 51–56
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AID is required for germinal center-derived lymphomagenesis
Laura Pasqualucci et al.
Nature Genetics 40, 108–112
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Coupling and coordination in gene expression processes: a systems biology view
Suzanne Komili & Pamela A. Silver
Nature Reviews Genetics 9, 38–48
(January 2008); doi:10.1038/nrg2223
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Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts
Masato Nakagawa et al.
Nature Biotechnology 26, 101–106
(January 2008); doi:10.1038/nbt1374
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Simpler and safer cell reprogramming
Martin F Pera & Kouichi Hasegawa
Nature Biotechnology 26, 59–60
(January 2008); doi:10.1038/nbt0108-59
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Trisomy represses ApcMin-mediated tumours in mouse models of Down's syndrome
Thomas E. Sussan, Annan Yang, Fu Li, Michael C. Ostrowski & Roger H. Reeves
Nature 451, 73–75
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Poly(ADP-ribose)-binding zinc finger motifs in DNA repair/checkpoint proteins
Ivan Ahel et al.
Nature 451, 81–85
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Phosphorylation of histone H3 at threonine 11 establishes a novel chromatin mark for transcriptional regulation
Eric Metzger et al.
Nature Cell Biology 10, 53–60
(January 2008); doi:10.1038/ncb1668
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Thrilling transcription through threonine phosphorylation
Luciano Di Croce & Ramin Shiekhattar
Nature Cell Biology 10, 5–6
(January 2008); doi:10.1038/ncb0108-5
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