Jan 132012

1.The genetic basis of early T-cell precursor acute lymphoblastic leukaemia.
Zhang J, Ding L, Holmfeldt L, Wu G, Heatley SL, Payne-Turner D, Easton J, Chen X, Wang J, Rusch M, Lu C, Chen SC, Wei L, Collins-Underwood JR, Ma J, Roberts KG, Pounds SB, Ulyanov A, Becksfort J, Gupta P, Huether R, Kriwacki RW, Parker M, McGoldrick DJ, Zhao D, Alford D, Espy S, Bobba KC, Song G, Pei D, Cheng C, Roberts S, Barbato MI, Campana D, Coustan-Smith E, Shurtleff SA, Raimondi SC, Kleppe M, Cools J, Shimano KA, Hermiston ML, Doulatov S, Eppert K, Laurenti E, Notta F, Dick JE, Basso G, Hunger SP, Loh ML, Devidas M, Wood B, Winter S, Dunsmore KP, Fulton RS, Fulton LL, Hong X, Harris CC, Dooling DJ, Ochoa K, Johnson KJ, Obenauer JC, Evans WE, Pui CH, Naeve CW, Ley TJ, Mardis ER, Wilson RK, Downing JR, Mullighan CG.
Nature. 2012 Jan 11;481(7380):157-63. doi: 10.1038/nature10725.
PMID: 22237106 [PubMed - in process]

2.Epigenetic regulation of hypoxic sensing disrupts cardiorespiratory homeostasis.
Nanduri J, Makarenko V, Reddy VD, Yuan G, Pawar A, Wang N, Khan SA, Zhang X, Kinsman B, Peng YJ, Kumar GK, Fox AP, Godley LA, Semenza GL, Prabhakar NR.
Proc Natl Acad Sci U S A. 2012 Jan 9. [Epub ahead of print]
PMID: 22232674 [PubMed - as supplied by publisher]

3.Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development.
Bonn S, Zinzen RP, Girardot C, Gustafson EH, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, Wilczyński B, Riddell A, Furlong EE.
Nat Genet. 2012 Jan 8. doi: 10.1038/ng.1064. [Epub ahead of print]
PMID: 22231485 [PubMed - as supplied by publisher]

4.Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint.
Gu SG, Pak J, Guang S, Maniar JM, Kennedy S, Fire A.
Nat Genet. 2012 Jan 8. doi: 10.1038/ng.1039. [Epub ahead of print]
PMID: 22231482 [PubMed - as supplied by publisher]

5.Chromodomains read the arginine code of post-translational targeting.
Holdermann I, Meyer NH, Round A, Wild K, Sattler M, Sinning I.
Nat Struct Mol Biol. 2012 Jan 8. doi: 10.1038/nsmb.2196. [Epub ahead of print]
PMID: 22231402 [PubMed - as supplied by publisher]

6.Symmetric dimethylation of H3R2 is a newly identified histone mark that supports euchromatin maintenance.
Migliori V, Mu Ller J, Phalke S, Low D, Bezzi M, Mok WC, Sahu SK, Gunaratne J, Capasso P, Bassi C, Cecatiello V, De Marco A, Blackstock W, Kuznetsov V, Amati B, Mapelli M, Guccione E.
Nat Struct Mol Biol. 2012 Jan 8. doi: 10.1038/nsmb.2209. [Epub ahead of print]
PMID: 22231400 [PubMed - as supplied by publisher]

7.Structure of HDAC3 bound to co-repressor and inositol tetraphosphate.
Watson PJ, Fairall L, Santos GM, Schwabe JW.
Nature. 2012 Jan 9. doi: 10.1038/nature10728. [Epub ahead of print]
PMID: 22230954 [PubMed - as supplied by publisher]

8.Human histone acetyltransferase HAT1 preferentially acetylates H4 molecules in H3.1-H4 dimers over H3.3-H4 dimers.
Zhang H, Han J, Kang B, Burgess R, Zhang Z.
J Biol Chem. 2012 Jan 7. [Epub ahead of print]
PMID: 22228774 [PubMed - as supplied by publisher] Free Article

9.Decapping of Long Noncoding RNAs Regulates Inducible Genes.
Geisler S, Lojek L, Khalil AM, Baker KE, Coller J.
Mol Cell. 2012 Jan 4. [Epub ahead of print]
PMID: 22226051 [PubMed - as supplied by publisher]

10.Compensatory functions of histone deacetylase 1 (HDAC1) and HDAC2 regulate transcription and apoptosis during mouse oocyte development.
Ma P, Pan H, Montgomery RL, Olson EN, Schultz RM.
Proc Natl Acad Sci U S A. 2012 Jan 5. [Epub ahead of print]
PMID: 22223663 [PubMed - as supplied by publisher]

11.Intronic promoter drives the BORIS-regulated expression of FerT in colon carcinoma cells.
Makovski A, Yaffe E, Shpungin S, Nir U.
J Biol Chem. 2012 Jan 5. [Epub ahead of print]
PMID: 22223638 [PubMed - as supplied by publisher] Free Article

12.Histone deacetylase 1 enhances microRNA processing via deacetylation of DGCR8.
Wada T, Kikuchi J, Furukawa Y.
EMBO Rep. 2012 Jan 6. doi: 10.1038/embor.2011.247. [Epub ahead of print]
PMID: 22222205 [PubMed - as supplied by publisher]

13.Trithorax group proteins: switching genes on and keeping them active.
Schuettengruber B, Martinez AM, Iovino N, Cavalli G.
Nat Rev Mol Cell Biol. 2011 Nov 23;12(12):799-814. doi: 10.1038/nrm3230. Review.
PMID: 22108599 [PubMed - indexed for MEDLINE]

14.Selective repression of MEF2 activity by PKA-dependent proteolysis of HDAC4.
Backs J, Worst BC, Lehmann LH, Patrick DM, Jebessa Z, Kreusser MM, Sun Q, Chen L, Heft C, Katus HA, Olson EN.
J Cell Biol. 2011 Oct 31;195(3):403-15.
PMID: 22042619 [PubMed - indexed for MEDLINE]

15.Phosphorylation at serine 331 is required for Aurora B activation.
Petsalaki E, Akoumianaki T, Black EJ, Gillespie DA, Zachos G.
J Cell Biol. 2011 Oct 31;195(3):449-66. Epub 2011 Oct 24.
PMID: 22024163 [PubMed - indexed for MEDLINE]

16.Deletion of the de novo DNA methyltransferase Dnmt3a promotes lung tumor progression.
Gao Q, Steine EJ, Barrasa MI, Hockemeyer D, Pawlak M, Fu D, Reddy S, Bell GW, Jaenisch R.
Proc Natl Acad Sci U S A. 2011 Nov 1;108(44):18061-6. Epub 2011 Oct 19.
PMID: 22011581 [PubMed - indexed for MEDLINE]

17.Transcriptome analysis of the Arabidopsis megaspore mother cell uncovers the importance of RNA helicases for plant germline development.
Schmidt A, Wuest SE, Vijverberg K, Baroux C, Kleen D, Grossniklaus U.
PLoS Biol. 2011 Sep;9(9):e1001155. Epub 2011 Sep 20.
PMID: 21949639 [PubMed - indexed for MEDLINE] Free PMC Article

18.Binding of the JmjC demethylase JARID1B to LSD1/NuRD suppresses angiogenesis and metastasis in breast cancer cells by repressing chemokine CCL14.
Li Q, Shi L, Gui B, Yu W, Wang J, Zhang D, Han X, Yao Z, Shang Y.
Cancer Res. 2011 Nov 1;71(21):6899-908. Epub 2011 Sep 21.
PMID: 21937684 [PubMed - indexed for MEDLINE]

19.SIRT1 is essential for oncogenic signaling by estrogen/estrogen receptor α in breast cancer.
Elangovan S, Ramachandran S, Venkatesan N, Ananth S, Gnana-Prakasam JP, Martin PM, Browning DD, Schoenlein PV, Prasad PD, Ganapathy V, Thangaraju M.
Cancer Res. 2011 Nov 1;71(21):6654-64. Epub 2011 Sep 15.
PMID: 21920899 [PubMed - indexed for MEDLINE]

20.HDAC4 protein regulates HIF1α protein lysine acetylation and cancer cell response to hypoxia.
Geng H, Harvey CT, Pittsenbarger J, Liu Q, Beer TM, Xue C, Qian DZ.
J Biol Chem. 2011 Nov 4;286(44):38095-102. Epub 2011 Sep 14.
PMID: 21917920 [PubMed - indexed for MEDLINE]

21.Verticillin A overcomes apoptosis resistance in human colon carcinoma through DNA methylation-dependent upregulation of BNIP3.
Liu F, Liu Q, Yang D, Bollag WB, Robertson K, Wu P, Liu K.
Cancer Res. 2011 Nov 1;71(21):6807-16. Epub 2011 Sep 12.
PMID: 21911457 [PubMed - indexed for MEDLINE]

22.Caenorhabditis elegans histone methyltransferase MET-2 shields the male X chromosome from checkpoint machinery and mediates meiotic sex chromosome inactivation.
Checchi PM, Engebrecht J.
PLoS Genet. 2011 Sep;7(9):e1002267. Epub 2011 Sep 1.
PMID: 21909284 [PubMed - indexed for MEDLINE] Free PMC Article

23.An iterative genetic and dynamical modelling approach identifies novel features of the gene regulatory network underlying melanocyte development.
Greenhill ER, Rocco A, Vibert L, Nikaido M, Kelsh RN.
PLoS Genet. 2011 Sep;7(9):e1002265. Epub 2011 Sep 1.
PMID: 21909283 [PubMed - indexed for MEDLINE] Free PMC Article

24.A pre-mRNA-associating factor links endogenous siRNAs to chromatin regulation.
Burkhart KB, Guang S, Buckley BA, Wong L, Bochner AF, Kennedy S.
PLoS Genet. 2011 Aug;7(8):e1002249. Epub 2011 Aug 25.
PMID: 21901112 [PubMed - indexed for MEDLINE] Free PMC Article

25.Definition of a FoxA1 Cistrome that is crucial for G1 to S-phase cell-cycle transit in castration-resistant prostate cancer.
Zhang C, Wang L, Wu D, Chen H, Chen Z, Thomas-Ahner JM, Zynger DL, Eeckhoute J, Yu J, Luo J, Brown M, Clinton SK, Nephew KP, Huang TH, Li W, Wang Q.
Cancer Res. 2011 Nov 1;71(21):6738-48. Epub 2011 Sep 7. Erratum in: Cancer Res. 2011 Dec 15;71(24):7718.
PMID: 21900400 [PubMed - indexed for MEDLINE]

26.Structure of human SMYD2 protein reveals the basis of p53 tumor suppressor methylation.
Wang L, Li L, Zhang H, Luo X, Dai J, Zhou S, Gu J, Zhu J, Atadja P, Lu C, Li E, Zhao K.
J Biol Chem. 2011 Nov 4;286(44):38725-37. Epub 2011 Aug 31.
PMID: 21880715 [PubMed - indexed for MEDLINE]

27.Condensins I and II are essential for construction of bivalent chromosomes in mouse oocytes.
Lee J, Ogushi S, Saitou M, Hirano T.
Mol Biol Cell. 2011 Sep;22(18):3465-77. Epub 2011 Jul 27.
PMID: 21795393 [PubMed - indexed for MEDLINE] Free PMC Article

28.Crystal structure of the N-terminal region of human Ash2L shows a winged-helix motif involved in DNA binding.
Chen Y, Wan B, Wang KC, Cao F, Yang Y, Protacio A, Dou Y, Chang HY, Lei M.
EMBO Rep. 2011 Jun 10;12(8):797-803. doi: 10.1038/embor.2011.101.
PMID: 21660059 [PubMed - indexed for MEDLINE]

Jan 062012

1.Histone H3K9 Trimethylase Eggless Controls Germline Stem Cell Maintenance and Differentiation.
Wang X, Pan L, Wang S, Zhou J, McDowell W, Park J, Haug J, Staehling K, Tang H, Xie T.
PLoS Genet. 2011 Dec;7(12):e1002426. Epub 2011 Dec 22.
PMID: 22216012 [PubMed - in process]

2.Structure and operation of the DNA-translocating type I DNA restriction enzymes.
Kennaway CK, Taylor JE, Song CF, Potrzebowski W, Nicholson W, White JH, Swiderska A, Obarska-Kosinska A, Callow P, Cooper LP, Roberts GA, Artero JB, Bujnicki JM, Trinick J, Kneale GG, Dryden DT.
Genes Dev. 2012 Jan 1;26(1):92-104.
PMID: 22215814 [PubMed - in process]

3.PRC2 directly methylates GATA4 and represses its transcriptional activity.
He A, Shen X, Ma Q, Cao J, von Gise A, Zhou P, Wang G, Marquez VE, Orkin SH, Pu WT.
Genes Dev. 2012 Jan 1;26(1):37-42.
PMID: 22215809 [PubMed - in process]

4.Insights into the role of Bromodomain, testis-specific (Brdt) in acetylated histone H4 dependent chromatin remodeling in mammalian spermiogenesis.
Dhar S, Thota A, Rao MR.
J Biol Chem. 2012 Jan 3. [Epub ahead of print]
PMID: 22215678 [PubMed - as supplied by publisher]

5.Lysine methyltransferase G9a methylates the transcription factor MyoD and regulates skeletal muscle differentiation.
Ling BM, Bharathy N, Chung TK, Kok WK, Li S, Tan YH, Rao VK, Gopinadhan S, Sartorelli V, Walsh MJ, Taneja R.
Proc Natl Acad Sci U S A. 2012 Jan 3. [Epub ahead of print]
PMID: 22215600 [PubMed - as supplied by publisher]

6.Bivalent recognition of nucleosomes by the tandem PHD fingers of the CHD4 ATPase is required for CHD4-mediated repression.
Musselman CA, Ramírez J, Sims JK, Mansfield RE, Oliver SS, Denu JM, Mackay JP, Wade PA, Hagman J, Kutateladze TG.
Proc Natl Acad Sci U S A. 2012 Jan 3. [Epub ahead of print]
PMID: 22215588 [PubMed - as supplied by publisher]

7.Epigenetics: Dynamic DNA methylation.
Stower H.
Nat Rev Genet. 2012 Jan 4. doi: 10.1038/nrg3156. [Epub ahead of print] No abstract available.
PMID: 22215132 [PubMed - as supplied by publisher]

8.Epigenetics and the environment: emerging patterns and implications.
Feil R, Fraga MF.
Nat Rev Genet. 2012 Jan 4. doi: 10.1038/nrg3142. [Epub ahead of print]
PMID: 22215131 [PubMed - as supplied by publisher]

9.MicroRNA-1 is a candidate tumor suppressor and prognostic marker in human prostate cancer.
Hudson RS, Yi M, Esposito D, Watkins SK, Hurwitz AA, Yfantis HG, Lee DH, Borin JF, Naslund MJ, Alexander RB, Dorsey TH, Stephens RM, Croce CM, Ambs S.
Nucleic Acids Res. 2011 Dec 30. [Epub ahead of print]
PMID: 22210864 [PubMed - as supplied by publisher] Free Article

10.Among B-type Cyclins Only CLB5 and CLB6 Promote Premeiotic S-phase in Saccharomyces cerevisiae.
Decesare JM, Stuart DT.
Genetics. 2011 Dec 29. [Epub ahead of print]
PMID: 22209902 [PubMed - as supplied by publisher] Free Article

11.Assembly of Drosophila Centromeric Nucleosomes Requires CID Dimerization.
Zhang W, Colmenares SU, Karpen GH.
Mol Cell. 2011 Dec 28. [Epub ahead of print]
PMID: 22209075 [PubMed - as supplied by publisher]

12.Assembling pieces of the centromere epigenetics puzzle.
González-Barrios R, Soto-Reyes E, Herrera LA.
Epigenetics. 2012 Jan 1;7(1). [Epub ahead of print]
PMID: 22207360 [PubMed - as supplied by publisher] Free Article

13.DNA replication, RNAi and epigenetic inheritance.
Gonzalez M, Li F.
Epigenetics. 2012 Jan 1;7(1). [Epub ahead of print]
PMID: 22207359 [PubMed - as supplied by publisher]

14.The 3D tissue microenvironment modulates DNA methylation and E-cadherin expression in squamous cell carcinoma.
Desrochers TM, Shamis Y, Alt-Holland A, Kudo Y, Takata T, Wang G, Jackson-Grusby L, Garlick JA.
Epigenetics. 2012 Jan 1;7(1). [Epub ahead of print]
PMID: 22207358 [PubMed - as supplied by publisher]

15.Clinical and public health research using methylated DNA Immunoprecipitation (MeDIP): A comparison of commercially available kits to examine differential DNA methylation across the genome.
Brebi-Mieville P, Ili-Gangas C, Leal-Rojas P, Noordhuis MG, Soudry E, Perez J, Roa JC, Sidransky D, Guerrero-Preston R.
Epigenetics. 2012 Jan 1;7(1). [Epub ahead of print]
PMID: 22207357 [PubMed - as supplied by publisher]

16.Local chromatin dynamics of transcription factors imply cell-lineage specific functions during cellular differentiation.
Tian R, Feng J, Cai X, Zhang Y.
Epigenetics. 2012 Jan 1;7(1). [Epub ahead of print]
PMID: 22207356 [PubMed - as supplied by publisher] Free Article

17.Current status and future prospects for epigenetic psychopharmacology.
Boks MP, de Jong NM, Kas MJ, Vinkers CH, Fernandes C, Kahn RS, Mill J, Ophoff RA.
Epigenetics. 2012 Jan 1;7(1). [Epub ahead of print]
PMID: 22207355 [PubMed - as supplied by publisher]

18.Aging and epigenetics: Longitudinal changes in gene-specific DNA methylation.
Madrigano J, Baccarelli A, Mittleman MA, Sparrow D, Vokonas PS, Tarantini L, Schwartz J.
Epigenetics. 2012 Jan 1;7(1). [Epub ahead of print]
PMID: 22207354 [PubMed - as supplied by publisher]

19.Role of DNMT3B in the regulation of early neural and neural crest specifiers.
Martins-Taylor K, Schroeder DI, Lasalle JM, Lalande M, Xu RH.
Epigenetics. 2012 Jan 1;7(1). [Epub ahead of print]
PMID: 22207353 [PubMed - as supplied by publisher]

20.Role of DNA methylation in the regulation of the RANKL-OPG system in human bone.
Delgado-Calle J, Sañudo C, Fernández AF, García-Renedo R, Fraga MF, Riancho JA.
Epigenetics. 2012 Jan 1;7(1). [Epub ahead of print]
PMID: 22207352 [PubMed - as supplied by publisher]

21.Monozygotic twins discordant for constitutive BRCA1 promoter methylation, childhood cancer and secondary cancer.
Galetzka D, Hansmann T, El Hajj N, Weis E, Irmscher B, Ludwig M, Schneider-Raetzke B, Kohlschmidt N, Beyer V, Bartsch O, Zechner U, Spix C, Haaf T.
Epigenetics. 2012 Jan 1;7(1). [Epub ahead of print]
PMID: 22207351 [PubMed - as supplied by publisher] Free Article

22.Small GTPase Rab5 participates in chromosome congression and regulates localization of the centromere-associated protein CENP-F to kinetochores.
Serio G, Margaria V, Jensen S, Oldani A, Bartek J, Bussolino F, Lanzetti L.
Proc Natl Acad Sci U S A. 2011 Oct 18;108(42):17337-42. Epub 2011 Oct 10.
PMID: 21987812 [PubMed - indexed for MEDLINE]

23.Cross-species hybridization of microarrays for studying tumor transcriptome of brain metastasis.
Park ES, Kim SJ, Kim SW, Yoon SL, Leem SH, Kim SB, Kim SM, Park YY, Cheong JH, Woo HG, Mills GB, Fidler IJ, Lee JS.
Proc Natl Acad Sci U S A. 2011 Oct 18;108(42):17456-61. Epub 2011 Oct 10.
PMID: 21987811 [PubMed - indexed for MEDLINE]

24.Dynamic nucleosome-depleted regions at androgen receptor enhancers in the absence of ligand in prostate cancer cells.
Andreu-Vieyra C, Lai J, Berman BP, Frenkel B, Jia L, Jones PA, Coetzee GA.
Mol Cell Biol. 2011 Dec;31(23):4648-62. Epub 2011 Oct 3.
PMID: 21969603 [PubMed - indexed for MEDLINE]

25.The NF90/NF45 complex participates in DNA break repair via nonhomologous end joining.
Shamanna RA, Hoque M, Lewis-Antes A, Azzam EI, Lagunoff D, Pe’ery T, Mathews MB.
Mol Cell Biol. 2011 Dec;31(23):4832-43. Epub 2011 Oct 3.
PMID: 21969602 [PubMed - indexed for MEDLINE]

26.Mammalian Ino80 mediates double-strand break repair through its role in DNA end strand resection.
Gospodinov A, Vaissiere T, Krastev DB, Legube G, Anachkova B, Herceg Z.
Mol Cell Biol. 2011 Dec;31(23):4735-45. Epub 2011 Sep 26.
PMID: 21947284 [PubMed - indexed for MEDLINE]

27.SIRT1 deacetylates the DNA methyltransferase 1 (DNMT1) protein and alters its activities.
Peng L, Yuan Z, Ling H, Fukasawa K, Robertson K, Olashaw N, Koomen J, Chen J, Lane WS, Seto E.
Mol Cell Biol. 2011 Dec;31(23):4720-34. Epub 2011 Sep 26.
PMID: 21947282 [PubMed - indexed for MEDLINE]

28.Histone H3 trimethylation at lysine 36 is associated with constitutive and facultative heterochromatin.
Chantalat S, Depaux A, Héry P, Barral S, Thuret JY, Dimitrov S, Gérard M.
Genome Res. 2011 Sep;21(9):1426-37. Epub 2011 Jul 29.
PMID: 21803857 [PubMed - indexed for MEDLINE]

29.Efficiently identifying genome-wide changes with next-generation sequencing data.
Huang W, Umbach DM, Vincent Jordan N, Abell AN, Johnson GL, Li L.
Nucleic Acids Res. 2011 Oct;39(19):e130. Epub 2011 Jul 29.
PMID: 21803788 [PubMed - indexed for MEDLINE] Free PMC Article

30.Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing.
Lee EJ, Pei L, Srivastava G, Joshi T, Kushwaha G, Choi JH, Robertson KD, Wang X, Colbourne JK, Zhang L, Schroth GP, Xu D, Zhang K, Shi H.
Nucleic Acids Res. 2011 Oct;39(19):e127. Epub 2011 Jul 23.
PMID: 21785137 [PubMed - indexed for MEDLINE] Free PMC Article

31.FGF-2 regulates cell proliferation, migration, and angiogenesis through an NDY1/KDM2B-miR-101-EZH2 pathway.
Kottakis F, Polytarchou C, Foltopoulou P, Sanidas I, Kampranis SC, Tsichlis PN.
Mol Cell. 2011 Jul 22;43(2):285-98.
PMID: 21777817 [PubMed - indexed for MEDLINE]

32.PHD finger recognition of unmodified histone H3R2 links UHRF1 to regulation of euchromatic gene expression.
Rajakumara E, Wang Z, Ma H, Hu L, Chen H, Lin Y, Guo R, Wu F, Li H, Lan F, Shi YG, Xu Y, Patel DJ, Shi Y.
Mol Cell. 2011 Jul 22;43(2):275-84.
PMID: 21777816 [PubMed - indexed for MEDLINE]

33.The initiation factor TFE and the elongation factor Spt4/5 compete for the RNAP clamp during transcription initiation and elongation.
Grohmann D, Nagy J, Chakraborty A, Klose D, Fielden D, Ebright RH, Michaelis J, Werner F.
Mol Cell. 2011 Jul 22;43(2):263-74.
PMID: 21777815 [PubMed - indexed for MEDLINE] Free PMC Article

34.NF-κB induction of the SUMO protease SENP2: A negative feedback loop to attenuate cell survival response to genotoxic stress.
Lee MH, Mabb AM, Gill GB, Yeh ET, Miyamoto S.
Mol Cell. 2011 Jul 22;43(2):180-91.
PMID: 21777808 [PubMed - indexed for MEDLINE]

35.A quantitative model of nucleosome dynamics.
Forties RA, North JA, Javaid S, Tabbaa OP, Fishel R, Poirier MG, Bundschuh R.
Nucleic Acids Res. 2011 Oct;39(19):8306-13. Epub 2011 Jul 14.
PMID: 21764779 [PubMed - indexed for MEDLINE] Free PMC Article

36.Liganded pregnane X receptor represses the human sulfotransferase SULT1E1 promoter through disrupting its chromatin structure.
Kodama S, Hosseinpour F, Goldstein JA, Negishi M.
Nucleic Acids Res. 2011 Oct;39(19):8392-403. Epub 2011 Jul 14.
PMID: 21764778 [PubMed - indexed for MEDLINE] Free PMC Article

37.Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features.
Cayrou C, Coulombe P, Vigneron A, Stanojcic S, Ganier O, Peiffer I, Rivals E, Puy A, Laurent-Chabalier S, Desprat R, Méchali M.
Genome Res. 2011 Sep;21(9):1438-49. Epub 2011 Jul 12.
PMID: 21750104 [PubMed - indexed for MEDLINE]

38.Key features of the two-intron Saccharomyces cerevisiae gene SUS1 contribute to its alternative splicing.
Hossain MA, Rodriguez CM, Johnson TL.
Nucleic Acids Res. 2011 Oct;39(19):8612-27. Epub 2011 Jul 12.
PMID: 21749978 [PubMed - indexed for MEDLINE] Free PMC Article

39.Histone H3 tail acetylation modulates ATP-dependent remodeling through multiple mechanisms.
Chatterjee N, Sinha D, Lemma-Dechassa M, Tan S, Shogren-Knaak MA, Bartholomew B.
Nucleic Acids Res. 2011 Oct;39(19):8378-91. Epub 2011 Jul 11.
PMID: 21749977 [PubMed - indexed for MEDLINE] Free PMC Article

40.Hyperexpansion of GAA repeats affects post-initiation steps of FXN transcription in Friedreich’s ataxia.
Kim E, Napierala M, Dent SY.
Nucleic Acids Res. 2011 Oct;39(19):8366-77. Epub 2011 Jul 10.
PMID: 21745819 [PubMed - indexed for MEDLINE] Free PMC Article

41.The USP7/Dnmt1 complex stimulates the DNA methylation activity of Dnmt1 and regulates the stability of UHRF1.
Felle M, Joppien S, Németh A, Diermeier S, Thalhammer V, Dobner T, Kremmer E, Kappler R, Längst G.
Nucleic Acids Res. 2011 Oct;39(19):8355-65. Epub 2011 Jul 10.
PMID: 21745816 [PubMed - indexed for MEDLINE] Free PMC Article

42.Histone variant H3.3 stimulates HSP70 transcription through cooperation with HP1γ.
Kim H, Heo K, Choi J, Kim K, An W.
Nucleic Acids Res. 2011 Oct;39(19):8329-41. Epub 2011 Jul 8.
PMID: 21742762 [PubMed - indexed for MEDLINE] Free PMC Article

43.Histone modifications influence mediator interactions with chromatin.
Zhu X, Zhang Y, Bjornsdottir G, Liu Z, Quan A, Costanzo M, Dávila López M, Westholm JO, Ronne H, Boone C, Gustafsson CM, Myers LC.
Nucleic Acids Res. 2011 Oct;39(19):8342-54. Epub 2011 Jul 8.
PMID: 21742760 [PubMed - indexed for MEDLINE] Free PMC Article

44.Mi-2/NuRD complex function is required for normal S phase progression and assembly of pericentric heterochromatin.
Sims JK, Wade PA.
Mol Biol Cell. 2011 Sep;22(17):3094-102. Epub 2011 Jul 7.
PMID: 21737684 [PubMed - indexed for MEDLINE] Free PMC Article

Dec 302011

1.A DETAILED STRUCTURAL-FUNCTIONAL ANALYSIS OF KRUPPEL-LIKE FACTOR 16 (KLF16) REVEALS NOVEL MECHANISMS FOR SILENCING SP/KLF-SITES INVOLVED IN METABOLISM AND ENDOCRINOLOGY. Daftary GS, Lomberk GA, Buttar NS, Allen TW, Grzenda A, Zhang J, Zheng Y, Mathison AJ, Gada RP, Iovanna JL, Billadeau DD, Prendergast FG, Urrutia R. J Biol Chem. 2011 Dec 27. [Epub ahead of print] PMID: 22203677 [PubMed - as supplied by publisher] 2.Cdc6 expression represses E-cadherin transcription and activates adjacent replication origins. Sideridou M, Zakopoulou R, Evangelou K, Liontos M, Kotsinas A, Rampakakis E, Gagos S, Kahata K, Grabusic K, Gkouskou K, Trougakos IP, Kolettas E, Georgakilas AG, Volarevic S, Eliopoulos AG, Zannis-Hadjopoulos M, Moustakas A, Gorgoulis VG. J Cell Biol. 2011 Dec 26;195(7):1123-40. PMID: 22201124 [PubMed - in process] 3.Dnmt3a silences hematopoietic stem cell self-renewal. Trowbridge JJ, Orkin SH. Nat Genet. 2011 Dec 27;44(1):13-4. doi: 10.1038/ng.1043. PMID: 22200773 [PubMed - in process] 4.Type III restriction endonuclease EcoP15I is a heterotrimeric complex containing one Res subunit with several DNA-binding regions and ATPase activity. Wyszomirski KH, Curth U, Alves J, Mackeldanz P, Möncke-Buchner E, Schutkowski M, Krüger DH, Reuter M. Nucleic Acids Res. 2011 Dec 23. [Epub ahead of print] PMID: 22199260 [PubMed - as supplied by publisher] Free [...]

Dec 232011

1.The deficiency of H3K79 histone methyltransferase DOT1L inhibits cell proliferation. Kim W, Kim R, Park G, Park JW, Kim JE. J Biol Chem. 2011 Dec 21. [Epub ahead of print] PMID: 22190683 [PubMed - as supplied by publisher] 2.A role for neuronal cAMP responsive-element binding (CREB)-1 in brain responses to calorie restriction. Fusco S, Ripoli C, Podda MV, Ranieri SC, Leone L, Toietta G, McBurney MW, Schütz G, Riccio A, Grassi C, Galeotti T, Pani G. Proc Natl Acad Sci U S A. 2011 Dec 21. [Epub ahead of print] PMID: 22190495 [PubMed - as supplied by publisher] 3.DNA methyltransferase 3a limits the expression of interleukin-13 in T helper 2 cells and allergic airway inflammation. Yu Q, Zhou B, Zhang Y, Nguyen ET, Du J, Glosson NL, Kaplan MH. Proc Natl Acad Sci U S A. 2011 Dec 21. [Epub ahead of print] PMID: 22190484 [PubMed - as supplied by publisher] 4.Gene silencing H-NS paralogue StpA forms a rigid protein filament along DNA that blocks DNA accessibility. Lim CJ, Whang YR, Kenney LJ, Yan J. Nucleic Acids Res. 2011 Dec 19. [Epub ahead of print] PMID: 22187157 [PubMed - as supplied by publisher] Free Article 5.Caenorhabditis elegans Heterochromatin Protein 1 [...]

Dec 162011

1.DNA-binding factors shape the mouse methylome at distal regulatory regions. Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, Wirbelauer C, Oakeley EJ, Gaidatzis D, Tiwari VK, Schübeler D. Nature. 2011 Dec 14. doi: 10.1038/nature10716. [Epub ahead of print] PMID: 22170606 [PubMed - as supplied by publisher] 2.Regulation of the Potential Marker for Intestinal Cells, Bmi1, by beta-Catenin and the Zinc Finger Protein KLF4: Implications for Colon Cancer. Yu T, Chen X, Zhang W, Colon D, Shi J, Napier D, Rychahou P, Lu W, Lee EY, Weiss HL, Evers BM, Liu C. J Biol Chem. 2011 Dec 14. [Epub ahead of print] PMID: 22170051 [PubMed - as supplied by publisher] 3.IKKα contributes to UVB-induced VEGF expression by regulating AP-1 transactivation. Dong W, Li Y, Gao M, Hu M, Li X, Mai S, Guo N, Yuan S, Song L. Nucleic Acids Res. 2011 Dec 14. [Epub ahead of print] PMID: 22169952 [PubMed - as supplied by publisher] 4.Epigenetic Mechanisms of Groucho/Grg/TLE Mediated Transcriptional Repression. Patel SR, Bhumbra SS, Paknikar RS, Dressler GR. Mol Cell. 2011 Dec 6. [Epub ahead of print] PMID: 22169276 [PubMed - as supplied by publisher] 5.Cdk Activity Couples Epigenetic Centromere Inheritance to Cell Cycle [...]

Dec 092011

1.A charge-based interaction conserved within the H3K4 methyltransferase complexes is needed for protein stability, histone methylation, and gene expression. Mersman DP, Du HN, Fingerman IM, South PF, Briggs SD. J Biol Chem. 2011 Dec 6. [Epub ahead of print] PMID: 22147691 [PubMed - as supplied by publisher] 2.MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain. Thambirajah AA, Ng MK, Frehlick LJ, Li A, Serpa JJ, Petrotchenko EV, Silva-Moreno B, Missiaen KK, Borchers CH, Adam Hall J, Mackie R, Lutz F, Gowen BE, Hendzel M, Georgel PT, Ausió J. Nucleic Acids Res. 2011 Dec 5. [Epub ahead of print] PMID: 22144686 [PubMed - as supplied by publisher] Free Article 3.The zinc finger protein ZFP57 requires its cofactor to recruit DNA methyltransferases and maintains the DNA methylation imprint in * embryonic stem cells via its transcriptional repression domain. Zuo X, Sheng J, Lau HT, McDonald CM, Andrade M, Cullen DE, Bell FT, Iacovino M, Kyba M, Xu G, Li X. J Biol Chem. 2011 Dec 5. [Epub ahead of print] PMID: 22144682 [PubMed - as supplied by publisher] Free Article 4.Glucose and insulin induction of bile acid synthesis: mechanisms and implication in diabetes and [...]

Dec 022011

1.The replication-independent H3-H4 chaperones HIR, ASF1 and RTT106 co-operate to maintain promoter fidelity. Silva AC, Xu X, Kim HS, Fillingham J, Kislinger T, Mennella TA, Keogh MC. J Biol Chem. 2011 Nov 29. [Epub ahead of print] PMID: 22128187 [PubMed - as supplied by publisher] Free Article 2.Stem Cell Gene SALL4 Suppresses Transcription through Recruitment of DNA Methyltransferases. Yang J, Corsello TR, Ma Y. J Biol Chem. 2011 Nov 29. [Epub ahead of print] PMID: 22128185 [PubMed - as supplied by publisher] Free Article 3.BRD4 jump-starts transcription after mitotic silencing. Voigt P, Reinberg D. Genome Biol. 2011 Nov 29;12(11):133. [Epub ahead of print] PMID: 22126464 [PubMed - as supplied by publisher] 4.Heritable Epigenetic Variation among Maize Inbreds. Eichten SR, Swanson-Wagner RA, Schnable JC, Waters AJ, Hermanson PJ, Liu S, Yeh CT, Jia Y, Gendler K, Freeling M, Schnable PS, Vaughn MW, Springer NM. PLoS Genet. 2011 Nov;7(11):e1002372. Epub 2011 Nov 17. PMID: 22125494 [PubMed - in process] Free PMC Article 5.Molecular cloning and characterization of the repetitive DNA sequences that comprise the constitutive heterochromatin of the W chromosomes of medaka fishes. Takehana Y, Naruse K, Asada Y, Matsuda Y, Shin-I T, Kohara Y, Fujiyama A, Hamaguchi S, Sakaizumi M. Chromosome [...]

In a dazzling visual display, Janssen et al. demonstrate a link a between chromosome missegregation and DNA-level structural defects, such as deletions and translocations, in human cells. The experimenters connect segregation errors, examining both induced missegregation in immortalized cell lines and endogenous errors in tumor cell lines, with structural damage using DNA damage markers such as γH2AX and 53BP1. Analysis of DNA damage marker immunofluorescence in real time suggested that DNA damage occurred at cytokinesis due to mechanical stress at the cleavage furrow. Janssen and peers confirmed these observations by inhibiting cytokinesis (DNA damage was reduced) and by observing the spatial and temporal occurrence of damage in relation to cytokinesis (damage occurred mainly at cytokinesis and when missegregating chromosomes became “trapped” in the cleavage furrow). Reasoning that chromosome breakage should activate double strand break repair, the experimenters demonstrated that chemically induced missegregations resulted in autophosphorylation of ATM and phosphorylation of Chk2 (two components of double strand break repair). Missegregation errors were also shown to cause p53 activation, demonstrating a connection between segregation and errors DNA damage checkpoint activation. The investigators also examined overall chromosome morphology under the induced segregation error conditions and observed an increase in the number of structural [...]

Nov 282011

1.Jarid2 (JUMONJI, at rich interactive domain 2) regulates notch1 expression via histone modification in the developing heart. Mysliwiec MR, Carlson CD, Tietjen J, Hung H, Ansari AZ, Lee Y. J Biol Chem. 2011 Nov 21. [Epub ahead of print] PMID: 22110129 [PubMed - as supplied by publisher] Free Article 2.The histone acetyltransferase TIP60 interacts with c-Myb and inactivates its transcriptional activity in human leukemia. Zhao H, Jin S, Gewirtz AM. J Biol Chem. 2011 Nov 21. [Epub ahead of print] PMID: 22110127 [PubMed - as supplied by publisher] Free Article 3.High-resolution mapping of open chromatin in the rice genome. Zhang W, Wu Y, Schnable JC, Zeng Z, Freeling M, Crawford GE, Jiang J. Genome Res. 2011 Nov 22. [Epub ahead of print] PMID: 22110044 [PubMed - as supplied by publisher] 4.Recognition of methylated DNA through methyl-CpG binding domain proteins. Zou X, Ma W, Solov’yov IA, Chipot C, Schulten K. Nucleic Acids Res. 2011 Nov 22. [Epub ahead of print] PMID: 22110028 [PubMed - as supplied by publisher] Free Article 5.DNAtraffic–a new database for systems biology of DNA dynamics during the cell life. Kuchta K, Barszcz D, Grzesiuk E, Pomorski P, Krwawicz J. Nucleic Acids Res. 2011 Nov 22. [Epub ahead [...]

Nov 182011

1.Developmental control of gene copy number by repression of replication initiation and fork progression. Sher N, Bell GW, Li S, Nordman J, Eng T, Eaton ML, Macalpine DM, Orr-Weaver TL. Genome Res. 2011 Nov 16. [Epub ahead of print] PMID: 22090375 [PubMed - as supplied by publisher] 2.DBTSS: DataBase of Transcriptional Start Sites progress report in 2012. Yamashita R, Sugano S, Suzuki Y, Nakai K. Nucleic Acids Res. 2011 Nov 15. [Epub ahead of print] PMID: 22086958 [PubMed - as supplied by publisher] 3.Pre-B cell to macrophage transdifferentiation without significant promoter DNA methylation changes. Rodríguez-Ubreva J, Ciudad L, Gómez-Cabrero D, Parra M, Bussmann LH, di Tullio A, Kallin EM, Tegnér J, Graf T, Ballestar E. Nucleic Acids Res. 2011 Nov 15. [Epub ahead of print] PMID: 22086955 [PubMed - as supplied by publisher] 4.The 19S proteasome subcomplex promotes the targeting of NuA4 HAT to the promoters of ribosomal protein genes to facilitate the recruitment of TFIID for transcriptional initiation in vivo. Uprety B, Lahudkar S, Malik S, Bhaumik SR. Nucleic Acids Res. 2011 Nov 15. [Epub ahead of print] PMID: 22086954 [PubMed - as supplied by publisher] 5.Multigenerational programming in the glucocorticoid programmed rat is associated with generation-specific and parent [...]

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