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Transcription Factors (66):
- Transcription Factor DP1
- Receptors, Thyroid Hormone
- Proto-Oncogene Proteins c-myb
- Paired Box Transcription Factors
- Nuclear Receptor Coactivator 2
- Tristetraprolin
- Transcription Factors, General
- MSX1 Transcription Factor
- G-Box Binding Factors
- Trans-Activators
- T-Box Domain Proteins
- Smad Proteins
- Sigma Factor
- Myeloid-Lymphoid Leukemia Protein
- I-kappa B Proteins
- Basic Helix-Loop-Helix Transcription Factors
- Winged-Helix Transcription Factors
- Peroxisome Proliferator-Activated Receptors
- Otx Transcription Factors
- MADS Domain Proteins
- Leucine-Responsive Regulatory Protein
- Host Cell Factor C1
- Cyclic AMP Receptor Protein
- Transcriptional Elongation Factors
- Rho Factor
- Receptors, Retinoic Acid
- POU Domain Factors
- Inhibitor of Differentiation Proteins
- Core Binding Factors
- TCF Transcription Factors
- Receptors, Aryl Hydrocarbon
- NFI Transcription Factors
- Fushi Tarazu Transcription Factors
- Early Growth Response Transcription Factors
- Adenovirus E1A Proteins
- Transcription Factor AP-2
- BRCA1 Protein
- Steroidogenic Factor 1
- STAT Transcription Factors
- Repressor Proteins
- Receptors, Notch
- Receptors, Calcitriol
- Proto-Oncogene Proteins c-ets
- Proto-Oncogene Proteins c-bcl-6
- Interferon Regulatory Factors
- Goosecoid Protein
- Antennapedia Homeodomain Protein
- Proto-Oncogene Proteins c-rel
- Nuclear Respiratory Factors
- NFATC Transcription Factors
- Interferon-Stimulated Gene Factor 3
- Immunoglobulin J Recombination Signal Sequence-Binding Protein
- GATA Transcription Factors
- SOX Transcription Factors
- Receptors, Steroid
- p300-CBP Transcription Factors
- NF-kappa B
- Kruppel-Like Transcription Factors
- Hepatocyte Nuclear Factors
- Erythroid-Specific DNA-Binding Factors
- E2F Transcription Factors
- beta Catenin
- Basic-Leucine Zipper Transcription Factors
- Adenovirus E1B Proteins
- Onecut Transcription Factors
- Nuclear Factor 90 Proteins
Recent article
Transcription Factors
Biochemical Pharmacology (82)11 2011
Abstract
We analyzed the effects of IFN-α2b and TGF-β1 treatments on Wnt/β-catenin pathway, Smads proteins levels, β-catenin/TCF4/Smads interaction and proliferation and apoptotic death in HepG2/C3A and Huh7 cell lines. IFN-α2b and TGF-β1 attenuated Wnt/β-catenin signal by decreasing β-catenin and Fr...
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PMID: 21843516
PDF is available here.
PDF is available here.
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Human Molecular Genetics (20)21 2011
Abstract
We previously found that loss-of-function mutations in the transcription factor GLIS2, a putative vertebrate ortholog of Drosophila Ci, cause nephronophthisis type 7 in humans and mice. Kidney tubular cells in Glis2-knockout mice acquire mesenchymal phenotype, but the cellular mechanisms of this tra...
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PMID: 21816948
PDF is available here.
PDF is available here.
Abstract
We conclude that Pax6 independently of Arx and Foxa2 is critical for α-cell function by coordinating glucagon gene expression as well as glucagon biosynthesis and secretion....
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PMID: 21824254
PDF is available here.
PDF is available here.
FEBS Journal (278)19 2011
Abstract
Chromatin remodelling is the ATP-dependent change in nucleosome organisation driven by Snf2 family ATPases. The biochemistry of this process depends on the behaviours of ATP-dependent motor proteins and their dynamic nucleosome substrates, which brings significant technical and conce...
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PMID: 21810178
PDF is available here.
PDF is available here.
Molecular Immunology (48)15-16 2011
Abstract
We investigated gene regulation at the IL-3/GM-CSF gene cluster. We found BRG1, a SWI/SNF remodeling ATPase, bound a distal element, CNSa. BRG1 binding was strongest in differentiated, stimulated T helper cells, paralleling IL-3 and GM-CSF expression. Depletion of BRG1 reduced IL-3 and GM-CSF transc...
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PMID: 21831442
PDF is available here.
PDF is available here.
Abstract
We report that sustained inhibition of the transforming growth factor beta type I receptor (also termed activin receptor-like kinase or ALK) using a chemical inhibitor selective for ALK4/5/7 (ALKi) leads to the cardiac differentiation of hESCs under feeder-free and serum-free conditions. Treatment w...
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PMID: 21208046
PDF is available here.
PDF is available here.
Genes & Development (25)16 2011
Abstract
We have determined the cistrome and transcriptome for the nuclear receptor liver receptor homolog-1 (LRH-1) in exocrine pancreas. Chromatin immunoprecipitation (ChIP)-seq and RNA-seq analyses reveal that LRH-1 directly induces expression of genes encoding digestive enzymes and secretory and mitochon...
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PMID: 21852532
PDF is available here.
PDF is available here.
Abstract
Journal of Cell Biology (194)3 2011
Abstract
We report that mitochondria lacking the mitochondrial import protein 1 (Mim1) are impaired in the biogenesis of multispanning outer membrane proteins, whereas overexpression of Mim1 stimulates their import. The Mim1 complex cooperates with the receptor Tom70 in binding of precursor proteins and prom...
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PMID: 21825073
PDF is available here.
PDF is available here.
Abstract
Aspects relevant to immune T-cell differentiation and fate determination have been examined and discussed in the context of transcription factors, initiating cytokines in association with cognate antigen activation. It appears that the differentiation optional program, in light of re...
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PMID: 21843087
PDF is available here.
PDF is available here.
Nature Cell Biology (13)8 2011
Abstract
How the unique chromatin configuration of embryonic stem cells (ESCs) integrates inputs from exogenous stimuli to maintain pluripotency remains largely unknown. The ESC-specific ATP-dependent chromatin-remodelling (esBAF) complex maintains the accessibility of the target sites of Sta...
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PMID: 21808242
PDF is available here.
PDF is available here.
Journal of Neuroscience (31)31 2011
Abstract
We generated mice (termed "Nes-Met") in which met is inactivated from midembryonic stages onward in the CNS only. Adult animals showed motor behavioral defects suggestive of impaired innervation of pectoral muscles. Correspondingly, in neonatal spinal cords of Nes-Met mutants, we observed death of a...
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PMID: 21813676
PDF is available here.
PDF is available here.
Abstract
We built a dynamical model to test whether pure diffusion could account for the observed co-localization of genes within a defined subnuclear region. A simple standard Brownian motion model in two and three dimensions shows that preferential co-localization is possible for co-regulated genes without...
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PMID: 21760760
PDF is available here.
PDF is available here.
Abstract
We propose that CUL7, OBSL1, and CCDC8 are members of a pathway controlling mammalian growth....
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PMID: 21737058
PDF is available here.
PDF is available here.
PLoS Pathogens (7)7 2011
Abstract
We performed high throughput sequencing of cDNA generated from sRNA transcripts isolated from a strain ectopically expressing ToxT, the major transcriptional regulator within the virulence gene regulon. We compared this data set with ToxT binding sites determined by pulldown and deep sequencing to i...
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PMID: 21779167
PDF is available here.
PDF is available here.
Abstract
We transduced SATB2 into murine adult stem cells, and found that SATB2 significantly increased expression levels of bone matrix proteins, osteogenic transcription factors, and a potent angiogenic factor, vascular endothelial growth factor. Using an osterix (Osx) promoter-luciferase construct and cal...
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PMID: 21385070
PDF is available here.
PDF is available here.
Abstract
Alcohol abuse is the leading etiologic factor of pancreatitis, although many heavy drinkers do not develop pancreatic damage. Alcohol promotes pancreatitis through a combination of remote (e.g., increased gut permeability to bacterial products such as lipopolysaccharide) and more pro...
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PMID: 21460613
PDF is available here.
PDF is available here.
Protein & Cell (2)7 2011
Abstract
We have previously reported that mTORC2 mediates growth factor dependent phosphorylation of Akt and facilitates Akt dependent phosphorylation and inactivation of transcription factors FoxO1 and FoxO3a. We have recently explored the functions of mTORC2 in B cells and show that mTORC2 plays a key role...
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PMID: 21822797
PDF is available here.
PDF is available here.
Rinsho Ketsueki (52)7 2011
Abstract
Biochimica et Biophysica Acta (1809)9 2011
Abstract
We review the available data and integrate the results with structural and biochemical studies of related enzymes to derive a model for Mot1's catalytic action consistent with the broad literature on enzymes in this family. We propose that the Mot1 ATPase domain is tethered to TBP by a flexible, spr...
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PMID: 21658482
PDF is available here.
PDF is available here.
Abstract
We report here the regulation of members of the NR4A family of nuclear receptors by the BRAF-MEK-ERK cascade in melanoma cells. Expression profiling of melanoma cells in which both the NR4A1 and NR4A2 family members have been down-regulated by siRNA revealed alterations in genes associated with prol...
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PMID: 21362156
PDF is available here.
PDF is available here.
Abstract
We review the cellular signaling networks that regulate the activity of transcription factors during brain development and discuss the functional roles of specific activity-regulated transcription factors in specific stages of synapse formation, refinement, and maturation. Interestingly, a number of...
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PMID: 21555405
PDF is available here.
PDF is available here.
Abstract
We review the cellular signaling networks that regulate the activity of transcription factors during brain development and discuss the functional roles of specific activity-regulated transcription factors in specific stages of synapse formation, refinement, and maturation. Interestingly, a number of...
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PMID: 21555405
PDF is available here.
PDF is available here.
PLoS Genetics (7)6 2011
Abstract
We show through chromatin immunoprecipitation (ChIP) that SPT5L/KTF1, a silencing factor and a homolog of SPT5 elongation factors, binds chromatin at loci subject to transcriptional silencing. Chromatin binding of SPT5L/KTF1 occurs downstream of RNA Polymerase V, but independently from the presence...
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PMID: 21738482
PDF is available here.
PDF is available here.
Abstract
Parkinson's disease (PD), a common degenerative disease in humans, is known to result from loss of dopamine neurons in the substantia nigra and is characterized by severe motor symptoms of tremor, rigidity, bradykinsia and postural instability. Although levodopa administration, surgi...
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PMID: 21495962
PDF is available here.
PDF is available here.
Abstract
We selected gelatin as ECM (extracellular matrix) to support differentiation of mES (mouse embryonic stem) cells into TE (trophectoderm), as gelatin was less expensive and widely used. We found that 0.2% and 1.5% gelatin were the suitable concentrations to induce TE differentiation by means of detec...
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PMID: 21091439
PDF is available here.
PDF is available here.
Rinsho Ketsueki (52)6 2011
Abstract
Xenobiotica (41)5 2011
Abstract
Studies described in the recent literature support the idea that gene therapy can lead to genuine clinical benefits when mediated by plasmid delivery in conjunction with electroporation. Plasmid-mediated muscle-targeted gene transfer offers the potential of a cost-effective pharmaceutical-grade ther...
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PMID: 18370221
PDF is available here.
PDF is available here.
Abstract
We show that AFCs express pluripotency markers (Nanog, Sox2, and Oct3/4) as well as retinal transcription factor genes (Et, Lhx2, Tll1, Six6, Otx2, Pax6, and Fgf15). AFCs from amniotic fluid of Fgf15.gfp, Nrl.gfp, and Crx.gfp embryos cultured in retinal proliferation and differentiation conditions f...
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PMID: 20939691
PDF is available here.
PDF is available here.
Abstract
We were referred a difficult diagnostic case of acute promyelocytic leukemia with no pathogenic X-RARA fusion identified by routine metaphase cytogenetics or interphase fluorescence in situ hybridization (FISH). The case patient was enrolled in an institutional review board-approved protocol, with c...
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PMID: 21505136
PDF is available here.
PDF is available here.
Abstract
We suggested that the human peripheral blood mononuclear cells (PBMC) network can be delineated by cellular reconstruction to guide identification of candidate genes. Based on 285 microarrays (7370 genes) from 98 heart transplant patients enrolled in the Cardiac Allograft Rejection Gene Expression O...
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PMID: 20497491
PDF is available here.
PDF is available here.
Abstract
We discuss specificities of SIRT1 effects in the liver versus pancreatic β-cells, ultimately converging towards metabolic homeostasis at the organism level....
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PMID: 21483037
PDF is available here.
PDF is available here.
Nature Immunology (12)4 2011
Abstract
We report that CD4+ T cell help in the form of IL-2 is required for IL-10 production by CTLs, but not for the induction of CTL effector cytokines. We show that IL-2 derived from CD4+ helper T cells cooperates with innate immune cell-derived IL-27 to amplify IL-10 production by CTLs through a Blimp-1...
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PMID: 21297642
PDF is available here.
PDF is available here.
Epigenetics (6)4 2011
Abstract
We previously described an extensive methylation-acetylation switch on cell cycle promoters using a single nucleosome ChIP assay. A key issue is how PTMs are locally positioned. We report an analysis on the role of the NF-Y CCAAT transcription factor on histone acetylation. Whereas H3K9 and H3K14 ac...
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PMID: 21304275
PDF is available here.
PDF is available here.
Abstract
Abstract
Eukaryotic Cell (10)3 2011
Abstract
We characterized Swi6p, Swi4p and Mbp1p, the closest orthologues of SBF (Swi6p and Swi4p) and MBF (Swi6p and Mbp1p) components in S. cerevisiae. The mbp1Δ/Δ cells showed minor growth defects, whereas swi4Δ/Δ and swi6Δ/Δ yeast cells dramatically increased in size, suggesting a G(1) phase delay....
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PMID: 21257795
PDF is available here.
PDF is available here.
Abstract
We demonstrate that FFAs can activate endoplasmic reticulum (ER) stress pathway by examination of ER stress sensor activation and marker gene expression. Chemical chaperone tauroursodeoxycholic acid (TUDCA) can reduce FFA-induced adipocyte inflammation and improve insulin signaling whereas overexpre...
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PMID: 20829802
PDF is available here.
PDF is available here.
Cell Cycle (10)4 2011
Abstract
We perform an extensive analysis of the developing central nervous system in global p63-/- mice and their wildtype littermates. Brain and spinal cord of embryos and newborn mice were assessed in vivo for neuroanatomy, histology, apoptosis, proliferation, stemness and differentiation, and in vitro fo...
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PMID: 21293190
PDF is available here.
PDF is available here.
Abstract
We demonstrate that Tbx6-dependent regulation of Sox2 determines the fate of axial stem cells. In wild-type embryos, enhancer N1 of the neural primordial gene Sox2 is activated in the caudal lateral epiblast, and the cells staying in the superficial layer sustain N1 activity and activate Sox2 expres...
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PMID: 21331042
PDF is available here.
PDF is available here.
Abstract
We show that both AMPK and calcineurin modulate longevity exclusively through post-translational modification of CRTC-1, the sole C. elegans CRTC. We demonstrate that CRTC-1 is a direct AMPK target, and interacts with the CREB homologue-1 (CRH-1) transcription factor in vivo. The pro-longevity effec...
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PMID: 21331044
PDF is available here.
PDF is available here.
Cell Stem Cell (8)2 2011
Abstract
We report here that breast epithelial cells derived from patients harboring deleterious mutations in BRCA1 (BRCA1(mut /+) give rise to tumors with increased basal differentiation relative to cells from BRCA1+/+ patients. Molecular analysis of disease-free breast tissues from BRCA1(mut /+) patients r...
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PMID: 21295272
PDF is available here.
PDF is available here.
Abstract
We identify five distinct classes of fru neuron that trigger or compose the song. Our data suggest that P1 and pIP10 neurons in the brain mediate the decision to sing, and to act upon this decision, while the thoracic neurons dPR1, vPR6, and vMS11 are components of a central pattern generator that t...
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PMID: 21315261
PDF is available here.
PDF is available here.
Abstract
We determined the cellular substrate for male courtship behavior by quasinatural and artificial stimulation of brain neurons. Activation of fruitless (fru)-expressing neurons via stimulation of thermosensitive dTrpA1 channels induced an entire series of courtship acts in male Drosophila placed alone...
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PMID: 21315260
PDF is available here.
PDF is available here.
Abstract
We show that hypoxia induces the expression of Snail via HIF. In silico analysis identified a potential hypoxia-response element (HRE) close to the minimal promoter of the human and mouse genome of the snail gene. Gel shift assays demonstrated that a specific hypoxia-inducible complex is formed with...
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PMID: 21257819
PDF is available here.
PDF is available here.
Abstract
We define the gene expression network topology of cardiac hypertrophy and failure and the extent of recapitulation of fetal gene expression programs in failing and hypertrophied adult myocardium.
We assembled all myocardial transcript data in the Gene Expression Omnibus (n=1617). Bec...
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PMID: 21127201
PDF is available here.
PDF is available here.
Abstract
We have established a tethering system, in which the Gal4 DNA binding domain (DBD) of the Flag:Gal4 DBD:Ote▵LEM fusion protein physically interacts with the Gal4 binding sites upstream of bamP-gfp to artificially recruit the reporter gene gfp to the nuclear membrane. Our data demonstrated that the...
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PMID: 21356524
PDF is available here.
PDF is available here.
Abstract
We identify a mechanism in which EZH2 expression-mediated downregulation of DNA damage repair leads to accumulation of recurrent RAF1 gene amplification in BTICs, which activates p-ERK-β-catenin signaling to promote BTIC expansion. We further reveal that AZD6244, a clinical trial drug that inhibits...
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PMID: 21215703
PDF is available here.
PDF is available here.
Developmental Cell (20)1 2011
Abstract
The histone H3 lysine 27 (H3K27) methyltransferase EZH2 is essential for stem cell maintenance and proliferation. Recent insights suggest that the cyclin-dependent kinase CDK1 phosphorylates EZH2 at specific threonine residues by sensing developmental cues to mediate self-renewal or...
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PMID: 21238919
PDF is available here.
PDF is available here.
Abstract
We have defined eight major activation patterns in nodules and identified associated potential regulatory genes. We have shown that transcription reprogramming during consecutive stages of nodule differentiation occurs in four major phases, respectively associated with (i) early signalling events an...
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PMID: 21304580
PDF is available here.
PDF is available here.
Abstract
Cancer stem cells (CSCs) can proliferate and self-renew extensively due to their ability to express anti-apoptotic and drug resistant proteins, thus sustaining tumor growth. Therefore, the strategy to eradicate CSCs might have significant clinical implications. The objectives of this study were to ex...
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PMID: 21304978
PDF is available here.
PDF is available here.
Abstract
The NTERA2 cl D1 (NT2) cell line, derived from human teratocarcinoma, exhibits similar properties as embryonic stem (ES) cells or very early neuroepithelial progenitors. NT2 cells can be induced to become postmitotic central nervous system neurons (NT2N) with retinoic acid. Although neurons derived f...
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PMID: 21283767
PDF is available here.
PDF is available here.
Abstract
We also demonstrate that two key transcription factor genes known to be regulated by Wnt signaling and to be vital for the generation and function of dopaminergic neurons; i.e., Lmx1a and Engrailed 1, are down-regulated in the HPRT knockdown SH-SY5Y cells. In addition to the Wnt signaling aberration...
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PMID: 21305049
PDF is available here.
PDF is available here.
Abstract
We quantified and enriched ALDH1(+) cells within HNSCC cell lines and subsequently characterized their phenotypical and functional properties like invasion capacity and epithelial-mesenchymal transition (EMT). Spheroid culture enriched CSC from five HNSCC cell lines by up to 5-fold. In spheroid-deri...
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PMID: 21304586
PDF is available here.
PDF is available here.
Abstract
We address these issues by studying five populations: the popular Sprague-Dawley strain, sub-strains of Long-Evans and Wistar rats, and two lines derived from crosses between the Long-Evans and Wistar sub-strains. Using three independent techniques - variance analysis, linear modelling, and unsuperv...
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PMID: 21760882
PDF is available here.
PDF is available here.
Abstract
We report the regulatory response of C. crescentus to carbon starvation, based on combined high-throughput proteome and transcriptome analyses. Our results identify cell cycle changes in gene expression in response to carbon starvation that involve the prominent role of the FixK FNR/CAP family trans...
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PMID: 21494595
PDF is available here.
PDF is available here.
Fortschritte der Arzneimittelforschung. Progress in drug research. Progres des recherches pharmaceutiques (67) 2011
Abstract
We discuss three mechanisms through which histone methylation can be removed from the chromatin template. We describe how these "erasure" mechanisms are linked to pathways that are known to be misregulated in diseases, such as cancer. We further describe how errors in the removal of histone methylat...
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PMID: 21141725
PDF is available here.
PDF is available here.
Abstract
We have used pathway-restricted gene expression profiles derived from RAS oncogene-transformed cells and from RAS-expressing cancer cells to identify regulators downstream of the MAPK pathway.We describe the role of epigenetic regulation exemplified by the control of several immune genes in generic...
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PMID: 21094659
PDF is available here.
PDF is available here.
Abstract
Glial cells missing 2 (Gcm2) is a master regulatory gene of parathyroid gland development, and it is exclusively expressed in the parathyroid gland. Diagnostic application of anti-Gcm2 antibody has not been reported yet. In this study, a total of 58 cases of parathyroid lesions including 40 adenomas...
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PMID: 21164298
PDF is available here.
PDF is available here.
Epigenetics (6)1 2011
Abstract
We compared two commonly used approaches to enrich for methylated DNA regions of the genome, namely methyl-DNA immunoprecipitation (MeDIP) that is based on enrichment with antibodies specific for 5'-methylcytosine (5MeC), and capture of methylated DNA using a methyl-CpG binding domain-based (MBD) pr...
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PMID: 20818161
PDF is available here.
PDF is available here.