Intestinal master transcription factor CDX2 controls chromatin access for partner transcription factor binding.

Abstract:

:Tissue-specific gene expression requires modulation of nucleosomes, allowing transcription factors to occupy cis elements that are accessible only in selected tissues. Master transcription factors control cell-specific genes and define cellular identities, but it is unclear if they possess special abilities to regulate cell-specific chromatin and if such abilities might underlie lineage determination and maintenance. One prevailing view is that several transcription factors enable chromatin access in combination. The homeodomain protein CDX2 specifies the embryonic intestinal epithelium, through unknown mechanisms, and partners with transcription factors such as HNF4A in the adult intestine. We examined enhancer chromatin and gene expression following Cdx2 or Hnf4a excision in mouse intestines. HNF4A loss did not affect CDX2 binding or chromatin, whereas CDX2 depletion modified chromatin significantly at CDX2-bound enhancers, disrupted HNF4A occupancy, and abrogated expression of neighboring genes. Thus, CDX2 maintains transcription-permissive chromatin, illustrating a powerful and dominant effect on enhancer configuration in an adult tissue. Similar, hierarchical control of cell-specific chromatin states is probably a general property of master transcription factors.

journal_name

Mol Cell Biol

authors

Verzi MP,Shin H,San Roman AK,Liu XS,Shivdasani RA

doi

10.1128/MCB.01185-12

subject

Has Abstract

pub_date

2013-01-01 00:00:00

pages

281-92

issue

2

eissn

0270-7306

issn

1098-5549

pii

MCB.01185-12

journal_volume

33

pub_type

杂志文章
  • Histone deacetylase 1 can repress transcription by binding to Sp1.

    abstract::The members of the Sp1 transcription factor family can act as both negative and positive regulators of gene expression. Here we show that Sp1 can be a target for histone deacetylase 1 (HDAC1)-mediated transcriptional repression. The histone deacetylase inhibitor trichostatin A activates the chromosomally integrated mu...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.19.8.5504

    authors: Doetzlhofer A,Rotheneder H,Lagger G,Koranda M,Kurtev V,Brosch G,Wintersberger E,Seiser C

    更新日期:1999-08-01 00:00:00

  • The HML mating-type cassette of Saccharomyces cerevisiae is regulated by two separate but functionally equivalent silencers.

    abstract::Mating-type genes resident in the silent cassette HML at the left arm of chromosome III are repressed by the action of four SIR gene products, most likely mediated through two cis-acting sites located on opposite sides of the locus. We showed that deletion of either of these two cis-acting sites from the chromosome di...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.9.11.4621

    authors: Mahoney DJ,Broach JR

    更新日期:1989-11-01 00:00:00

  • Transposition of the yeast retroviruslike element Ty3 is dependent on the cell cycle.

    abstract::Host cell cycle genes provide important functions to retroviruses and retroviruslike elements. To define some of these functions, the cell cycle dependence of transposition of the yeast retroviruslike element Ty3 was examined. Ty3 is unique among retroviruslike elements because of the specificity of its integration, w...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.14.12.8229

    authors: Menees TM,Sandmeyer SB

    更新日期:1994-12-01 00:00:00

  • NFATx, a novel member of the nuclear factor of activated T cells family that is expressed predominantly in the thymus.

    abstract::The nuclear factor of activated T cells (NFAT) regulates cytokine gene expression in T cells through cis-acting elements located in the promoters of cytokine genes. Here, we report the cDNA cloning, chromosomal localization, and initial characterization of a transcription factor related to NFATp and NFATc. The novel m...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.15.5.2697

    authors: Masuda ES,Naito Y,Tokumitsu H,Campbell D,Saito F,Hannum C,Arai K,Arai N

    更新日期:1995-05-01 00:00:00

  • RotundRacGAP functions with Ras during spermatogenesis and retinal differentiation in Drosophila melanogaster.

    abstract::Our analysis of rotund (rn) null mutations in Drosophila melanogaster revealed that deletion of the rn locus affects both spermatid and retinal differentiation. In the male reproductive system, the absence of RnRacGAP induced small testes, empty seminal vesicles, short testicular cysts, reduced amounts of interspermat...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.21.18.6280-6291.2001

    authors: Bergeret E,Pignot-Paintrand I,Guichard A,Raymond K,Fauvarque MO,Cazemajor M,Griffin-Shea R

    更新日期:2001-09-01 00:00:00

  • Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits.

    abstract::BUD23 was identified from a bioinformatics analysis of Saccharomyces cerevisiae genes involved in ribosome biogenesis. Deletion of BUD23 leads to severely impaired growth, reduced levels of the small (40S) ribosomal subunit, and a block in processing 20S rRNA to 18S rRNA, a late step in 40S maturation. Bud23 belongs t...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.01674-07

    authors: White J,Li Z,Sardana R,Bujnicki JM,Marcotte EM,Johnson AW

    更新日期:2008-05-01 00:00:00

  • Mutational analysis of the DNA binding, dimerization, and transcriptional activation domains of MEF2C.

    abstract::There are four members of the myocyte enhancer factor 2 (MEF2) family of transcription factors in vertebrates, MEF2A, -B, -C, and -D, which have homology within a MADS box at their amino termini and an adjacent motif known as the MEF2 domain. These factors activate muscle gene expression by binding as homo- and hetero...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.16.6.2627

    authors: Molkentin JD,Black BL,Martin JF,Olson EN

    更新日期:1996-06-01 00:00:00

  • Structure and regulation of KGD1, the structural gene for yeast alpha-ketoglutarate dehydrogenase.

    abstract::Nuclear respiratory-defective mutants of Saccharomyces cerevisiae have been screened for lesions in the mitochondrial alpha-ketoglutarate dehydrogenase complex. Strains assigned to complementation group G70 were ascertained to be deficient in enzyme activity due to mutations in the KGD1 gene coding for the alpha-ketog...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.9.6.2695

    authors: Repetto B,Tzagoloff A

    更新日期:1989-06-01 00:00:00

  • Biphasic and dosage-dependent regulation of osteoclastogenesis by β-catenin.

    abstract::Wnt/β-catenin signaling is a critical regulator of skeletal physiology. However, previous studies have mainly focused on its roles in osteoblasts, while its specific function in osteoclasts is unknown. This is a clinically important question because neutralizing antibodies against Wnt antagonists are promising new dru...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.05980-11

    authors: Wei W,Zeve D,Suh JM,Wang X,Du Y,Zerwekh JE,Dechow PC,Graff JM,Wan Y

    更新日期:2011-12-01 00:00:00

  • Overlapping roles of pocket proteins in the myocardium are unmasked by germ line deletion of p130 plus heart-specific deletion of Rb.

    abstract::The pocket protein family of tumor suppressors, and Rb specifically, have been implicated as controlling terminal differentiation in many tissues, including the heart. To establish the biological functions of Rb in the heart and overcome the early lethality caused by germ line deletion of Rb, we used a Cre/loxP system...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.25.6.2486-2497.2005

    authors: MacLellan WR,Garcia A,Oh H,Frenkel P,Jordan MC,Roos KP,Schneider MD

    更新日期:2005-03-01 00:00:00

  • Structurally normal corneas in aldehyde dehydrogenase 3a1-deficient mice.

    abstract::We have constructed an ALDH3a1 null mouse to investigate the role of this enzyme that comprises nearly one-half of the total water-soluble protein in the mouse corneal epithelium. ALDH3a1-deficient mice are viable and fertile, have a corneal epithelium with a water-soluble protein content approximately half that of wi...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.22.3.849-855.2002

    authors: Nees DW,Wawrousek EF,Robison WG Jr,Piatigorsky J

    更新日期:2002-02-01 00:00:00

  • The small nucle(ol)ar RNA cap trimethyltransferase is required for ribosome synthesis and intact nucleolar morphology.

    abstract::Nucleolar morphogenesis is a poorly defined process. Here we report that the Saccharomyces cerevisiae nucleolar trimethyl guanosine synthase I (Tgs1p), which specifically selects the m(7)G cap structure of snRNAs and snoRNAs for m(2,2,7)G conversion, is required not only for efficient pre-mRNA splicing but also for pr...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.24.18.7976-7986.2004

    authors: Colau G,Thiry M,Leduc V,Bordonné R,Lafontaine DL

    更新日期:2004-09-01 00:00:00

  • Promoter and enhancer elements from the rat elastase I gene function independently of each other and of heterologous enhancers.

    abstract::An elastase-human growth hormone (hGH) fusion gene containing 205 base pairs of elastase 5' flanking region is expressed exclusively in pancreatic acinar cells of transgenic mice. This paper shows that the promoter region (-72 to +8) and the enhancer (-205 to -73) function independently of each other. The elastase enh...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.7.10.3466

    authors: Ornitz DM,Hammer RE,Davison BL,Brinster RL,Palmiter RD

    更新日期:1987-10-01 00:00:00

  • The 5' untranslated region of mRNA for ribosomal protein S19 is involved in its translational regulation during Xenopus development.

    abstract::During Xenopus development, the synthesis of ribosomal proteins is regulated at the translational level. To identify the region of the ribosomal protein mRNAs responsible for their typical translational behavior, we constructed a fused gene in which the upstream sequences (promoter) and the 5' untranslated sequence (f...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.10.2.816

    authors: Mariottini P,Amaldi F

    更新日期:1990-02-01 00:00:00

  • Selective translational control and nonspecific posttranscriptional regulation of ribosomal protein gene expression during development and regeneration of rat liver.

    abstract::Mammalian liver development is accompanied by a transition from rapid growth in the fetus to a quiescent state in the adult. However, extensive proliferation can be induced in the adult liver by partial hepatectomy. In this study, we examined the regulation of ribosomal protein (rp) gene expression in the developing a...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.12.5.2203

    authors: Aloni R,Peleg D,Meyuhas O

    更新日期:1992-05-01 00:00:00

  • Modulation of transcriptional regulation by LEF-1 in response to Wnt-1 signaling and association with beta-catenin.

    abstract::Wnt signaling is thought to be mediated via interactions between beta-catenin and members of the LEF-1/TCF family of transcription factors. Here we study the mechanism of transcriptional regulation by LEF-1 in response to a Wnt-1 signal under conditions of endogenous beta-catenin in NIH 3T3 cells, and we examine wheth...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.18.8.4807

    authors: Hsu SC,Galceran J,Grosschedl R

    更新日期:1998-08-01 00:00:00

  • Phosphorylation of distinct sites in MeCP2 modifies cofactor associations and the dynamics of transcriptional regulation.

    abstract::Mutations in the gene encoding methyl-CpG-binding protein 2 (MeCP2) lead to disrupted neuronal function and can cause the neurodevelopmental disorder Rett syndrome. MeCP2 is a transcriptional regulator that binds to methylated DNA and is most abundant in neuronal nuclei. The mechanisms by which MeCP2 regulates gene ex...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.06728-11

    authors: Gonzales ML,Adams S,Dunaway KW,LaSalle JM

    更新日期:2012-07-01 00:00:00

  • Serum response factor is required for immediate-early gene activation yet is dispensable for proliferation of embryonic stem cells.

    abstract::Addition of serum to mitogen-starved cells activates the cellular immediate-early gene (IEG) response. Serum response factor (SRF) contributes to such mitogen-stimulated transcriptional induction of many IEGs during the G0-G1 cell cycle transition. SRF is also believed to be essential for cell cycle progression, as im...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.21.8.2933-2943.2001

    authors: Schratt G,Weinhold B,Lundberg AS,Schuck S,Berger J,Schwarz H,Weinberg RA,Rüther U,Nordheim A

    更新日期:2001-04-01 00:00:00

  • Mouse testes contain two size classes of actin mRNA that are differentially expressed during spermatogenesis.

    abstract::Using several actin isotype-specific cDNA probes, we found actin mRNA of two size classes, 2.1 and 1.5 kilobases (kb), in extracts of polyadenylated and nonpolyadenylated RNA from sexually mature CD-1 mouse testes. Although the 2.1-kb sequence was present in both meiotic and postmeiotic testicular cell types, it decre...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.5.7.1649

    authors: Waters SH,Distel RJ,Hecht NB

    更新日期:1985-07-01 00:00:00

  • A new means of inducibly inactivating a cellular protein.

    abstract::This paper presents a general means of eliminating the function of a single protein without relying on genetic alterations in its structure or level of synthesis. The strategy is based on the inducible cellular expression of neutralizing antibody to inactivate the protein selectively. The feasibility of this approach ...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.8.6.2638

    authors: Carlson JR

    更新日期:1988-06-01 00:00:00

  • Family of human alpha-interferon-like sequences.

    abstract::An interferon-alpha-like sequence was isolated from a human genomic library by hybridization with a 15-base oligonucleotide. The sequence also showed homology to alpha-interferon and was most closely related to the leukocyte interferon-M gene fragment. The original isolate cross-hybridized to a family of sequences, 10...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.5.3.510

    authors: Feinstein SI,Mory Y,Chernajovsky Y,Maroteaux L,Nir U,Lavie V,Revel M

    更新日期:1985-03-01 00:00:00

  • Evidence for impaired retinoic acid receptor-thyroid hormone receptor AF-2 cofactor activity in human lung cancer.

    abstract::Retinoic acid (RA) is required for normal airway epithelial cell growth and differentiation both in vivo and in vitro. One of the earliest events following the exposure of bronchial epithelial cells to RA is the strong induction of RA receptor beta (RAR beta) mRNA. Previous work established that many lung cancer cell ...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.15.7.3945

    authors: Moghal N,Neel BG

    更新日期:1995-07-01 00:00:00

  • Identification in vivo of different rate-limiting steps associated with transcriptional activators in the presence and absence of a GAGA element.

    abstract::We analyzed the impact of a GAGA element on a transgenic promoter in Drosophila melanogaster that was activated by proteins composed of the Tet(on) DNA binding domain and either the heat shock factor (HSF) activation domain or a potent subdomain of VP16. Permanganate footprinting was used to monitor polymerase II (Pol...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.25.9.3543-3552.2005

    authors: Wang YV,Tang H,Gilmour DS

    更新日期:2005-05-01 00:00:00

  • Nonsense codons can reduce the abundance of nuclear mRNA without affecting the abundance of pre-mRNA or the half-life of cytoplasmic mRNA.

    abstract::The abundance of the mRNA for human triosephosphate isomerase (TPI) is decreased to approximately 20% of normal by frameshift and nonsense mutations that cause translation to terminate at a nonsense codon within the first three-fourths of the reading frame. Results of previous studies inhibiting RNA synthesis with act...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.13.3.1892

    authors: Cheng J,Maquat LE

    更新日期:1993-03-01 00:00:00

  • The histidyl-tRNA synthetase-related sequence in the eIF-2 alpha protein kinase GCN2 interacts with tRNA and is required for activation in response to starvation for different amino acids.

    abstract::Protein kinase GCN2 is a multidomain protein that contains a region homologous to histidyl-tRNA synthetases juxtaposed to the kinase catalytic moiety. Previous studies have shown that in response to histidine starvation, GCN2 phosphorylates eukaryotic initiation factor 2 (eIF-2), to induce the translational expression...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.15.8.4497

    authors: Wek SA,Zhu S,Wek RC

    更新日期:1995-08-01 00:00:00

  • Functional expression and RNA binding analysis of the interferon-induced, double-stranded RNA-activated, 68,000-Mr protein kinase in a cell-free system.

    abstract::Eukaryotic viruses have devised numerous strategies to downregulate activity of the interferon-induced, double-stranded (dsRNA)-activated protein kinase (referred to as p68 on the basis of its Mr of 68,000 in human cells). Viruses must exert this control to avoid extensive phosphorylation of the alpha subunit of eukar...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.11.11.5497

    authors: Katze MG,Wambach M,Wong ML,Garfinkel M,Meurs E,Chong K,Williams BR,Hovanessian AG,Barber GN

    更新日期:1991-11-01 00:00:00

  • ELF-2, a new member of the Eph ligand family, is segmentally expressed in mouse embryos in the region of the hindbrain and newly forming somites.

    abstract::The Eph receptors are the largest known family of receptor tyrosine kinases and are notable for distinctive expression patterns in the nervous system and in early vertebrate development. However, all were identified as orphan receptors, and only recently have there been descriptions of a corresponding family of ligand...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.15.9.4921

    authors: Bergemann AD,Cheng HJ,Brambilla R,Klein R,Flanagan JG

    更新日期:1995-09-01 00:00:00

  • Group IVA Cytosolic Phospholipase A2 Regulates the G2-to-M Transition by Modulating the Activity of Tumor Suppressor SIRT2.

    abstract::The G2-to-M transition (or prophase) checkpoint of the cell cycle is a critical regulator of mitotic entry. SIRT2, a tumor suppressor gene, contributes to the control of this checkpoint by blocking mitotic entry under cellular stress. However, the mechanism underlying both SIRT2 activation and regulation of the G2-to-...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.00184-15

    authors: Movahedi Naini S,Sheridan AM,Force T,Shah JV,Bonventre JV

    更新日期:2015-11-01 00:00:00

  • Cleavage of eukaryotic translation initiation factor 4G by exogenously added hybrid proteins containing poliovirus 2Apro in HeLa cells: effects on gene expression.

    abstract::Efficient cleavage of both forms of eukaryotic initiation factor 4G (eIF4G-1 and eIF4G-2) has been achieved in HeLa cells by incubation with hybrid proteins containing poliovirus 2Apro. Entry of these proteins into cells is promoted by adenovirus particles. Substantial levels of ongoing translation on preexisting cell...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.19.4.2445

    authors: Novoa I,Carrasco L

    更新日期:1999-04-01 00:00:00

  • Negative regulation of transcription in vitro by a glucocorticoid response element is mediated by a trans-acting factor.

    abstract::In vitro experiments with cell extracts prepared from a mouse mammary epithelial cell line demonstrated that a cis-acting glucocorticoid response element (GRE) of the mouse mammary tumor virus represses transcription from its homologous promoter. Competition transcription experiments, in which a molar excess of a rest...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.8.9.3872

    authors: Langer SJ,Ostrowski MC

    更新日期:1988-09-01 00:00:00