Rpd3- and spt16-mediated nucleosome assembly and transcriptional regulation on yeast ribosomal DNA genes.

Abstract:

:Ribosomal DNA (rDNA) genes in eukaryotes are organized into multicopy tandem arrays and transcribed by RNA polymerase I. During cell proliferation, ∼50% of these genes are active and have a relatively open chromatin structure characterized by elevated accessibility to psoralen cross-linking. In Saccharomyces cerevisiae, transcription of rDNA genes becomes repressed and chromatin structure closes when cells enter the diauxic shift and growth dramatically slows. In this study, we found that nucleosomes are massively depleted from the active rDNA genes during log phase and reassembled during the diauxic shift, largely accounting for the differences in psoralen accessibility between active and inactive genes. The Rpd3L histone deacetylase complex was required for diauxic shift-induced H4 and H2B deposition onto rDNA genes, suggesting involvement in assembly or stabilization of the entire nucleosome. The Spt16 subunit of FACT, however, was specifically required for H2B deposition, suggesting specificity for the H2A/H2B dimer. Miller chromatin spreads were used for electron microscopic visualization of rDNA genes in an spt16 mutant, which was found to be deficient in the assembly of normal nucleosomes on inactive genes and the disruption of nucleosomes on active genes, consistent with an inability to fully reactivate polymerase I (Pol I) transcription when cells exit stationary phase.

journal_name

Mol Cell Biol

authors

Johnson JM,French SL,Osheim YN,Li M,Hall L,Beyer AL,Smith JS

doi

10.1128/MCB.00112-13

subject

Has Abstract

pub_date

2013-07-01 00:00:00

pages

2748-59

issue

14

eissn

0270-7306

issn

1098-5549

pii

MCB.00112-13

journal_volume

33

pub_type

杂志文章
  • Identification of the mitogen-activated protein kinase phosphorylation sites on human Sos1 that regulate interaction with Grb2.

    abstract::The Son of sevenless proteins (Sos) are guanine nucleotide exchange factors involved in the activation of Ras by cytoplasmic and receptor tyrosine kinases. Growth factor stimulation rapidly induces the phosphorylation of Sos on multiple serine and threonine sites. Previous studies have demonstrated that growth factor-...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.16.10.5674

    authors: Corbalan-Garcia S,Yang SS,Degenhardt KR,Bar-Sagi D

    更新日期:1996-10-01 00:00:00

  • Interaction between the yeast mitochondrial and nuclear genomes influences the abundance of novel transcripts derived from the spacer region of the nuclear ribosomal DNA repeat.

    abstract::We have identified stable transcripts from the so-called nontranscribed spacer region (NTS) of the nuclear ribosomal DNA repeat in certain respiration-deficient strains of Saccharomyces cerevisiae. These RNAs, which are transcribed from the same strand as is the 37S rRNA precursor, are 500 to 800 nucleotides long and ...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.9.5.1897

    authors: Parikh VS,Conrad-Webb H,Docherty R,Butow RA

    更新日期:1989-05-01 00:00:00

  • Isolation and characterization of revertants from four different classes of aryl hydrocarbon hydroxylase-deficient hepa-1 mutants.

    abstract::Revertants were selected from aryl hydrocarbon hydroxylase (AHH)-deficient recessive mutants belonging to three complementation groups and from a dominant mutant of the Hepa-1 cell line. The recessive mutants had low spontaneous reversion frequencies (less than 4 X 10(-7] that were increased by mutagenesis. The majori...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.4.8.1597

    authors: Van Gurp JR,Hankinson O

    更新日期:1984-08-01 00:00:00

  • Embryonic lethality, decreased erythropoiesis, and defective octamer-dependent promoter activation in Oct-1-deficient mice.

    abstract::Oct-1 is a sequence-specific DNA binding transcription factor that is believed to regulate a large group of tissue-specific and ubiquitous genes. Both Oct-1 and the related but tissue-restricted Oct-2 protein bind to a DNA sequence termed the octamer motif (5'-ATGCAAAT-3') with equal affinity in vitro. To address the ...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.24.3.1022-1032.2004

    authors: Wang VE,Schmidt T,Chen J,Sharp PA,Tantin D

    更新日期:2004-02-01 00:00:00

  • Can ACG serve as an initiation codon for protein synthesis in eucaryotic cells?

    abstract::An ACG codon, which replaces the AUG codon used to initiate the synthesis of bacteriophage T7 gene 0.3 protein, was shown to function as a low-efficiency initiation codon in a wheat germ cell-free protein-synthesizing system. ...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.5.12.3621

    authors: Anderson CW,Buzash-Pollert E

    更新日期:1985-12-01 00:00:00

  • Both the SH2 and SH3 domains of human CRK protein are required for neuronal differentiation of PC12 cells.

    abstract::Human CRK protein is a homolog of the chicken v-crk oncogene product and consists mostly of src homology region 2 (SH2) and SH3, which are shared by many proteins, in particular those involved in signal transduction. SH2 has been shown to bind specifically to phosphotyrosine-containing peptides. We report here that bo...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.13.7.4409

    authors: Tanaka S,Hattori S,Kurata T,Nagashima K,Fukui Y,Nakamura S,Matsuda M

    更新日期:1993-07-01 00:00:00

  • A family of insulin-like growth factor II mRNA-binding proteins represses translation in late development.

    abstract::Insulin-like growth factor II (IGF-II) is a major fetal growth factor. The IGF-II gene generates multiple mRNAs with different 5' untranslated regions (5' UTRs) that are translated in a differential manner during development. We have identified a human family of three IGF-II mRNA-binding proteins (IMPs) that exhibit m...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.19.2.1262

    authors: Nielsen J,Christiansen J,Lykke-Andersen J,Johnsen AH,Wewer UM,Nielsen FC

    更新日期:1999-02-01 00:00:00

  • Saccharomyces cerevisiae transcription elongation mutants are defective in PUR5 induction in response to nucleotide depletion.

    abstract::IMP dehydrogenase (IMPDH) is the rate-limiting enzyme in the de novo synthesis of guanine nucleotides. It is a target of therapeutically useful drugs and is implicated in the regulation of cell growth rate. In the yeast Saccharomyces cerevisiae, mutations in components of the RNA polymerase II (Pol II) transcription e...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.20.20.7427-7437.2000

    authors: Shaw RJ,Reines D

    更新日期:2000-10-01 00:00:00

  • Transcriptional and posttranscriptional control of c-myc gene expression in WEHI 231 cells.

    abstract::Incubation of WEHI 231 cells, derived from a murine B-cell lymphoma, with antisera directed against its surface immunoglobulin results in the inhibition of growth within 24 h. Previously, we demonstrated that this treatment selectively affects cytoplasmic levels of c-myc mRNA (J. E. McCormack, V. H. Pepe, R. B. Kent, ...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.6.11.4112

    authors: Levine RA,McCormack JE,Buckler A,Sonenshein GE

    更新日期:1986-11-01 00:00:00

  • G1 transcription factors are differentially regulated in Saccharomyces cerevisiae by the Swi6-binding protein Stb1.

    abstract::Stage-specific transcriptional programs are an integral feature of cell cycle regulation. In the budding yeast Saccharomyces cerevisiae, over 120 genes are coordinately induced in late G(1) phase by two heterodimeric transcription factors called SBF and MBF. Activation of SBF and MBF is an upstream initiator of key ce...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.23.14.5064-5077.2003

    authors: Costanzo M,Schub O,Andrews B

    更新日期:2003-07-01 00:00:00

  • Alternative excision products originating from a single integration of polyomavirus DNA.

    abstract::The Cyp cell line consists of mouse cells transformed by a thermosensitive polyomavirus (Py) genome and routinely propagated at 39 degrees C. Cyp cells are readily induced to synthesize free Py DNA by being transferred to 33 degrees C. In one subclone (C12/a1/S48, or S48) of this line, such induction resulted in the i...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.5.10.2608

    authors: Huberdeau D,Sylla BS,Herring-Gillam E,Bourgaux-Ramoisy D,Bourgaux P

    更新日期:1985-10-01 00:00:00

  • Mutations in the yeast KEX2 gene cause a Vma(-)-like phenotype: a possible role for the Kex2 endoprotease in vacuolar acidification.

    abstract::Mutants of Saccharomyces cerevisiae that lack vacuolar proton-translocating ATPase (V-ATPase) activity show a well-defined set of Vma- (stands for vacuolar membrane ATPase activity) phenotypes that include pH-conditional growth, increased calcium sensitivity, and the inability to grow on nonfermentable carbon sources....

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.18.3.1534

    authors: Oluwatosin YE,Kane PM

    更新日期:1998-03-01 00:00:00

  • Construction and characterization of Chinese hamster cell EmtA EmtB double mutants.

    abstract::Starting with hybrid cell lines between a Chinese hamster cell EmtA mutant and a Chinese hamster cell EmtB mutant, we have constructed cell lines that are homozygous for mutant alleles at both the emtA locus and the emtB locus, by using a two-step segregation protocol. The EmtA EmtB double mutants are approximately 10...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.3.5.761

    authors: Chang S,Wasmuth JJ

    更新日期:1983-05-01 00:00:00

  • Expression profiling of murine acute promyelocytic leukemia cells reveals multiple model-dependent progression signatures.

    abstract::Leukemia results from the expansion of self-renewing hematopoietic cells that are thought to contain mutations that contribute to disease initiation and progression. Studies of the gene expression profiles of human acute myeloid leukemia samples has allowed their classification based on the presence of translocations ...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.24.24.10882-10893.2004

    authors: Walter MJ,Park JS,Lau SK,Li X,Lane AA,Nagarajan R,Shannon WD,Ley TJ

    更新日期:2004-12-01 00:00:00

  • RAP30/74: a general initiation factor that binds to RNA polymerase II.

    abstract::We have previously shown by affinity chromatography that RAP30 and RAP74 are the mammalian proteins that have the highest affinity for RNA polymerase II. Here we show that RAP30 binds to RAP74 and that the RAP30-RAP74 complex (RAP30/74) is required for accurate initiation by RNA polymerase II. RAP30/74 is required for...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.8.4.1602

    authors: Burton ZF,Killeen M,Sopta M,Ortolan LG,Greenblatt J

    更新日期:1988-04-01 00:00:00

  • Expression pattern, regulation, and biological role of runt domain transcription factor, run, in Caenorhabditis elegans.

    abstract::The Caenorhabditis elegans run gene encodes a Runt domain factor. Runx1, Runx2, and Runx3 are the three known mammalian homologs of run. Runx1, which plays an essential role in hematopoiesis, has been identified at the breakpoint of chromosome translocations that are responsible for human leukemia. Runx2 plays an esse...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.22.2.547-554.2002

    authors: Nam S,Jin YH,Li QL,Lee KY,Jeong GB,Ito Y,Lee J,Bae SC

    更新日期:2002-01-01 00:00:00

  • Thyrotropin-induced mitogenesis is Ras dependent but appears to bypass the Raf-dependent cytoplasmic kinase cascade.

    abstract::Cellular growth control requires the coordination and integration of multiple signaling pathways which are likely to be activated concomitantly. Mitogenic signaling initiated by thyrotropin (TSH) in thyroid cells seems to require two distinct signaling pathways, a cyclic AMP (cAMP)-dependent signaling pathway and a Ra...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.15.3.1162

    authors: al-Alawi N,Rose DW,Buckmaster C,Ahn N,Rapp U,Meinkoth J,Feramisco JR

    更新日期:1995-03-01 00:00:00

  • 4.5S RNA is encoded by hundreds of tandemly linked genes, has a short half-life, and is hydrogen bonded in vivo to poly(A)-terminated RNAs in the cytoplasm of cultured mouse cells.

    abstract::4.5S RNA is a group of RNAs 90 to 94 nucleotides long (length polymorphism due to a varying number of UMP residues at the 3' end) that form hydrogen bonds with poly(A)-terminated RNAs isolated from mouse, hamster, or rat cells (W. R. Jelinek and L. Leinwand, Cell 15:205-214, 1978; F. Harada, N. Kato, and H.-O. Hoshino...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.6.5.1508

    authors: Schoeniger LO,Jelinek WR

    更新日期:1986-05-01 00:00:00

  • Disruption of the c/ebp alpha gene in adult mouse liver.

    abstract::The liver-enriched transcription factor C/EBP alpha has been implicated in the regulation of numerous liver-specific genes. It was previously reported that mice carrying a homozygous null mutation at the c/ebp alpha locus died as neonates due to the absence of hepatic glycogen and the resulting hypoglycemia. However, ...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.17.10.6014

    authors: Lee YH,Sauer B,Johnson PF,Gonzalez FJ

    更新日期:1997-10-01 00:00:00

  • Phospholipase Cgamma2 contributes to light-chain gene activation and receptor editing.

    abstract::Phospholipase Cgamma2 (PLCgamma2) is critical for pre-B-cell receptor (pre-BCR) and BCR signaling. Current studies discovered that PLCgamma2-deficient mice had reduced immunoglobulin lambda (Iglambda) light-chain usage throughout B-cell maturation stages, including transitional type 1 (T1), transitional type 2 (T2), a...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.02273-06

    authors: Bai L,Chen Y,He Y,Dai X,Lin X,Wen R,Wang D

    更新日期:2007-09-01 00:00:00

  • Role of transcription factor NFAT in glucose and insulin homeostasis.

    abstract::Compromised immunoregulation contributes to obesity and complications in metabolic pathogenesis. Here, we demonstrate that the nuclear factor of activated T cell (NFAT) group of transcription factors contributes to glucose and insulin homeostasis. Expression of two members of the NFAT family (NFATc2 and NFATc4) is ind...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.00580-06

    authors: Yang TT,Suk HY,Yang X,Olabisi O,Yu RY,Durand J,Jelicks LA,Kim JY,Scherer PE,Wang Y,Feng Y,Rossetti L,Graef IA,Crabtree GR,Chow CW

    更新日期:2006-10-01 00:00:00

  • Extrachromosomal replication of shuttle vectors in Dictyostelium discoideum.

    abstract::We cloned a 12.3-kilobase (kb) endogenous plasmid, Ddp1, found in several wild-type and laboratory strains of Dictyostelium discoideum into pBR322. The cloned plasmids have been used to cotransform D. discoideum cells with B10S, a transformation vector carrying a gene fusion conferring resistance to G418. Whereas B10S...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.5.11.3241

    authors: Firtel RA,Silan C,Ward TE,Howard P,Metz BA,Nellen W,Jacobson A

    更新日期:1985-11-01 00:00:00

  • Posttranscriptional regulation of chicken ccn2 gene expression by nucleophosmin/B23 during chondrocyte differentiation.

    abstract::CCN2/CTGF is a multifunctional factor that plays a crucial role in the growth and differentiation of chondrocytes. The chicken ccn2 gene is regulated not only at the transcriptional level but also by the interaction between a posttranscriptional element in the 3' untranslated region (3'-UTR) and a cofactor. In the pre...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.00495-08

    authors: Mukudai Y,Kubota S,Kawaki H,Kondo S,Eguchi T,Sumiyoshi K,Ohgawara T,Shimo T,Takigawa M

    更新日期:2008-10-01 00:00:00

  • A compartmentalized phosphorylation/dephosphorylation system that regulates U snRNA export from the nucleus.

    abstract::PHAX (phosphorylated adaptor for RNA export) is the key regulator of U snRNA nuclear export in metazoa. Our previous work revealed that PHAX is phosphorylated in the nucleus and is exported as a component of the U snRNA export complex to the cytoplasm, where it is dephosphorylated (M. Ohno, A. Segref, A. Bachi, M. Wil...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.01189-07

    authors: Kitao S,Segref A,Kast J,Wilm M,Mattaj IW,Ohno M

    更新日期:2008-01-01 00:00:00

  • Domains in human splicing factors SF3a60 and SF3a66 required for binding to SF3a120, assembly of the 17S U2 snRNP, and prespliceosome formation.

    abstract::The active 17S U2 small nuclear ribonucleoprotein particle (snRNP), which binds to the intron branch site during the formation of the prespliceosome, is assembled in vitro by sequential interactions of the essential splicing factors SF3b and SF3a with the 12S U2 snRNP. We have analyzed the function of individual subun...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.21.19.6406-6417.2001

    authors: Nesic D,Krämer A

    更新日期:2001-10-01 00:00:00

  • Two upstream activation sequences control the expression of the XPR2 gene in the yeast Yarrowia lipolytica.

    abstract::We have initiated a study of the promoter region of the alkaline extracellular protease gene (XPR2) from Yarrowia lipolytica to identify upstream sequences possibly involved in carbon, nitrogen, and peptone control of XPR2 expression. Deletion analysis showed that the TATA box and two major upstream activation sequenc...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.14.1.327

    authors: Blanchin-Roland S,Cordero Otero RR,Gaillardin C

    更新日期:1994-01-01 00:00:00

  • The forkhead transcription factor FOXM1 controls cell cycle-dependent gene expression through an atypical chromatin binding mechanism.

    abstract::There are nearly 50 forkhead (FOX) transcription factors encoded in the human genome and, due to sharing a common DNA binding domain, they are all thought to bind to similar DNA sequences. It is therefore unclear how these transcription factors are targeted to specific chromatin regions to elicit specific biological e...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.00881-12

    authors: Chen X,Müller GA,Quaas M,Fischer M,Han N,Stutchbury B,Sharrocks AD,Engeland K

    更新日期:2013-01-01 00:00:00

  • Two distant and precisely positioned domains promote transcription of Xenopus laevis rRNA genes: analysis with linker-scanning mutants.

    abstract::To examine the internal organization of the promoter of the Xenopus laevis rRNA gene, we constructed a series of linker-scanning mutants that traverse the rDNA initiation region. The mutant genes, which have 3 to 11 clustered base substitutions set within an otherwise unaltered rDNA promoter sequence, were injected in...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.6.12.4585

    authors: Windle JJ,Sollner-Webb B

    更新日期:1986-12-01 00:00:00

  • A dual role for the dREAM/MMB complex in the regulation of differentiation-specific E2F/RB target genes.

    abstract::E2F and RB proteins regulate the expression of genes involved in cell cycle progression, apoptosis, differentiation, and development. Recent studies indicate that they function as part of an evolutionarily conserved multiprotein complex termed dREAM/DREAM/LINC. Here we characterize the role of the Drosophila complex, ...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.06314-11

    authors: Lee H,Ragusano L,Martinez A,Gill J,Dimova DK

    更新日期:2012-06-01 00:00:00

  • The CACCC-binding protein KLF3/BKLF represses a subset of KLF1/EKLF target genes and is required for proper erythroid maturation in vivo.

    abstract::The CACCC-box binding protein erythroid Krüppel-like factor (EKLF/KLF1) is a master regulator that directs the expression of many important erythroid genes. We have previously shown that EKLF drives transcription of the gene for a second KLF, basic Krüppel-like factor, or KLF3. We have now tested the in vivo role of K...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.00173-12

    authors: Funnell AP,Norton LJ,Mak KS,Burdach J,Artuz CM,Twine NA,Wilkins MR,Power CA,Hung TT,Perdomo J,Koh P,Bell-Anderson KS,Orkin SH,Fraser ST,Perkins AC,Pearson RC,Crossley M

    更新日期:2012-08-01 00:00:00