Composite patterns in neutral/neutral two-dimensional gels demonstrate inefficient replication origin usage.

Abstract:

:The neutral/neutral two-dimensional (2-D) gel replicon mapping technique has been used to great advantage to localize and characterize origins of replication. Interestingly, many yeast origins display a composite pattern consisting of both a bubble arc and a single-fork arc. Moreover, in every instance in which neutral/neutral 2-D gels have been used to analyze origins in higher eukaryotic cells, two or more adjacent fragments display these composite patterns. We believe that composite patterns signal inefficient origin usage in yeast cells because the replicators in question are not active in every cell cycle and in higher eukaryotic replicons because initiation sites are chosen from among many potential sites lying within a zone. However, others have suggested that the single-fork arcs in these composite gel patterns arise from nicking activity that converts replication bubbles to branched structures that comigrate with bona fide single forks. Here, we have used three different replicon mapping strategies to show that broken simian virus 40 replication bubbles trace unique arcs that are clearly distinguishable from classic, intact single forks. Thus, it is likely that composite 2-D gel patterns represent origins that are inefficiently utilized.

journal_name

Mol Cell Biol

authors

Kalejta RF,Hamlin JL

doi

10.1128/mcb.16.9.4915

subject

Has Abstract

pub_date

1996-09-01 00:00:00

pages

4915-22

issue

9

eissn

0270-7306

issn

1098-5549

journal_volume

16

pub_type

杂志文章
  • Differential regulation of transcription through distinct Suppressor of Hairless DNA binding site architectures during Notch signaling in proneural clusters.

    abstract::In Drosophila melanogaster, achaete (ac) and m8 are model basic helix-loop-helix activator (bHLH A) and repressor genes, respectively, that have the opposite cell expression pattern in proneural clusters during Notch signaling. Previous studies have shown that activation of m8 transcription in specific cells within pr...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.00003-10

    authors: Cave JW,Xia L,Caudy M

    更新日期:2011-01-01 00:00:00

  • Identification of an octamer-binding site in the mouse kappa light-chain immunoglobulin enhancer.

    abstract::A 215-base-pair (bp) region of the mouse MOPC 41 kappa light-chain immunoglobulin gene enhancer has been analyzed for specific binding of lymphoid and nonlymphoid nuclear factors. Mobility shift assays with a series of overlapping DNA fragments have mapped DNA-binding sites for three unique factors. The B-cell-specifi...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.9.10.4239

    authors: Currie RA,Roeder RG

    更新日期:1989-10-01 00:00:00

  • A weak spliceosome-binding domain of Yju2 functions in the first step and bypasses Prp16 in the second step of splicing.

    abstract::Yju2 is an essential splicing factor required for the first catalytic step after the action of Prp2. We dissected the structure of Yju2 and found that the amino (Yju2-N) and carboxyl (Yju2-C) halves of the protein can be separated and reconstituted for Yju2 function both in vivo and in vitro. Yju2-N has a weak affinit...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.00035-13

    authors: Chiang TW,Cheng SC

    更新日期:2013-05-01 00:00:00

  • Genetic interaction between transcription elongation factor TFIIS and RNA polymerase II.

    abstract::Little is known about the regions of RNA polymerase II (RNAPII) that are involved in the process of transcript elongation and interaction with elongation factors. One elongation factor, TFIIS, stimulates transcript elongation by binding to RNAPII and facilitating its passage through intrinsic pausing sites in vitro. I...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.12.9.4142

    authors: Archambault J,Lacroute F,Ruet A,Friesen JD

    更新日期:1992-09-01 00:00:00

  • A Novel Interaction of Ecdysoneless (ECD) Protein with R2TP Complex Component RUVBL1 Is Required for the Functional Role of ECD in Cell Cycle Progression.

    abstract::Ecdysoneless (ECD) is an evolutionarily conserved protein whose germ line deletion is embryonic lethal. Deletion of Ecd in cells causes cell cycle arrest, which is rescued by exogenous ECD, demonstrating a requirement of ECD for normal mammalian cell cycle progression. However, the exact mechanism by which ECD regulat...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.00594-15

    authors: Mir RA,Bele A,Mirza S,Srivastava S,Olou AA,Ammons SA,Kim JH,Gurumurthy CB,Qiu F,Band H,Band V

    更新日期:2015-12-28 00:00:00

  • Regulation of albumin gene expression in a series of rat hepatocyte cell lines immortalized by simian virus 40 and maintained in chemically defined medium.

    abstract::A series of simian virus 40 (SV40)-immortalized hepatocyte cell lines were characterized for albumin production, the regulation of albumin production, and the expression of other liver-specific genes. This series of cell lines is particularly useful for studying the regulation of hepatocyte gene expression because the...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.7.10.3740

    authors: Woodworth CD,Isom HC

    更新日期:1987-10-01 00:00:00

  • Osteoclast progenitors reside in the peroxisome proliferator-activated receptor γ-expressing bone marrow cell population.

    abstract::Osteoclasts are bone-resorbing cells essential for skeletal development, homeostasis, and regeneration. They derive from hematopoietic progenitors in the monocyte/macrophage lineage and differentiate in response to RANKL. However, the precise nature of osteoclast progenitors is a longstanding and important question. U...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.05979-11

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

    更新日期:2011-12-01 00:00:00

  • Human Cdc34 and Rad6B ubiquitin-conjugating enzymes target repressors of cyclic AMP-induced transcription for proteolysis.

    abstract::Ubiquitin-mediated proteolysis controls diverse physiological processes in eukaryotes. However, few in vivo targets of the mammalian Cdc34 and Rad6 ubiquitin-conjugating enzymes are known. A yeast-based genetic assay to identify proteins that interact with human Cdc34 resulted in three cDNAs encoding bZIP DNA binding ...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.19.7.5001

    authors: Pati D,Meistrich ML,Plon SE

    更新日期:1999-07-01 00:00:00

  • Plk is a functional homolog of Saccharomyces cerevisiae Cdc5, and elevated Plk activity induces multiple septation structures.

    abstract::Plk is a mammalian serine/threonine protein kinase whose activity peaks at the onset of M phase. It is closely related to other mammalian kinases, Snk, Fnk, and Prk, as well as to Xenopus laevis Plx1, Drosophila melanogaster polo, Schizosaccharomyces pombe Plo1, and Saccharomyces cerevisiae Cdc5. The M phase of the ce...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.17.6.3408

    authors: Lee KS,Erikson RL

    更新日期:1997-06-01 00:00:00

  • Specific acetylation of chromosomal protein HMG-17 by PCAF alters its interaction with nucleosomes.

    abstract::Nonhistone chromosomal proteins HMG-14 and HMG-17 are closely related nucleosomal binding proteins that unfold the higher-order chromatin structure, thereby enhancing the transcription and replication potential of chromatin. Here we report that PCAF, a transcription coactivator with intrinsic histone acetyltransferase...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.19.5.3466

    authors: Herrera JE,Sakaguchi K,Bergel M,Trieschmann L,Nakatani Y,Bustin M

    更新日期:1999-05-01 00:00:00

  • Proliferative activation of quiescent Rat-1A cells by delta FosB.

    abstract::Fos and Jun transcription factors are induced during the normal course of the proliferative response of quiescent cells to serum or to growth factors. We have shown that delta FosB, an alternatively spliced form of FosB, is formed as rapidly as FosB in serum-stimulated Rat-1A cells. Although delta FosB lacks the C-ter...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.13.7.4157

    authors: Nakabeppu Y,Oda S,Sekiguchi M

    更新日期:1993-07-01 00:00:00

  • Multiple proteins interact with the fushi tarazu proximal enhancer.

    abstract::The expression of the Drosophila segmentation gene fushi tarazu (ftz) is controlled at the level of transcription. The proximal enhancer, located approximately 3.4 kb upstream of the transcription start site, directs lacZ fusion gene expression in a ftz-like seven-stripe pattern in transgenic fly embryos. We have take...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.13.9.5549

    authors: Han W,Yu Y,Altan N,Pick L

    更新日期:1993-09-01 00:00:00

  • Molecular cloning of casein kinase II alpha subunit from Dictyostelium discoideum and its expression in the life cycle.

    abstract::A Dictyostelium discoideum cDNA encoding an alpha-type subunit of casein kinase II was isolated, and its cDNA was used to study developmental expression of casein kinase II during the Dictyostelium life cycle. The 1.3-kb cDNA insert contained an open reading frame of 337 amino acids (M(r) 39,900). The deduced amino ac...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.12.12.5711

    authors: Kikkawa U,Mann SK,Firtel RA,Hunter T

    更新日期:1992-12-01 00:00:00

  • Mutational analysis of the hsp70-interacting protein Hip.

    abstract::The hsp70-interacting protein Hip participates in the assembly pathway for progesterone receptor complexes. During assembly, Hip appears at early assembly stages in a transient manner that parallels hsp70 interactions. In this study, a cDNA for human Hip was used to develop various mutant Hip forms in the initial mapp...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.16.11.6200

    authors: Prapapanich V,Chen S,Toran EJ,Rimerman RA,Smith DF

    更新日期:1996-11-01 00:00:00

  • Dax1 binds to Oct3/4 and inhibits its transcriptional activity in embryonic stem cells.

    abstract::Embryonic stem (ES) cells are pluripotent cells derived from the inner cell mass of blastocysts. Transcription factor Oct3/4 is an indispensable factor in the self-renewal of ES cells. In this study, we searched for a protein that would interact with Oct3/4 in ES cells and identified an orphan nuclear hormone receptor...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.01863-08

    authors: Sun C,Nakatake Y,Akagi T,Ura H,Matsuda T,Nishiyama A,Koide H,Ko MS,Niwa H,Yokota T

    更新日期:2009-08-01 00:00:00

  • Transfer and amplification of a mutant beta-tubulin gene results in colcemid dependence: use of the transformant to demonstrate regulation of beta-tubulin subunit levels by protein degradation.

    abstract::Total genomic DNA from a temperature-sensitive, colcemid-resistant Chinese hamster ovary (CHO) cell mutant expressing an electrophoretic variant beta-tubulin was used to transform wild-type CHO cells to colcemid-resistant cells at 37 degrees C. Southern blot analysis of the transformant demonstrated the three- to five...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.6.5.1422

    authors: Whitfield C,Abraham I,Ascherman D,Gottesman MM

    更新日期:1986-05-01 00:00:00

  • Loss of YY1 impacts the heterochromatic state and meiotic double-strand breaks during mouse spermatogenesis.

    abstract::The progression of spermatogenesis involves global changes in chromatin structure and conformation. However, our understanding of the regulation of chromatin changes in germ cells remains limited. Here we describe both in vivo RNA interference and genetic mouse knockout studies that identify a critical role for Yin Ya...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.00679-09

    authors: Wu S,Hu YC,Liu H,Shi Y

    更新日期:2009-12-01 00:00:00

  • Reciprocal regulation of the tandemly duplicated PHO5/PHO3 gene cluster within the acid phosphatase multigene family of Saccharomyces cerevisiae.

    abstract::We characterized the organization and expression of PHO5 and PHO3, the tightly linked repressible and constitutive acid phosphatase genes of Saccharomyces cerevisiae. The "constitutive" gene, PHO3, is expressed only when PHO5 is not. Altering PHO5 expression, either through promoter deletions or through mutations in t...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.6.6.1855

    authors: Tait-Kamradt AG,Turner KJ,Kramer RA,Elliott QD,Bostian SJ,Thill GP,Rogers DT,Bostian KA

    更新日期:1986-06-01 00:00:00

  • 14-3-3 interaction with histone H3 involves a dual modification pattern of phosphoacetylation.

    abstract::Histone modifications occur in precise patterns and are proposed to signal the recruitment of effector molecules that profoundly impact chromatin structure, gene regulation, and cell cycle events. The linked modifications serine 10 phosphorylation and lysine 14 acetylation on histone H3 (H3S10phK14ac), modifications c...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.01457-07

    authors: Walter W,Clynes D,Tang Y,Marmorstein R,Mellor J,Berger SL

    更新日期:2008-04-01 00:00:00

  • Identification of a cis-acting DNA antisilencer element which modulates vimentin gene expression.

    abstract::Vimentin is a tissue-specific, developmentally regulated member of the intermediate filament protein family normally expressed in cells of mesenchymal origin. Transcription factors which recognize specific cis-acting elements of the chicken gene include Sp-1 and the 95-kDa silencer protein which binds to a 40-bp silen...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.12.5.2230

    authors: Stover DM,Zehner ZE

    更新日期:1992-05-01 00:00:00

  • Human MDM2 isoforms translated differentially on constitutive versus p53-regulated transcripts have distinct functions in the p53/MDM2 and TSG101/MDM2 feedback control loops.

    abstract::Proteins encoded by the mdm2 gene, which has a pivotal role in the regulation of growth and differentiation, exist principally in human and murine cells as two isoforms that migrate in gels as 75-kDa and 90-kDa proteins. There is limited understanding of the respective biological roles of these isoforms, their molecul...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.00235-06

    authors: Cheng TH,Cohen SN

    更新日期:2007-01-01 00:00:00

  • Cotranscriptional processing of Drosophila histone mRNAs.

    abstract::The 3' ends of metazoan histone mRNAs are generated by specialized processing machinery that cleaves downstream of a conserved stem-loop structure. To examine how this reaction might be influenced by transcription, we used a Drosophila melanogaster in vitro system that supports both processes. In this system the compl...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.23.12.4046-4055.2003

    authors: Adamson TE,Price DH

    更新日期:2003-06-01 00:00:00

  • DNA-binding activities of the Drosophila melanogaster even-skipped protein are mediated by its homeo domain and influenced by protein context.

    abstract::The homeo box gene even-skipped (eve) encodes a 376-amino-acid protein that binds with high affinity to sequences located near the 5' termini of the eve and en genes. The 5' en sites are A + T rich and contain copies of the 10-base-pair (bp) consensus sequence T-C-A-A-T-T-A-A-A-T. In contrast, the 5' eve sites are G +...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.8.11.4598

    authors: Hoey T,Warrior R,Manak J,Levine M

    更新日期:1988-11-01 00:00:00

  • An open reading frame element mediates posttranscriptional regulation of tropoelastin and responsiveness to transforming growth factor beta1.

    abstract::Elastin, an extracellular component of arteries, lung, and skin, is produced during fetal and neonatal growth. We reported previously that the cessation of elastin production is controlled by a posttranscriptional mechanism. Although tropoelastin pre-mRNA is transcribed at the same rate in neonates and adults, marked ...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.19.11.7314

    authors: Zhang M,Pierce RA,Wachi H,Mecham RP,Parks WC

    更新日期:1999-11-01 00:00:00

  • An unconventional human Ccr4-Caf1 deadenylase complex in nuclear cajal bodies.

    abstract::mRNA deadenylation is a key process in the regulation of translation and mRNA turnover. In Saccharomyces cerevisiae, deadenylation is primarily carried out by the Ccr4p and Caf1p/Pop2p subunits of the Ccr4-Not complex, which is conserved in eukaryotes including humans. Here we have identified an unconventional human C...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.01483-06

    authors: Wagner E,Clement SL,Lykke-Andersen J

    更新日期:2007-03-01 00:00:00

  • The C proteins of HeLa 40S nuclear ribonucleoprotein particles exist as anisotropic tetramers of (C1)3 C2.

    abstract::The C proteins (C1 and C2) of HeLa 40S heterogeneous nuclear ribonucleoprotein particles copurify under native conditions as a stable complex with a fixed molar protein ratio (S.F. Barnett, W.M. LeStourgeon, and D.L. Friedman, J. Biochem. Biophys. Methods 16:87-97, 1988). Gel filtration chromatography and velocity sed...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.9.2.492

    authors: Barnett SF,Friedman DL,LeStourgeon WM

    更新日期:1989-02-01 00:00:00

  • Interactions of the Mcm1 MADS box protein with cofactors that regulate mating in yeast.

    abstract::The yeast Mcm1 protein is a member of the MADS box family of transcriptional regulatory factors, a class of DNA-binding proteins that control numerous cellular and developmental processes in yeast, Drosophila melanogaster, plants, and mammals. Although these proteins bind DNA on their own, they often combine with diff...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.22.13.4607-4621.2002

    authors: Mead J,Bruning AR,Gill MK,Steiner AM,Acton TB,Vershon AK

    更新日期:2002-07-01 00:00:00

  • Properties and possible functions of the adenylate cyclase in plasma membranes of Saccharomyces cerevisiae.

    abstract::We have examined the possible role of adenosine 3',5'-phosphate (cAMP) in functions associated with the plasma membranes of Saccharomyces cerevisiae. Purified membranes from this source contained an adenylate cyclase which was insensitive to activation by fluoride or guanine nucleotides, only weakly responsive to chan...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.2.12.1481

    authors: Jaynes PK,McDonough JP,Mahler HR

    更新日期:1982-12-01 00:00:00

  • The nematode eukaryotic translation initiation factor 4E/G complex works with a trans-spliced leader stem-loop to enable efficient translation of trimethylguanosine-capped RNAs.

    abstract::Eukaryotic mRNA translation begins with recruitment of the 40S ribosome complex to the mRNA 5' end through the eIF4F initiation complex binding to the 5' m(7)G-mRNA cap. Spliced leader (SL) RNA trans splicing adds a trimethylguanosine (TMG) cap and a sequence, the SL, to the 5' end of mRNAs. Efficient translation of T...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.01437-09

    authors: Wallace A,Filbin ME,Veo B,McFarland C,Stepinski J,Jankowska-Anyszka M,Darzynkiewicz E,Davis RE

    更新日期:2010-04-01 00:00:00

  • RYBP represses endogenous retroviruses and preimplantation- and germ line-specific genes in mouse embryonic stem cells.

    abstract::Polycomb repressive complexes (PRCs) are important chromatin regulators of embryonic stem (ES) cell function. RYBP binds Polycomb H2A monoubiquitin ligases Ring1A and Ring1B and has been suggested to assist PRC localization to their targets. Moreover, constitutive inactivation of RYBP precludes ES cell formation. Usin...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.06441-11

    authors: Hisada K,Sánchez C,Endo TA,Endoh M,Román-Trufero M,Sharif J,Koseki H,Vidal M

    更新日期:2012-03-01 00:00:00