Fine-structure analysis of activation-induced deaminase accessibility to class switch region R-loops.

Abstract:

:Activation-induced deaminase (AID) is essential for class switch recombination and somatic hypermutation, and it has the ability to deaminate single-stranded DNA at cytidines. Mammalian class switch regions form R-loops upon transcription in the physiological orientation. The displaced DNA strand of an R-loop is forced to wrap around the RNA-DNA hybrid; hence, it may not have complete exposure to proteins. A fundamental question concerns the extent to which AID is accessible to the displaced strand of a transcription-generated R-loop. We used a minimal R-loop to carry out high-resolution analysis of the precise locations of AID action. We found that AID deaminates on the displaced DNA strand across the entire length of the R-loop. Displaced strand locations with a WRC (where W is A or T and R is A or G) sequence are preferred targets, but there are clear exceptions. These WRC deviations may be due to steric constraints on the accessibility of AID to these sites as the displaced strand twists around the RNA-DNA duplex. This phenomenon may explain the lack of WRC site preference at the mutations surrounding class switch recombination junctions.

journal_name

Mol Cell Biol

authors

Yu K,Roy D,Bayramyan M,Haworth IS,Lieber MR

doi

10.1128/MCB.25.5.1730-1736.2005

subject

Has Abstract

pub_date

2005-03-01 00:00:00

pages

1730-6

issue

5

eissn

0270-7306

issn

1098-5549

pii

25/5/1730

journal_volume

25

pub_type

杂志文章
  • Saccharomyces cerevisiae Mob1p is required for cytokinesis and mitotic exit.

    abstract::The Saccharomyces cerevisiae mitotic exit network (MEN) is a conserved set of genes that mediate the transition from mitosis to G(1) by regulating mitotic cyclin degradation and the inactivation of cyclin-dependent kinase (CDK). Here, we demonstrate that, in addition to mitotic exit, S. cerevisiae MEN gene MOB1 is req...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.21.20.6972-6983.2001

    authors: Luca FC,Mody M,Kurischko C,Roof DM,Giddings TH,Winey M

    更新日期:2001-10-01 00:00:00

  • Repression of GCN5 histone acetyltransferase activity via bromodomain-mediated binding and phosphorylation by the Ku-DNA-dependent protein kinase complex.

    abstract::GCN5, a putative transcriptional adapter in humans and yeast, possesses histone acetyltransferase (HAT) activity which has been linked to GCN5's role in transcriptional activation in yeast. In this report, we demonstrate a functional interaction between human GCN5 (hGCN5) and the DNA-dependent protein kinase (DNA-PK) ...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.18.3.1349

    authors: Barlev NA,Poltoratsky V,Owen-Hughes T,Ying C,Liu L,Workman JL,Berger SL

    更新日期:1998-03-01 00:00:00

  • pp39mos is associated with p34cdc2 kinase in c-mosxe-transformed NIH 3T3 cells.

    abstract::We investigated the possible interactions between pp39mos and p34cdc2 kinase in NIH 3T3 cells transformed by c-mosxe. pp39mos is coprecipitated with p34cdc2 when using either anti-PSTAIR antibody or p13suc1-Sepharose beads. Likewise, p34cdc2 is coprecipitated with pp39mos when using anti-mos antibody. However, pp39mos...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.12.8.3583

    authors: Zhou R,Daar I,Ferris DK,White G,Paules RS,Vande Woude G

    更新日期:1992-08-01 00:00:00

  • Cooperation of p27(Kip1) and p18(INK4c) in progestin-mediated cell cycle arrest in T-47D breast cancer cells.

    abstract::The steroid hormone progesterone regulates proliferation and differentiation in the mammary gland and uterus by cell cycle phase-specific actions. The long-term effect of progestins on T-47D breast cancer cells is inhibition of cellular proliferation. This is accompanied by decreased G(1) cyclin-dependent kinase (CDK)...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.20.7.2581-2591.2000

    authors: Swarbrick A,Lee CS,Sutherland RL,Musgrove EA

    更新日期:2000-04-01 00:00:00

  • Human Rvb1/Tip49 is required for the histone acetyltransferase activity of Tip60/NuA4 and for the downregulation of phosphorylation on H2AX after DNA damage.

    abstract::The role of chromatin-remodeling factors in transcription is well established, but the link between chromatin-remodeling complexes and DNA repair remains unexplored. Human Rvb1 and Rvb2 are highly conserved AAA(+) ATP binding proteins that are part of various chromatin-remodeling complexes, such as Ino80, SNF2-related...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.01983-07

    authors: Jha S,Shibata E,Dutta A

    更新日期:2008-04-01 00:00:00

  • The absence of Tssc6, a member of the tetraspanin superfamily, does not affect lymphoid development but enhances in vitro T-cell proliferative responses.

    abstract::The tetraspanins are a family of integral membrane proteins with four transmembrane domains. These molecules form multimolecular networks on the surfaces of many different cell types. Gene-targeting studies have revealed a role for tetraspanins in B- and T-lymphocyte function. We have isolated and deleted a novel tetr...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.22.14.5006-5018.2002

    authors: Tarrant JM,Groom J,Metcalf D,Li R,Borobokas B,Wright MD,Tarlinton D,Robb L

    更新日期:2002-07-01 00:00:00

  • Genetic requirements for RAD51- and RAD54-independent break-induced replication repair of a chromosomal double-strand break.

    abstract::Broken chromosomes can be repaired by several homologous recombination mechanisms, including gene conversion and break-induced replication (BIR). In Saccharomyces cerevisiae, an HO endonuclease-induced double-strand break (DSB) is normally repaired by gene conversion. Previously, we have shown that in the absence of R...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.21.6.2048-2056.2001

    authors: Signon L,Malkova A,Naylor ML,Klein H,Haber JE

    更新日期:2001-03-01 00:00:00

  • Binding and uptake of diphtheria toxin by toxin-resistant Chinese hamster ovary and mouse cells.

    abstract::We investigated two phenotypically distinct types of diphtheria toxin-resistant mutants of Chinese hamster cells and compared their resistance with that of naturally resistant mouse cells. All are resistant due to a defect in the process of internalization and delivery of toxin to its target in the cytosol, elongation...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.3.7.1283

    authors: Didsbury JR,Moehring JM,Moehring TJ

    更新日期:1983-07-01 00:00:00

  • Mcm1 promotes replication initiation by binding specific elements at replication origins.

    abstract::Minichromosome maintenance protein 1 (Mcm1) is required for efficient replication of autonomously replicating sequence (ARS)-containing plasmids in yeast cells. Reduced DNA binding activity in the Mcm1-1 mutant protein (P97L) results in selective initiation of a subset of replication origins and causes instability of ...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.24.14.6514-6524.2004

    authors: Chang VK,Donato JJ,Chan CS,Tye BK

    更新日期:2004-07-01 00:00:00

  • Determination of the spectrum of mutations induced by defined-wavelength solar UVB (313-nm) radiation in mammalian cells by use of a shuttle vector.

    abstract::Mutations induced by UVB (313-nm) radiation, a wavelength in the region of peak effectiveness for sunlight-induced skin cancer in humans, have been analyzed at the sequence level in simian cells by using a plasmid shuttle vector (pZ189). We find that significant differences exist between the types of mutations induced...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.8.12.5425

    authors: Keyse SM,Amaudruz F,Tyrrell RM

    更新日期:1988-12-01 00:00:00

  • Lipid raft targeting of hematopoietic protein tyrosine phosphatase by protein kinase C theta-mediated phosphorylation.

    abstract::Protein kinase C theta (PKC theta) is unique among PKC isozymes in its translocation to the center of the immune synapse in T cells and its unique downstream signaling. Here we show that the hematopoietic protein tyrosine phosphatase (HePTP) also accumulates in the immune synapse in a PKC theta-dependent manner upon a...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.26.5.1806-1816.2006

    authors: Nika K,Charvet C,Williams S,Tautz L,Bruckner S,Rahmouni S,Bottini N,Schoenberger SP,Baier G,Altman A,Mustelin T

    更新日期:2006-03-01 00:00:00

  • Endothelial Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4 Is Critical for Lymphatic Vascular Development and Function.

    abstract::The molecular mechanisms underlying lymphatic vascular development and function are not well understood. Recent studies have suggested a role for endothelial cell (EC) mitogen-activated protein kinase kinase kinase kinase 4 (Map4k4) in developmental angiogenesis and atherosclerosis. Here, we show that constitutive los...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.01121-15

    authors: Roth Flach RJ,Guo CA,Danai LV,Yawe JC,Gujja S,Edwards YJ,Czech MP

    更新日期:2016-05-31 00:00:00

  • Isolated clusters of paired tandemly repeated sequences in the Xenopus laevis genome.

    abstract::There exist in the Xenopus laevis genome clusters of tandemly repeated DNA sequences, consisting of two types of 393-base-pair repeating unit. Each such cluster contains several units of one of these paired tandem repeats (PTR-1), followed by several units of the other repeat (PTR-2). The number of repeats of each typ...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.4.2.254

    authors: Carroll D,Garrett JE,Lam BS

    更新日期:1984-02-01 00:00:00

  • RNA polymerase II carboxy-terminal domain phosphorylation is required for cotranscriptional pre-mRNA splicing and 3'-end formation.

    abstract::We investigated the role of RNA polymerase II (pol II) carboxy-terminal domain (CTD) phosphorylation in pre-mRNA processing coupled and uncoupled from transcription in Xenopus oocytes. Inhibition of CTD phosphorylation by the kinase inhibitors 5,6-dichloro-1beta-D-ribofuranosyl-benzimidazole and H8 blocked transcripti...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.24.20.8963-8969.2004

    authors: Bird G,Zorio DA,Bentley DL

    更新日期:2004-10-01 00:00:00

  • Transforming Growth Factor β-Induced Proliferative Arrest Mediated by TRIM26-Dependent TAF7 Degradation and Its Antagonism by MYC.

    abstract::Recognition of gene promoters by RNA polymerase II is mediated by general transcription factor IID (TFIID), which has been thought to be a static complex and to play a passive role in the regulation of gene expression under the instruction of gene-specific transcription factors. Here we show that transforming growth f...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.00449-17

    authors: Nakagawa T,Hosogane M,Nakagawa M,Morohoshi A,Funayama R,Nakayama K

    更新日期:2018-02-12 00:00:00

  • CD40 induces apoptosis in carcinoma cells through activation of cytotoxic ligands of the tumor necrosis factor superfamily.

    abstract::CD40, a tumor necrosis factor (TNF) receptor (TNFR) family member, conveys signals regulating diverse cellular responses, ranging from proliferation and differentiation to growth suppression and cell death. The ability of CD40 to mediate apoptosis in carcinoma cells is intriguing given the fact that the CD40 cytoplasm...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.20.15.5503-5515.2000

    authors: Eliopoulos AG,Davies C,Knox PG,Gallagher NJ,Afford SC,Adams DH,Young LS

    更新日期:2000-08-01 00:00:00

  • The microRNA 424/503 cluster reduces CDC25A expression during cell cycle arrest imposed by transforming growth factor β in mammary epithelial cells.

    abstract::Recently, we demonstrated that the microRNA 424(322)/503 [miR-424(322)/503] cluster is transcriptionally controlled by transforming growth factor β (TGF-β) in the mammary epithelium. Induction of this microRNA cluster impacts mammary epithelium fate by regulating apoptosis and insulin-like growth factor 1 (IGF1) signa...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.00611-14

    authors: Llobet-Navas D,Rodriguez-Barrueco R,de la Iglesia-Vicente J,Olivan M,Castro V,Saucedo-Cuevas L,Marshall N,Putcha P,Castillo-Martin M,Bardot E,Ezhkova E,Iavarone A,Cordon-Cardo C,Silva JM

    更新日期:2014-12-01 00:00:00

  • Identification of proteins associating with glycosylphosphatidylinositol- anchored T-cadherin on the surface of vascular endothelial cells: role for Grp78/BiP in T-cadherin-dependent cell survival.

    abstract::There is scant knowledge regarding how cell surface lipid-anchored T-cadherin (T-cad) transmits signals through the plasma membrane to its intracellular targets. This study aimed to identify membrane proteins colocalizing with atypical glycosylphosphatidylinositol (GPI)-anchored T-cad on the surface of endothelial cel...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.00157-08

    authors: Philippova M,Ivanov D,Joshi MB,Kyriakakis E,Rupp K,Afonyushkin T,Bochkov V,Erne P,Resink TJ

    更新日期:2008-06-01 00:00:00

  • Differential regulation of the rat phosphoenolpyruvate carboxykinase gene expression in several tissues of transgenic mice.

    abstract::The selective expression of a unique copy gene in several mammalian tissues has been approached by studying the regulatory sequences needed to control expression of the rat phosphoenolpyruvate carboxykinase (PEPCK) gene in transgenic mice. A transgene containing the entire PEPCK gene, including 2.2 kb of the 5'-flanki...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.12.3.1396

    authors: Eisenberger CL,Nechushtan H,Cohen H,Shani M,Reshef L

    更新日期:1992-03-01 00:00:00

  • Vascular endothelial growth factor activates nuclear factor of activated T cells in human endothelial cells: a role for tissue factor gene expression.

    abstract::Vascular endothelial growth factor (VEGF) is a potent angiogenic inducer that stimulates the expression of tissue factor (TF), the major cellular initiator of blood coagulation. Here we show that signaling triggered by VEGF induced DNA-binding and transcriptional activities of nuclear factor of activated T cells (NFAT...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.19.3.2032

    authors: Armesilla AL,Lorenzo E,Gómez del Arco P,Martínez-Martínez S,Alfranca A,Redondo JM

    更新日期:1999-03-01 00:00:00

  • Trm112 is required for Bud23-mediated methylation of the 18S rRNA at position G1575.

    abstract::Posttranscriptional and posttranslational modification of macromolecules is known to fine-tune their functions. Trm112 is unique, acting as an activator of both tRNA and protein methyltransferases. Here we report that in Saccharomyces cerevisiae, Trm112 is required for efficient ribosome synthesis and progression thro...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.06623-11

    authors: Figaro S,Wacheul L,Schillewaert S,Graille M,Huvelle E,Mongeard R,Zorbas C,Lafontaine DL,Heurgué-Hamard V

    更新日期:2012-06-01 00:00:00

  • cis-acting regulatory elements within gag genes of avian retroviruses.

    abstract::A cis-acting enhancer element has been detected within the gag gene of several avian retroviruses, including Rous sarcoma virus, Fujinami sarcoma virus, and the endogenous Rous-associated virus-0. A consensus enhancer core sequence, GTGGTTTG, is present in all of these viral genomes, approximately 900 bases downstream...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.7.1.388

    authors: Arrigo S,Yun M,Beemon K

    更新日期:1987-01-01 00:00:00

  • Positive control of sporulation-specific genes by the IME1 and IME2 products in Saccharomyces cerevisiae.

    abstract::In the yeast Saccharomyces cerevisiae, meiosis and spore formation require the induction of sporulation-specific genes. Two genes are thought to activate the sporulation program: IME1 and IME2 (inducer of meiosis). Both genes are induced upon entry into meiosis, and IME1 is required for IME2 expression. We report here...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.10.5.2104

    authors: Mitchell AP,Driscoll SE,Smith HE

    更新日期:1990-05-01 00:00:00

  • A nucleosome-positioning sequence is required for GCN4 to activate transcription in the absence of a TATA element.

    abstract::In the gal-his3 hybrid promoter his3-GG1, the yeast upstream activator protein GCN4 stimulates transcription when bound at the position normally occupied by the TATA element. This TATA-independent activation by GCN4 requires two additional elements in the gal enhancer region that are distinct from those involved in no...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.10.8.4256

    authors: Brandl CJ,Struhl K

    更新日期:1990-08-01 00:00:00

  • A model system for activation-induced alternative splicing of CD45 pre-mRNA in T cells implicates protein kinase C and Ras.

    abstract::Multiple isoforms of the protein tyrosine phosphatase CD45 are expressed on the surface of human T cells. Interestingly, the expression of these isoforms has been shown to vary significantly upon T-cell activation. In this report, we describe a novel cell line-based model system in which we can mimic the activation-in...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.20.1.70-80.2000

    authors: Lynch KW,Weiss A

    更新日期:2000-01-01 00:00:00

  • E2a/Pbx1 induces the rapid proliferation of stem cell factor-dependent murine pro-T cells that cause acute T-lymphoid or myeloid leukemias in mice.

    abstract::Oncoprotein E2a/Pbx1 is produced by the t(1;19) chromosomal translocation of human pre-B acute lymphoblastic leukemia. E2a/Pbx1 blocks differentiation of primary myeloid progenitors but, paradoxically, induces apoptosis in established pre-B-cell lines, and no transforming function of E2a/Pbx1 has been reported in cult...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.24.3.1256-1269.2004

    authors: Sykes DB,Kamps MP

    更新日期:2004-02-01 00:00:00

  • Coordinate regulation of IkappaB kinases by mitogen-activated protein kinase kinase kinase 1 and NF-kappaB-inducing kinase.

    abstract::IkappaB kinases (IKKalpha and IKKbeta) are key components of the IKK complex that mediates activation of the transcription factor NF-kappaB in response to extracellular stimuli such as inflammatory cytokines, viral and bacterial infection, and UV irradiation. Although NF-kappaB-inducing kinase (NIK) interacts with and...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.18.12.7336

    authors: Nemoto S,DiDonato JA,Lin A

    更新日期:1998-12-01 00:00:00

  • 5'-AMP-activated protein kinase (AMPK) is induced by low-oxygen and glucose deprivation conditions found in solid-tumor microenvironments.

    abstract::Low oxygen gradients (hypoxia and anoxia) are important determinants of pathological conditions under which the tissue blood supply is deficient or defective, such as in solid tumors. We have been investigating the relationship between the activation of hypoxia-inducible factor 1 (HIF-1), the primary transcriptional r...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/MCB.00166-06

    authors: Laderoute KR,Amin K,Calaoagan JM,Knapp M,Le T,Orduna J,Foretz M,Viollet B

    更新日期:2006-07-01 00:00:00

  • The mitogenic response to tumor necrosis factor alpha requires c-Jun/AP-1.

    abstract::In the present study, we addressed the role of the c-jun proto-oncogene in the mitogenic response of human fibroblasts and primary acute myelogenous leukemia blasts to tumor necrosis factor alpha (TNF-alpha). Our data indicate that TNF-alpha treatment of these cells is associated with transcriptional activation of c-j...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.13.7.4284

    authors: Brach MA,Gruss HJ,Sott C,Herrmann F

    更新日期:1993-07-01 00:00:00

  • Discrete functions of TRAF1 and TRAF2 in Drosophila melanogaster mediated by c-Jun N-terminal kinase and NF-kappaB-dependent signaling pathways.

    abstract::Two Drosophila tumor necrosis factor receptor-associated factors (TRAF), DTRAF1 and DTRAF2, are proposed to have similar functions with their mammalian counterparts as a signal mediator of cell surface receptors. However, their in vivo functions and related signaling pathways are not fully understood yet. Here, we sho...

    journal_title:Molecular and cellular biology

    pub_type: 杂志文章

    doi:10.1128/mcb.23.22.7982-7991.2003

    authors: Cha GH,Cho KS,Lee JH,Kim M,Kim E,Park J,Lee SB,Chung J

    更新日期:2003-11-01 00:00:00