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Topoisomerase IIalpha binding domains of adenomatous polyposis coli influence cell cycle progression and aneuploidy.
Wang Y, Coffey RJ, Osheroff N, Neufeld KL
(2010) PLoS One 5: e9994
MeSH Terms: Adenomatous Polyposis Coli, Adenomatous Polyposis Coli Protein, Aneuploidy, Antigens, Neoplasm, Binding Sites, Cell Cycle, Cell Line, Tumor, Codon, Nonsense, DNA Topoisomerases, Type II, DNA-Binding Proteins, Epithelial Cells, G2 Phase, Humans, Repetitive Sequences, Nucleic Acid, beta Catenin
Show Abstract · Added August 12, 2010
BACKGROUND - Truncating mutations in the tumor suppressor gene APC (Adenomatous Polyposis Coli) are thought to initiate the majority of colorectal cancers. The 15- and 20-amino acid repeat regions of APC bind beta-catenin and have been widely studied for their role in the negative regulation of canonical Wnt signaling. However, functions of APC in other important cellular processes, such as cell cycle control or aneuploidy, are only beginning to be studied. Our previous investigation implicated the 15-amino acid repeat region of APC (M2-APC) in the regulation of the G2/M cell cycle transition through interaction with topoisomerase IIalpha (topo IIalpha).
METHODOLOGY/PRINCIPAL FINDINGS - We now demonstrate that the 20-amino acid repeat region of APC (M3-APC) also interacts with topo IIalpha in colonic epithelial cells. Expression of M3-APC in cells with full-length endogenous APC causes cell accumulation in G2. However, cells with a mutated topo IIalpha isoform and lacking topo IIbeta did not arrest, suggesting that the cellular consequence of M2- or M3-APC expression depends on functional topoisomerase II. Both purified recombinant M2- and M3-APC significantly enhanced the activity of topo IIalpha. Of note, although M3-APC can bind beta-catenin, the G2 arrest did not correlate with beta-catenin expression or activity, similar to what was seen with M2-APC. More importantly, expression of either M2- or M3-APC also led to increased aneuploidy in cells with full-length endogenous APC but not in cells with truncated endogenous APC that includes the M2-APC region.
CONCLUSIONS/SIGNIFICANCE - Together, our data establish that the 20-amino acid repeat region of APC interacts with topo IIalpha to enhance its activity in vitro, and leads to G2 cell cycle accumulation and aneuploidy when expressed in cells containing full-length APC. These findings provide an additional explanation for the aneuploidy associated with many colon cancers that possess truncated APC.
1 Communities
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15 MeSH Terms
Initial sequence and comparative analysis of the cat genome.
Pontius JU, Mullikin JC, Smith DR, Agencourt Sequencing Team, Lindblad-Toh K, Gnerre S, Clamp M, Chang J, Stephens R, Neelam B, Volfovsky N, Schäffer AA, Agarwala R, Narfström K, Murphy WJ, Giger U, Roca AL, Antunes A, Menotti-Raymond M, Yuhki N, Pecon-Slattery J, Johnson WE, Bourque G, Tesler G, NISC Comparative Sequencing Program, O'Brien SJ
(2007) Genome Res 17: 1675-89
MeSH Terms: Animals, Cats, Dogs, Genome, Genomics, Humans, Mice, MicroRNAs, Microsatellite Repeats, Models, Genetic, Polymorphism, Single Nucleotide, Rats, Repetitive Sequences, Nucleic Acid
Show Abstract · Added February 22, 2011
The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome assemblies of six mammals (human, chimpanzee, mouse, rat, dog, and cow). The results resolved chromosomal positions for 663,480 contigs, 20,285 putative feline gene orthologs, and 133,499 conserved sequence blocks (CSBs). Additional annotated features include repetitive elements, endogenous retroviral sequences, nuclear mitochondrial (numt) sequences, micro-RNAs, and evolutionary breakpoints that suggest historic balancing of translocation and inversion incidences in distinct mammalian lineages. Large numbers of single nucleotide polymorphisms (SNPs), deletion insertion polymorphisms (DIPs), and short tandem repeats (STRs), suitable for linkage or association studies were characterized in the context of long stretches of chromosome homozygosity. In spite of the light coverage capturing approximately 65% of euchromatin sequence from the cat genome, these comparative insights shed new light on the tempo and mode of gene/genome evolution in mammals, promise several research applications for the cat, and also illustrate that a comparative approach using more deeply covered mammals provides an informative, preliminary annotation of a light (1.9-fold) coverage mammal genome sequence.
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13 MeSH Terms
Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis.
Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CM, Dorrance AE, Dou D, Dickerman AW, Dubchak IL, Garbelotto M, Gijzen M, Gordon SG, Govers F, Grunwald NJ, Huang W, Ivors KL, Jones RW, Kamoun S, Krampis K, Lamour KH, Lee MK, McDonald WH, Medina M, Meijer HJ, Nordberg EK, Maclean DJ, Ospina-Giraldo MD, Morris PF, Phuntumart V, Putnam NH, Rash S, Rose JK, Sakihama Y, Salamov AA, Savidor A, Scheuring CF, Smith BM, Sobral BW, Terry A, Torto-Alalibo TA, Win J, Xu Z, Zhang H, Grigoriev IV, Rokhsar DS, Boore JL
(2006) Science 313: 1261-6
MeSH Terms: Algal Proteins, Biological Evolution, DNA, Algal, Genes, Genome, Hydrolases, Photosynthesis, Phylogeny, Physical Chromosome Mapping, Phytophthora, Plant Diseases, Polymorphism, Single Nucleotide, Repetitive Sequences, Nucleic Acid, Sequence Analysis, DNA, Symbiosis, Toxins, Biological
Show Abstract · Added March 20, 2014
Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oömycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oömycete avirulence genes.
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16 MeSH Terms
The glucose-6-phosphatase catalytic subunit gene promoter contains both positive and negative glucocorticoid response elements.
Vander Kooi BT, Onuma H, Oeser JK, Svitek CA, Allen SR, Vander Kooi CW, Chazin WJ, O'Brien RM
(2005) Mol Endocrinol 19: 3001-22
MeSH Terms: Animals, Base Sequence, Catalysis, Dexamethasone, Gene Expression Regulation, Enzymologic, Genes, Reporter, Glucocorticoids, Glucose-6-Phosphatase, Mice, Molecular Sequence Data, Promoter Regions, Genetic, Protein Subunits, Rats, Receptors, Glucocorticoid, Repetitive Sequences, Nucleic Acid, Response Elements, Transcription Factors, Transcription, Genetic
Show Abstract · Added December 10, 2013
Glucose-6-phosphatase catalyzes the final step in the gluconeogenic and glycogenolytic pathways. Glucocorticoids stimulate glucose-6-phosphatase catalytic subunit (G6Pase) gene transcription and studies performed in H4IIE hepatoma cells demonstrate the presence of a glucocorticoid response unit (GRU) in the proximal G6Pase promoter. In vitro deoxyribonuclease I footprinting analyses show that the glucocorticoid receptor binds to three glucocorticoid response elements (GREs) in the -231 to -129 promoter region and transfection results indicate all three contribute to glucocorticoid induction of G6Pase gene transcription. Furthermore, binding sites for hepatocyte nuclear factor-1 and -4, CRE binding factors, and FKHR (FOXO1a) are required for the full glucocorticoid response. Chromatin immunoprecipitation assays show that dexamethasone treatment stimulates glucocorticoid receptor and FKHR binding to the endogenous G6Pase promoter. Surprisingly, although glucocorticoids stimulate G6Pase gene transcription, deoxyribonuclease I footprinting and transfection analyses demonstrate the presence of a negative GRE and an associated negative accessory factor element in the -271 to -225 promoter region, which inhibit the glucocorticoid response. This appears to be the first report of a promoter that contains both positive and negative GREs, which function within the same cellular environment. We hypothesize that targeted signaling to the negative accessory element within the GRU may provide tight regulation of the glucocorticoid stimulation.
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18 MeSH Terms
Mitochondrial DNA repeats constrain the life span of mammals.
Samuels DC
(2004) Trends Genet 20: 226-9
MeSH Terms: Animals, DNA, Mitochondrial, Gene Deletion, Genome, Humans, Longevity, Mammals, Mutation, Repetitive Sequences, Nucleic Acid, Time Factors
Added December 12, 2013
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10 MeSH Terms
Human Sgt1 binds HSP90 through the CHORD-Sgt1 domain and not the tetratricopeptide repeat domain.
Lee YT, Jacob J, Michowski W, Nowotny M, Kuznicki J, Chazin WJ
(2004) J Biol Chem 279: 16511-7
MeSH Terms: Amino Acid Sequence, Binding Sites, HSP90 Heat-Shock Proteins, Humans, Kinetochores, Molecular Sequence Data, Protein Binding, Protein Folding, Protein Structure, Tertiary, Protein Subunits, Recombinant Proteins, Repetitive Sequences, Nucleic Acid, SKP Cullin F-Box Protein Ligases, Sequence Alignment
Show Abstract · Added December 10, 2013
Sgt1 has been identified as a subunit of both core kinetochore and SCF (Skp1-Cul1-F-box) ubiquitin ligase complexes and is also implicated in plant disease resistance. Sgt1 has two putative HSP90 binding domains, a tetratricopeptide repeat and a p23-like CHORD and Sgt1 (CS) domain. Using NMR spectroscopy, we show that only the CS domain of human Sgt1 physically interacts with HSP90. The tetratricopeptide repeat domain does not bind to either HSP90 or HSP70. Determination of the three-dimensional structure showed that the Sgt1-CS domain shares the same beta-sandwich fold as p23 but lacks the last highly conserved beta-strand in p23. Analysis of the structures of Sgt1-CS and p23 revealed a similar charge distribution on one of two opposing surfaces that suggests that it is the binding region for HSP90 in Sgt1. Although ATP is absolutely required for p23 binding to HSP90, Sgt1 binds to HSP90 also in the absence of the non-hydrolyzable analog ATPgammaS. Our findings suggest the CS domain is a binding module for HSP90 distinct from p23-like domains, which implies that Sgt1 and related proteins function in recruiting heat shock protein activities to multiprotein assemblies.
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14 MeSH Terms
C-terminal sequences outside the tetratricopeptide repeat domain of FKBP51 and FKBP52 cause differential binding to Hsp90.
Cheung-Flynn J, Roberts PJ, Riggs DL, Smith DF
(2003) J Biol Chem 278: 17388-94
MeSH Terms: Amino Acid Sequence, Binding Sites, HSP90 Heat-Shock Proteins, Humans, Molecular Sequence Data, Protein Binding, Recombinant Proteins, Repetitive Sequences, Nucleic Acid, Sequence Analysis, Tacrolimus Binding Proteins
Show Abstract · Added March 9, 2015
Hsp90 assembles with steroid receptors and other client proteins in association with one or more Hsp90-binding cochaperones, some of which contain a common tetratricopeptide repeat (TPR) domain. Included in the TPR cochaperones are the Hsp70-Hsp90-organizing protein Hop, the FK506-binding immunophilins FKBP52 and FKBP51, the cyclosporin A-binding immunophilin CyP40, and protein phosphatase PP5. The TPR domains from these proteins have similar x-ray crystallographic structures and target cochaperone binding to the MEEVD sequence that terminates Hsp90. However, despite these similarities, the TPR cochaperones have distinctive properties for binding Hsp90 and assembling with Hsp90.steroid receptor complexes. To identify structural features that differentiate binding of FKBP51 and FKBP52 to Hsp90, we generated an assortment of truncation mutants and chimeras that were compared for coimmunoprecipitation with Hsp90. Although the core TPR domain (approximately amino acids 260-400) of FKBP51 and FKBP52 is required for Hsp90 binding, the C-terminal 60 amino acids (approximately 400-end) also influence Hsp90 binding. More specifically, we find that amino acids 400-420 play a critical role for Hsp90 binding by either FKBP. Within this 20-amino acid region, we have identified a consensus sequence motif that is also present in some other TPR cochaperones. Additionally, the final 30 amino acids of FKBP51 enhance binding to Hsp90, whereas the corresponding region of FKBP52 moderates binding to Hsp90. Taking into account the x-ray crystal structure for FKBP51, we conclude that the C-terminal regions of FKBP51 and FKBP52 outside the core TPR domains are likely to assume alternative conformations that significantly impact Hsp90 binding.
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10 MeSH Terms
The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions.
Eichman BF, Vargason JM, Mooers BH, Ho PS
(2000) Proc Natl Acad Sci U S A 97: 3971-6
MeSH Terms: Base Sequence, Crystallography, X-Ray, DNA, Models, Molecular, Nucleic Acid Conformation, Repetitive Sequences, Nucleic Acid
Show Abstract · Added April 7, 2017
Holliday junctions are important structural intermediates in recombination, viral integration, and DNA repair. We present here the single-crystal structure of the inverted repeat sequence d(CCGGTACCGG) as a Holliday junction at the nominal resolution of 2. 1 A. Unlike the previous crystal structures, this DNA junction has B-DNA arms with all standard Watson-Crick base pairs; it therefore represents the intermediate proposed by Holliday as being involved in homologous recombination. The junction is in the stacked-X conformation, with two interconnected duplexes formed by coaxially stacked arms, and is crossed at an angle of 41.4 degrees as a right-handed X. A sequence comparison with previous B-DNA and junction crystal structures shows that an ACC trinucleotide forms the core of a stable junction in this system. The 3'-C x G base pair of this ACC core forms direct and water-mediated hydrogen bonds to the phosphates at the crossover strands. Interactions within this core define the conformation of the Holliday junction, including the angle relating the stacked duplexes and how the base pairs are stacked in the stable form of the junction.
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6 MeSH Terms
Production and characterization of monoclonal antibodies to ARVCF.
Mariner DJ, Sirotkin H, Daniel JM, Lindman BR, Mernaugh RL, Patten AK, Thoreson MA, Reynolds AB
(1999) Hybridoma 18: 343-9
MeSH Terms: Abnormalities, Multiple, Amino Acid Sequence, Animals, Antibodies, Monoclonal, Antibody Affinity, Antibody Formation, Armadillos, Binding Sites, Blotting, Western, Cadherins, Catenins, Cell Adhesion Molecules, Cell Line, Craniofacial Abnormalities, DiGeorge Syndrome, Dogs, Fluorescent Antibody Technique, Gene Deletion, Haplorhini, Heart Defects, Congenital, Humans, Hybridomas, Intercellular Junctions, Mice, Molecular Sequence Data, Phosphoproteins, Precipitin Tests, Rats, Repetitive Sequences, Amino Acid, Repetitive Sequences, Nucleic Acid, Sequence Homology, Amino Acid, Species Specificity, Velopharyngeal Insufficiency
Show Abstract · Added March 5, 2014
We have generated the first monoclonal antibodies (MAbs) to Armadillo repeat gene deleted in velo-cardiofacial syndrome (ARVCF), a recently identified Armadillo repeat-containing protein closely related to the catenin p120ctn. Six ARVCF-specific MAbs were characterized for isotype, species cross-reactivity, and utility in assays including immunofluorescence, immunoprecipitation, and Western blotting. All six antibodies were isotyped as IgG1 and several cross-reacted with ARVCF from a variety of species including human, rat, dog, and monkey, but not mouse. Importantly, none of the ARVCF MAbs cross-reacted with p120ctn, despite the high homology between these proteins. MAbs 3B2 and 4B1 were consistently the best in all applications and will provide valuable tools for further study of the role of ARVCF in cells.
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33 MeSH Terms
An enhancer element in the EphA2 (Eck) gene sufficient for rhombomere-specific expression is activated by HOXA1 and HOXB1 homeobox proteins.
Chen J, Ruley HE
(1998) J Biol Chem 273: 24670-5
MeSH Terms: Animals, Base Sequence, Binding Sites, COS Cells, Cell Line, Consensus Sequence, DNA Primers, Embryonic and Fetal Development, Enhancer Elements, Genetic, Female, Gene Expression Regulation, Developmental, Homeodomain Proteins, Mice, Mice, Inbred C57BL, Mice, Inbred DBA, Mice, Transgenic, Molecular Sequence Data, Polymerase Chain Reaction, Repetitive Sequences, Nucleic Acid, Rhombencephalon, Transcription Factors, Transfection
Show Abstract · Added March 5, 2014
In the hindbrain of the mouse embryo, there is often coincident rhombomere-restricted expression of Eph receptor tyrosine kinases and Hox homeobox genes, raising the possibility of regulatory interactions. In this paper, we have identified cis-acting regulatory sequences of the EphA2 (Eck) gene, which direct node and hindbrain-specific expression in transgenic embryos. An 8-kilobase region of mouse genomic DNA element was sufficient to drive rhombomere 4 (r4)-specific expression while conferring patchy expression in the node. Further analysis localized the rhombomere-specific enhancer to a 0.9-kilobase sequence. This element contains multiple Hox-Pbx consensus binding sites that bind to both HOXA1/Pbx1 and HOXB1/Pbx1 proteins in vitro. Co-expression of either HOXA1 or HOXB1 with Pbx1 transactivated EphA2 enhancer-dependent reporter gene expression. These results, together with observations of reduced EphA2 expression in hoxa1 and hoxb1 double mutant mice, suggest that expression of EphA2 gene in rhombomere 4 is directly regulated by Hoxa1 and Hoxb1 homeobox transcription factors.
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22 MeSH Terms