Genomes and Genes
Summary: A method that is used to detect DNA-protein interactions. Proteins are separated by electrophoresis and blotted onto a nitrocellulose membrane similar to Western blotting (BLOTTING, WESTERN) but the proteins are identified when they bind labeled DNA PROBES (as with Southern blotting (BLOTTING, SOUTHERN)) instead of antibodies.
- Wu Y, Savelli S, Yang Y, Zhou B, Rovin B, Birmingham D, et al. Sensitive and specific real-time polymerase chain reaction assays to accurately determine copy number variations (CNVs) of human complement C4A, C4B, C4-long, C4-short, and RCCX modules: elucidation of C4 CNVs in 50 consanguineous subjects with defin. J Immunol. 2007;179:3012-25 pubmed..These C4 qPCR assays are proven to be robust, sensitive, and reliable, as they have contributed to the elucidation of C4 CNVs in >1000 human samples with autoimmune and neurological diseases. ..
- Khanam T, Raabe C, Kiefmann M, Handel S, Skryabin B, BROSIUS J. Can ID repetitive elements serve as cis-acting dendritic targeting elements? An in vivo study. PLoS ONE. 2007;2:e961 pubmed..Other mRNAs containing naturally inserted ID elements are also not found in neuronal dendrites. We conclude that the 5' ID domain from BC1 RNA is not a sufficient dendritic targeting element for mRNAs in vivo. ..
- Isono M, Chen S, Hong S, Iglesias de la Cruz M, Ziyadeh F. Smad pathway is activated in the diabetic mouse kidney and Smad3 mediates TGF-beta-induced fibronectin in mesangial cells. Biochem Biophys Res Commun. 2002;296:1356-65 pubmed..We conclude that hyperglycemia activates the intrarenal TGF-beta/Smad signaling pathway, which then promotes mesangial matrix gene expression in diabetic nephropathy. ..
- Maloney B, Ge Y, Petersen R, Hardy J, Rogers J, PÃ©rez Tur J, et al. Functional characterization of three single-nucleotide polymorphisms present in the human APOE promoter sequence: Differential effects in neuronal cells and on DNA-protein interactions. Am J Med Genet B Neuropsychiatr Genet. 2010;153B:185-201 pubmed publisher..Taken together, these results suggest that APOE expression levels are a risk factor for AD irrespective of APOEepsilon4 allele status. ..
- Cai R, Xu W, Dai B, Cai X, Xu R, Lu J. SATB1 binds an intronic MAR sequence in human PI3kgamma in vitro. Mol Biol Rep. 2010;37:1461-5 pubmed publisher..These results indicate that SATB1 may play antagonistic roles in PI3Kgamma transcriptional regulation. ..
- Yang G, Tian J, Li J. Fermentation of 1,3-propanediol by a lactate deficient mutant of Klebsiella oxytoca under microaerobic conditions. Appl Microbiol Biotechnol. 2007;73:1017-24 pubmed..56 g l-1, 0.62 mol mol-1, and 1.61 g l(-1) h-1, respectively. Furthermore, 60.11 g l(-1) 2,3-butanediol was also formed as major byproduct in the broth...
- Jenke B, Fetzer C, Stehle I, Jönsson F, Fackelmayer F, Conradt H, et al. An episomally replicating vector binds to the nuclear matrix protein SAF-A in vivo. EMBO Rep. 2002;3:349-54 pubmed..These data provide the first experimental evidence for the binding of an artificial episome to a nuclear matrix protein in vivo and the basis for understanding the mitotic stability of this novel vector class. ..
- Jiang D, Jarrett H, Haskins W. Methods for proteomic analysis of transcription factors. J Chromatogr A. 2009;1216:6881-9 pubmed publisher..The synergy of highly selective purification and analytical strategies has led to an explosion of knowledge about the TF proteome and the proteomes of other DNA- and RNA-binding proteins. ..
- Zahedi K, Prada A, Mulligan A, Prada J, Davis A. Normal transcription of the C1 inhibitor gene is dependent upon a polypurine-polypyrimidine region within the promoter. Inflammation. 2002;26:183-91 pubmed..Southwestern blot analysis detected four bands (M(r)s -130, 75, 65 and 20 kDa). These data suggest that the -98 to -9 region of the C1INH promoter interacts with at least four proteins, one of which is HNF-1alpha. ..
- Arockiasamy S, Ignacimuthu S. Regeneration of transgenic plants from two indica rice (Oryza sativa L.) cultivars using shoot apex explants. Plant Cell Rep. 2007;26:1745-53 pubmed..6 to 6.2% whereas in the case of PB1, it was from 7 to 8%. Progeny analysis of these plants showed a pattern of classical Mendelian inheritance for both hpt and GUS gene. ..
- Hoo R, Ngan E, Leung P, Chow B. Two Inr elements are important for mediating the activity of the proximal promoter of the human gonadotropin-releasing hormone receptor gene. Endocrinology. 2003;144:518-27 pubmed..Additional mechanisms are needed to modulate the efficiencies of individual promoters for developmental and/or tissue-specific regulations. ..
- Christmann M, Tomicic M, Aasland D, Kaina B. A role for UV-light-induced c-Fos: Stimulation of nucleotide excision repair and protection against sustained JNK activation and apoptosis. Carcinogenesis. 2007;28:183-90 pubmed..The data support the hypothesis that non-repaired DNA damage is the cause for the late and sustained activation of the MAP kinase pathway in response to genotoxins. ..
- Li Y, Bai F, Shan Z, Xu H, Qiao M. [Identification of two new genes involved in swimming motility of Pseudomonas aeruginosa]. Wei Sheng Wu Xue Bao. 2006;46:18-22 pubmed..Observation of these two mutants with an integrity flagellum under electron microscope showed that two new genes were not involved in construction of flagella, but probably in energy metabolism and gene regulation of swimming motility. ..
- Zhang H, Fu S, Busch A, Chen F, Qin L, Bromberg J. Identification of TNF-alpha-sensitive sites in HCMVie1 promoter. Exp Mol Pathol. 2001;71:106-14 pubmed..b>Southwestern blotting showed that three proteins (45, 30, and 20 kDa) bound to this TNF-alpha-sensitive element, separately...
- Papavassiliou A. Determination of a transcription factor-binding site by nuclease protection footprinting onto southwestern blots. Methods Mol Biol. 2009;543:201-18 pubmed publisher..Coupling SW and in situ (on-blot) DNase I footprinting methodologies has the dual potential of accurately determining the molecular mass of individual DNA-binding transcription factors and precisely mapping their cognate binding sites. ..
- Jiang D, Jia Y, Zhou Y, Jarrett H. Two-dimensional southwestern blotting and characterization of transcription factors on-blot. J Proteome Res. 2009;8:3693-701 pubmed publisherTwo-dimensional Southwestern blotting (2D-SW) described here combines several steps. Proteins are separated by two-dimensional gel electrophoresis and transferred to nitrocellulose (NC) or polyvinylidene fluoride (PVDF) membrane...
- Panzer U, Steinmetz O, Turner J, Meyer Schwesinger C, von Ruffer C, Meyer T, et al. Resolution of renal inflammation: a new role for NF-kappaB1 (p50) in inflammatory kidney diseases. Am J Physiol Renal Physiol. 2009;297:F429-39 pubmed publisher..In conclusion, our studies indicate that NF-kappaB subunit p50 proteins have critical in vivo functions in immunologically mediated renal disease by downregulating inflammation during the resolution period. ..
- Ohri S, Sharma D, Dixit A. Interaction of an approximately 40 kDa protein from regenerating rat liver with the -148 to -124 region of c-jun complexed with RLjunRP coincides with enhanced c-jun expression in proliferating rat liver. Eur J Biochem. 2004;271:4892-902 pubmed
- Zhu Y, Cai X, Wang Z, Hong M. An interaction between a MYC protein and an EREBP protein is involved in transcriptional regulation of the rice Wx gene. J Biol Chem. 2003;278:47803-11 pubmed..These results suggest that the OsBP-5 and OsEBP-89 proteins act synergistically, perhaps as a heterodimer, to regulate the transcription of the rice Wx gene. ..
- Coffman J, Yuh C. Identification of sequence-specific DNA binding proteins. Methods Cell Biol. 2004;74:653-75 pubmed
- López Meza J, Barboza Corona J, Del Rincón Castro M, Ibarra J. Sequencing and characterization of plasmid pUIBI-1 from Bacillus thuringiensis serovar entomocidus LBIT-113. Curr Microbiol. 2003;47:395-9 pubmed..7%). Detection of single-stranded DNA (ssDNA) intermediates indicated that pUIBI-1 replicates by the rolling-circle replication mechanism, as demonstrated by S1 treatment and Southern hybridization under non-denaturing conditions. ..
- Poch M, Al Kassim L, Smolinski S, Hines R. Two distinct classes of CCAAT box elements that bind nuclear factor-Y/alpha-actinin-4: potential role in human CYP1A1 regulation. Toxicol Appl Pharmacol. 2004;199:239-50 pubmed
- Gai Q, James C. Identification of a region on the adenovirus E1A gene responsible for induction by phorbol ester tumor promoter. In Vitro Cell Dev Biol Anim. 2001;37:465-70 pubmed..the TRE (-237 to -47) form specific DNA-protein complexes as demonstrated by gel shift analysis and Southwestern blotting. These experiments provide evidence that novel protein-DNA complexes are formed on a region of the E1A ..
- Subramanian M, Gonzalez R, Patil H, Ueda T, Lim J, Kraemer K, et al. The nucleosome-binding protein HMGN2 modulates global genome repair. FEBS J. 2009;276:6646-57 pubmed publisher..Our finding that HMGNs play a role in global DNA repair expands the role of these proteins in the maintenance of genome integrity. ..
- Labbe S, Harrisson J, SEGUIN C. Identification of sequence-specific DNA-binding proteins by southwestern blotting. Methods Mol Biol. 2009;543:151-61 pubmed publisherWe describe a Southwestern blotting method for characterization of both DNA-binding proteins and their specific sites...
- Hishikawa Y, Damavandi E, Izumi S, Koji T. Molecular histochemical analysis of estrogen receptor alpha and beta expressions in the mouse ovary: in situ hybridization and Southwestern histochemistry. Med Electron Microsc. 2003;36:67-73 pubmed..By employing these methods, more precise understanding of specific gene expression and evaluation of its biological significance in the ovary would be possible. ..
- Sugimoto K, Takeda S, Hirochika H. Transcriptional activation mediated by binding of a plant GATA-type zinc finger protein AGP1 to the AG-motif (AGATCCAA) of the wound-inducible Myb gene NtMyb2. Plant J. 2003;36:550-64 pubmed..We also found that the AGP1 binding activity is highly enhanced by adenine methylation of the AG-motif by bacterial dam methylase...
- Liang D, Ma X, Qu Z, Hull R. Nucleic acid binding property of the gene products of rice stripe virus. Virus Genes. 2005;31:203-9 pubmed..The central and C-terminal regions of pc4 bind nucleic acid. It has been suggested that this protein is a cell-to-cell movement protein and nucleic acid binding would be in accord with this function...
- Gonzalez Vioque E, Blazquez A, Fernandez Moreira D, Bornstein B, Bautista J, Arpa J, et al. Association of novel POLG mutations and multiple mitochondrial DNA deletions with variable clinical phenotypes in a Spanish population. Arch Neurol. 2006;63:107-11 pubmed..Molecular studies in the POLG gene should be addressed in patients with mitochondrial disease, particularly in those with PEO, and multiple mtDNA deletions. ..
- Jeong S, Rose A, Meier I. MFP1 is a thylakoid-associated, nucleoid-binding protein with a coiled-coil structure. Nucleic Acids Res. 2003;31:5175-85 pubmed..Importantly, it is associated in vivo with nucleoids, suggesting a function for MFP1 at the interface between chloroplast nucleoids and the developing thylakoid membrane system. ..
- Banerjee S, Fisher O, Lohia A, Ankri S. Entamoeba histolytica DNA methyltransferase (Ehmeth) is a nuclear matrix protein that binds EhMRS2, a DNA that includes a scaffold/matrix attachment region (S/MAR). Mol Biochem Parasitol. 2005;139:91-7 pubmed..We observed the presence of methylated cytosine within the 3'-end of EhMRS2. These data provide the first evidence that a member of the DNMT2 family interacts with a S/MAR containing DNA element. ..
- Hong S, Jeong H, Kim Y, Kim S, Choi K, Lee H, et al. Nuclear factor kappa B activation in glomeruli of posttransplant IgA nephropathy using southwestern histochemistry. Transplant Proc. 2003;35:179-80 pubmed
- Yamaza T, Masuda K, Tsukiyama Y, Nishijima K, Murakami R, Kido M, et al. NF-kappaB activation and iNOS expression in the synovial membrane of rat temporomandibular joints after induced synovitis. J Dent Res. 2003;82:183-8 pubmed..These findings indicate that excess mechanical stress increases NF-kappaB activation in the TMJ and suggest that active NF-kappaB is involved in the progression of TMJ inflammation. ..
- Brown T. Hybridization analysis of DNA blots. Curr Protoc Immunol. 2001;Chapter 10:Unit 10.6B pubmed publisher..An Alternate Protocol describes a similar method for probing DNA blots with a radiolabeled RNA probe. A Support Protocol for stripping blots to ready them for reprobing is also provided. ..
- Zarantonelli M, Carlier J, Alonso J, Taha M. Insertional inactivation of the lpxA gene involved in the biosynthesis of lipid A in Neisseria meningitidis resulted in lpxA/lpxA::aph-3' heterodiploids. FEMS Microbiol Lett. 2003;226:51-6 pubmed..The absence of lipooligosaccharide in these mutants may result from a negative transdominance effect of a truncated LpxA protein on the wild-type LpxA protein. ..
- Natarajan S, Nickles K, McEachern M. Screening for telomeric recombination in wild-type Kluyveromyces lactis. FEMS Yeast Res. 2006;6:442-8 pubmed..This suggests that the exchange of telomeric repeats is not a routine occurrence in K. lactis meiosis. ..
- Güner E, Watanabe M, Hashimoto N, Kadosaka T, Kawamura Y, Ezaki T, et al. Borrelia turcica sp. nov., isolated from the hard tick Hyalomma aegyptium in Turkey. Int J Syst Evol Microbiol. 2004;54:1649-52 pubmed..The G+C content of strain IST7T is 30.0 mol%. From these genetic features, a novel Borrelia species, Borrelia turcica sp. nov., is proposed; the type strain is IST7T (= JCM 11958T = DSM 16138T). ..
- Papantonis A, Sourmeli S, Lecanidou R. Chorion gene activation and repression is dependent on BmC/EBP expression and binding to cognate cis-elements. Biochem Biophys Res Commun. 2008;369:905-9 pubmed publisher..A biphasic function of BmC/EBP, according to which it may act as both an activator and a repressor during silkmoth choriogenesis, is considered under the light of the presented data. ..
- Chen B, Wang Y, You M. Characterization of two protein-binding sites in the second intron of the mouse K-ras gene. Exp Lung Res. 2005;31:179-92 pubmed..Southwestern blot analysis of DNA-protein complexes indicated that the 2 repeated regions might bind the same regulatory complex. ..
- Zhang W, Peacock C, Matlashewski G. A genomic-based approach combining in vivo selection in mice to identify a novel virulence gene in Leishmania. PLoS Negl Trop Dis. 2008;2:e248 pubmed publisher..These observations demonstrate that the levels of expression and sequence variations in genes ubiquitously shared between Leishmania species have the potential to significantly influence virulence and tissue tropism. ..
- Ryschkewitsch C, Jensen P, Hou J, Fahle G, Fischer S, Major E. Comparison of PCR-southern hybridization and quantitative real-time PCR for the detection of JC and BK viral nucleotide sequences in urine and cerebrospinal fluid. J Virol Methods. 2004;121:217-21 pubmed
- Pusch C, Wundrack I, Mullenbach R, Schempp W, Blin N. The 48 bp centromeric repeat is a functionally conserved motif in great apes and man showing protein-binding properties. Electrophoresis. 2002;23:20-6 pubmed..The complex is likely involved in the proper formation and/or function of mammalian centromeres. ..
- Grillo C, Coppari S, Turano C, Altieri F. The DNA-binding activity of protein disulfide isomerase ERp57 is associated with the a(') domain. Biochem Biophys Res Commun. 2002;295:67-73 pubmed
- Xing C, LaPorte J, Barbay J, Myers A. Identification of GAPDH as a protein target of the saframycin antiproliferative agents. Proc Natl Acad Sci U S A. 2004;101:5862-6 pubmed
- Rio R, Anderegg M, Graf J. Characterization of a catalase gene from Aeromonas veronii, the digestive-tract symbiont of the medicinal leech. Microbiology. 2007;153:1897-906 pubmed..The data suggest that although many colonization factors reoccur, each symbiotic system has also evolved specific mechanisms that affect symbiont-host dynamics...
- Honda S, Kobayashi T, Kajino K, Urakami S, Igawa M, Hino O. Ets protein Elf-1 bidirectionally suppresses transcriptional activities of the tumor suppressor Tsc2 gene and the repair-related Nth1 gene. Mol Carcinog. 2003;37:122-9 pubmed..Our observations suggest that mechanisms that inactivate Tsc2 gene expression, such as promoter suppression, may exist. ..
- Franke C, Gräfe D, Bartsch H, Bachmann M. Use of non-radioactive detection method for north- and southwestern blot. Methods Mol Biol. 2009;536:441-9 pubmed publisher..Here, we describe the use of a northwestern and southwestern blot protocol for the evaluation of the DNA and RNA binding abilities of a novel putative methyl transferase HSPC133 (METTL5). ..
- Choudhury S, Roy S, Saha P, Singh S, Sengupta D. Characterization of differential ripening pattern in association with ethylene biosynthesis in the fruits of five naturally occurring banana cultivars and detection of a GCC-box-specific DNA-binding protein. Plant Cell Rep. 2008;27:1235-49 pubmed publisher..Together, these results indicate the probable involvement of the GCC-box motif as the cis-acting ERE in the regulation of MA-ACS1 and MA-ACO1 during ripening in banana fruits via binding of specific ERE-binding protein. ..
- MacKay A, Mhanni A, McGowan R, Krone P. Immunological detection of changes in genomic DNA methylation during early zebrafish development. Genome. 2007;50:778-85 pubmed..Although zebrafish sperm DNA is strongly methylated, the zebrafish genome is not detectably methylated through cleavage and early blastula stages but is heavily remethylated in blastula and early gastrula stages. ..
- Huang Y, Wang M, Ou W, Fung C, Chen L, Chang D. Analysis of DNA-binding activity of the JC virus minor capsid protein VP2. J Neurovirol. 2003;9 Suppl 1:21-4 pubmed..b>Southwestern blotting was employed for the DNA-binding assay...
- Ashizawa M, Miyazaki M, Abe K, Furusu A, Isomoto H, Harada T, et al. Detection of nuclear factor-kappaB in IgA nephropathy using Southwestern histochemistry. Am J Kidney Dis. 2003;42:76-86 pubmed..Our results indicate that NF-kappaB is involved in the progression of tissue injury in IgA nephropathy through the induction of transcriptionally regulated genes. ..
- Kaur H, Jaso Friedmann L, Leary J, Praveen K, Brahmi Z, Evans D. Activation of natural killer-like YT-INDY cells by oligodeoxynucleotides and binding by homologous pattern recognition proteins. Scand J Immunol. 2005;62:361-70 pubmed..These experiments demonstrated that Po single base dG20 and CpG ODN bind to a (potential) new class of cell-surface proteins that mediate the activation of YT-INDY cells. ..