• DNase
  • Using this technology, systematic identification of hundreds of thousands of DNase I hypersensitive sites (DHS) per cell type has been possible, and this in turn has helped to precisely delineate genomic regulatory compartments. (ox.ac.uk)
  • RESULTS: We report a significant degree of sequence preference spanning sites cut by DNase I in a number of published data sets. (ox.ac.uk)
  • CONCLUSIONS: DNase I is a sequence-specific enzyme, with a specificity that may depend on experimental conditions. (ox.ac.uk)
  • Molecular characterization of this process identified a specific DNase (CAD, caspase-activated DNase) that cleaves chromosomal DNA in a caspase-dependent manner. (wikipedia.org)
  • RNA Isolation: RNA is isolated from tissue and mixed with deoxyribonuclease (DNase). (wikipedia.org)
  • Genetic
  • Genetic studies on site-specific endodeoxyribonucleases in Bacillus subtilis: multiple modification and restriction systems in transformants of Bacillus subtilis 168. (atcc.org)
  • Transformation is one of three processes for horizontal gene transfer, in which exogenous genetic material passes from bacterium to another, the other two being conjugation (transfer of genetic material between two bacterial cells in direct contact) and transduction (injection of foreign DNA by a bacteriophage virus into the host bacterium). (wikipedia.org)
  • Chromatin
  • In 1978, Zakharyan and Pogosyan presented a paper revealing that glucocorticoid-induced DNA degradation in rat lymphoid tissue, thymus, and spleen occurred in a specific pattern producing fragments of DNA that were electrophoretically similar to those observed after treatment of chromatin with microccoccal nuclease, which indicated internucleosomal cleavage pattern of DNA degradation occurred during apoptosis. (wikipedia.org)
  • protein
  • p>This indicates the type of evidence that supports the existence of the protein. (uniprot.org)
  • Cytochrome c'' (cyt c'') from Methylophilus methylotrophus is unusual insofar as the heme has two axial histidine ligands in the oxidized form but one is detached when the protein is reduced. (bireme.br)
  • The Restriction-modification system AhdI contains two convergent transcription units, one with genes encoding methyltransferase subunits M and S and another with genes encoding the controller (C) protein and the restriction endonuclease (R). We show that AhdI transcription is controlled by two independent regulatory loops that are well-optimized to ensure successful establishment in a naïve bacterial host. (nih.gov)
  • Transcription from the weak CR promoter is regulated by the C protein interaction with two DNA-binding sites. (nih.gov)
  • Because of high levels of cooperativity, both C protein-binding sites are always occupied in the absence of RNA polymerase, raising a question how activated transcription is achieved. (nih.gov)
  • We develop a mathematical model that is in quantitative agreement with the experiment and indicates that RNA polymerase outcompetes C protein from the promoter-proximal-binding site. (nih.gov)
  • Contacts between Bacillus subtilis catabolite regulatory protein CcpA and amyO target site. (naver.com)
  • The LACTB2 protein has a metallo β-lactamase (MBL) fold, with two zinc ions in the active site. (wikipedia.org)
  • Enforced expression of wild-type NCOA2 but not the LACTB2-NCOA2 fusion protein impaired the pro-tumorigenic phenotypes of CRC cells, whereas knockdown of endogenous NCOA2 in normal colonocytes had opposite effects. (wikipedia.org)
  • G G A T C C C C T A G G As of the end of 2010, there were 5 crystal structures of BamH I in the Protein Data Bank BamHI, type II restriction endonucleases, often requires divalent metals as cofactors to catalyze DNA cleavage. (wikipedia.org)
  • Gene map locus 19p13.1-q13.11 OMIM: 227240 GTPBP3: GTP binding protein 3 19p13.11 KLF2: Krüppel-like factor 2, also known as Lung Krüppel-like factor. (wikipedia.org)
  • Gene map locus 19q13.2 FCGBP: Fc fragment of IgG binding protein SARS2: seryl-tRNA synthetase 2, mitochondrial. (wikipedia.org)
  • Gene map locus 19q13.32 GLTSCR2: Glioma tumor suppressor candidate region gene 2 protein 19q13.33 A1BG: Plasma glycoprotein, unknown function. (wikipedia.org)
  • cleavage
  • Despite the lack of evidence suggesting an exact mechanism for the cleavage of DNA by HindIII, site-mutagenesis analysis coupled with more detailed studies of metal ion-mediated catalysis in EcoRV have led to the following proposed catalytic mechanism. (wikipedia.org)
  • The 3' to 5' human type endonuclease is known to be essential for the proper processing of histone pre-mRNA, in which U7 snRNP directs the single cleavage process. (wikipedia.org)
  • fragments
  • In vitro transcription from both fragments was independent of the presence of C.AhdI and initiated from the same start site as that determined in vivo (data not shown).Figure 8. (nih.gov)
  • This finding was consistent with the hypothesis that these DNA fragments were a specific degradation product of nuclear DNA. (wikipedia.org)
  • gene
  • Peg5/Neuronatin is an imprinted gene located on sub-distal chromosome 2 in the mouse. (naver.com)
  • it works with a 5' exonuclease (human gene Xrn2) to degrade the newly formed transcript downstream, leaving the polyadenylation site and simultaneously shooting the polymerase. (wikipedia.org)
  • Wild-type AAV has attracted considerable interest from gene therapy researchers due to a number of features. (wikipedia.org)
  • the other two are transduction, carried out by means of a bacteriophage, and conjugation, in which a gene is passed through direct contact between bacteria. (wikipedia.org)
  • A variety of parameters are considered when designing and conducting RNA-Seq experiments: Tissue specificity: Gene expression varies within and between tissues, and RNA-Seq measures this mix of cell types. (wikipedia.org)
  • ions
  • Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme. (naver.com)
  • Two-metal ion mechanism is one of the possible catalytic mechanisms of BamHI since the BamHI crystal structure has the ability to bind two metal ions at the active site, which is suitable for the classical two-metal ion mechanism to proceed. (wikipedia.org)
  • The two metal ions (A and B) are 4.1 apart from each other in the active site and are in-line with these residues. (wikipedia.org)
  • In general, when the two metal ions (A and B) are bonded to the active site, they help stabilize a cluster distribution of negative charges localized at the active site created by the leaving of an oxygen atom during the transition state. (wikipedia.org)
  • molecule
  • What was then needed was a tool that would cut DNA at specific sites, rather than at random sites along the length of the molecule, so that scientists could cut DNA molecules in a predictable and reproducible way. (wikipedia.org)
  • chromosome
  • LACTB2 is located on the 8th chromosome, with its specific location being 8q13.3. (wikipedia.org)
  • A tumor-specific LACTB2-NCOA2 fusion originating from intra-chromosomal rearrangement of chromosome 8 has been identified at both DNA and RNA levels. (wikipedia.org)
  • It can also infect non-dividing cells and has the ability to stably integrate into the host cell genome at a specific site (designated AAVS1) in the human chromosome 19. (wikipedia.org)
  • People normally have two copies of this chromosome. (wikipedia.org)
  • nucleotide sequence
  • An important development came when H.O. Smith, K.W. Wilcox, and T.J. Kelley, working at Johns Hopkins University in 1968, isolated and characterized the first restriction nuclease whose functioning depended on a specific DNA nucleotide sequence. (wikipedia.org)
  • locus
  • There are two primary classifications based on the locus of activity. (wikipedia.org)
  • The Se locus encodes a specific fucosyltransferase that is expressed in the epithelia of secretory tissues, such as salivary glands, the gastrointestinal tract, and the respiratory tract. (wikipedia.org)
  • There is an estimated 1 x 10−4 to 1 x 10−6 mutations per human gamete, which follows to finding at least one mutation at a specific locus per one million gametes. (wikipedia.org)
  • Binding Sites
  • Fragmentation of the RNA reduces 5' bias of randomly primed-reverse transcription and the influence of primer binding sites, with the downside that the 5' and 3' ends are converted to DNA less efficiently. (wikipedia.org)
  • catalytic
  • Both the APE1 active-site geometry and a complex with cleaved AP-DNA and Mn2+ support a testable structure-based catalytic mechanism. (wikipedia.org)
  • genome
  • The AAV genome integrates most frequently into the site mentioned, while random incorporations into the genome take place with a negligible frequency. (wikipedia.org)
  • specificity
  • The two major protocols in current use each show a different pattern, but for a given protocol the pattern of sequence specificity seems to be quite consistent. (ox.ac.uk)
  • polymerase
  • RNA polymerase is, therefore, recruited to HO in two steps and not as a holoenzyme. (ox.ac.uk)
  • Exonuclease II is associated with DNA polymerase I, which contains a 5' exonuclease that clips off the RNA primer contained immediately upstream from the site of DNA synthesis in a 5' → 3' manner. (wikipedia.org)
  • transcription
  • Transcription regulation of the type II restriction-modification system AhdI. (nih.gov)
  • The interaction with the promoter-distal high-affinity site activates transcription, while interaction with the weaker promoter-proximal site represses it. (nih.gov)
  • Pseudomonas aeruginosa AlgB, a two-component response regulator of the NtrC family, is required for algD transcription. (naver.com)
  • Activation of HO in yeast involves recruitment of transcription factors in two waves. (ox.ac.uk)
  • This process involves the exonuclease's catching up to the pol II and terminating the transcription. (wikipedia.org)
  • The two can be separated quite easily and often are during replication and transcription. (wikipedia.org)
  • overlaps
  • Inspection of the PahdIMS sequence revealed the presence of an AhdI site that partially overlaps with the −10 element of the promoter (Figure 1). (nih.gov)
  • histones
  • The histone fold domain is responsible for formation of head-to-tail heterodimers of two histones: H2A-H2B and H3-H4. (wikipedia.org)
  • As a result of the rotation, two ends of histones involved in DNA binding of the crescent shape H3-H4 are equivalent, yet they organize different stretches of DNA. (wikipedia.org)
  • stabilize
  • The N-terminal tails do not interact with a specific region of DNA but rather stabilize and guide the DNA wrapped around the octamer. (wikipedia.org)
  • downstream
  • In the case of the AhdI site embedded in PahdIMS, a non-template strand A between the extended −10 TG motif and the CATACT −10 element and the template strand A two bases downstream of the −10 element should be methylated (Figure 1). (nih.gov)
  • active site
  • Such a nuclease diffuses along DNA until it encounters a target, upon which the residues of its active site interact with the chemical groups of the DNA. (wikipedia.org)