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Transcriptionally Regulatory Sequences of Phylogenetic Significance
Published in S. K. Dutta, DNA Systematics, 2019
Promoters which are a portion of a transcriptional unit have been shown for genes transcribed by eukaryotic polymerase III.81 Internal promoters have been documented in genes for tRNA,82–84 5S ribosomal RNA,85,86 as well as adenovirus VA1 gene.87,88 For tRNAmet of Xenopus laevis, 2 sequences from +8 to +30 and from +51 to +72 are essential for transcription. For 5S genes, the promoter sequence has been deduced to lie between position + 55 and +80. For the VA1 gene, two intragenic promoter boxes have been identified between +10 and +69. This “split promoter” involves the sequences … TCCGTGGTC … and … ACCGGGGTTCGAACCC … 89 At least two other downstream sequences have also been assigned to pol III promoters. These are … TGGCTCAGTGG … and … GGTTCGATCCC … 90 However, other segments of flanking sequence 5′ to the tRNA genes from Xenopus laevis are inhibitory to the transcription of these tRNA genes in vitro.91 A number of protein factors have been identified which allow polymerase III to recognize one or more internal sequences of certain genes, yet make contact upstream as much as 50 bp away, to initiate transcription of the gene (see later). It is interesting to note that internal control elements also exist in prokaryotic genes. The gal operon of E. coli is an example.92 Whether control elements within a structural gene share a certain common mechanism or not is as yet unknown.
In Situ Hybridization
Published in Attila Lorincz, Nucleic Acid Testing for Human Disease, 2016
ISH targeting Aspergillus 5S ribosomal RNA (rRNA) identified 41 localized aspergillomas in the lung, brain, sinonasal tract, and ear, and two cases of invasive aspergillosis involving pleura and soft tissue of the scapular region.8.9 The diagnosis of Pneumocystis carinii by ISH was performed on FFPE human lung tissues and detected with the avidin–biotin peroxidase complex method. The reactions were positive in all 12 cases of P. carinii pneumonia, but in none of the infections with other pathogenic agents, including viruses (6 cases), mycobacteria (4 cases), protozoa (4 cases), and fungi (8 cases).129
The Cell and Cell Division
Published in Anthony R. Mundy, John M. Fitzpatrick, David E. Neal, Nicholas J. R. George, The Scientific Basis of Urology, 2010
There are three types of RNA polymerase (types I, II, and III). Type I RNA polymerase makes large ribosomal RNA and type III makes tRNA and the small 5S ribosomal RNA. Type II RNA polymerase is responsible for synthesis of the other types of RNA. Both ends of mRNA are modified. The 5′ end is “capped’’ by a methylated G nucleotide, whereas to the 3’ end a polyadenylated (poly-A) tail is added. The 5′ cap plays an important part in protein synthesis and protects the mRNA from degradation. The poly-A tail aids the export of mRNA, it may stabilize mRNA in the cytoplasm, and it serves a recognition signal for the ribosome. The primary RNA transcript from the gene is known as hnRNA, most of which is rapidly destroyed by removal and splicing of the remaining mRNA. The presence of the poly-A tail allows purification of the mRNA from other types of RNA, a fact that is useful in purifying mRNA for studies.
Association analysis of genetic polymorphisms and expression levels of selected genes involved in extracellular matrix turnover and angiogenesis with the risk of age-related macular degeneration
Published in Ophthalmic Genetics, 2018
Katarzyna Oszajca, Maciej Szemraj, Janusz Szemraj, Piotr Jurowski
Total RNA was extracted from the peripheral blood lymphocytes using RNA extraction reagent, TRIZOL (Invitrogen Life Technologies), according to the standard acid–guanidinium–phenol–chloroform method (24). The extracted RNA was analyzed by agarose gel electrophoresis and only cases with preserved 28S, 18S, and 5S ribosomal RNA bands indicating good RNA quality were used in the study. Total RNA was digested with DNase (GIBCO) at room temperature for 15 min. The amount of purified RNA was determined using spectrophotometry at 260 nm in a NanoDrop analyzer (ND-100; NanoDrop Technologies, Wilmington, DE, USA). The purity was verified according to the ratio of 260/280 nm measurements such that values between 1.8 and 2.1 indicated that the quality of the RNA obtained was optimal and suitable for the quantitative real-time polymerase chain reaction (PCR). The quality of isolated RNA was checked using 2100 Bioanalyzer (Agilent Technologies). The level of degradation of total RNA was determined with the use of an electrophoretogram and RIN values recorded. Only the samples with RNA Integrity Number (RIN) value >7 were subject to further analysis.