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Messenger RNA and hnRNA both have polv(A) tails

Posted by star on 2018-12-25 21:56:29
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    The next major advance in studying eukaryotic mRNA synthesis took place in the early 1970s as a result of efforts to characterize HeLa cell mRNA by digesting it with ribonucleases. The mRNA was extracted from cytoplasmic complexes known as polyribosomes or polysomes, each consisting of two or more ribosomes translating a single mRNA. Two different endonucleases, RNase TI (a product of the fungus Aspergillus oryzae) and pancreatic RNase, were used to digest the mRNA. RNase TI and pancreatic RNase cleave phosphodiester bonds on the 3’-sides of guanylate residues and pyrimidine nucleotide distribution within HeLa cell mRNA, one would expect to find the digests would contain a mixture of short oligonucleotides along with some mononucleotides. Although digesting HeLa cell mRNA with either T1 RNase or pancreatic RNase did indeed produce the expected digestion products, it also produced an entirely unexpected polynucleotide containing 150 to 200 adenylate groups. Further analysis showed that these poly (A) segments are attached to the 3’-end of mRNA. With the one notable exception of histone mRNA, all eukaryotic mRNAs have such 3'-poly (A) tails. Yeast poly (A) tails are usually between 50 and 70 nucleotides long, considerabiy shorter than mammalian poly (A) tails. Subsequent studies showed that a large proportion of the rapidly labeled hnRNA molecules also have poly (A) tails, supporting the idea that these hnRNA molecules are converted to mRNA.
    Poly (A) tails have a practical laboratory application; their baes paring properties can be uesd to separate mRNA and pre-mRNA from other kinds of RNA. This separation is accomplished by passing a mixture of RNA molecules, dissolved in a buffer solution containing a high salt concentration, through a column packed with cellulose fibers linked to oligo (dT). Messenger RNA molecules stick to the column because of base pairing between their poly (A) tails and oligo (dT). The s......


    Although a great deal is now known about structure-function relationships in DNA-binding domains from a wide variety of transcription activator proteins, much less is known about the activation domains (ADs) in these same transcription activator proteins. This disparity in knowledge reflects difficulties in studying activation domains. In contrast to DNA binding domains, which usually fold to form specific three-dimensional structures such as helix-turn-helix motifs or zinc fingers, activation domains tend to be random coils but may assume a defined structure when they interact with other components of the transcription machinery. Furthermore, activation domains do not appear to share common structural features such as conserved amino acid sequences. Activation domain function has been just as difficult to study as activation domain structure. Although activation domains work by binding to specific proteins in the transcription machinery, it is quite difficult to determine the physiological target. In fact, many activation domains appear to have several possible targets and it is quite possible that many of these targets are physiologically important.
    DNA-bound transcriptional activator proteins may work by one or both of the following mechanisms:
    1.Activation by recruitment model. The activation domain interacts with one or more components of the transcription machinery and stabilizes the binding of the component(s) to the template DNA.
    2.Activation by conformational change model. Tne activation domain somehow induces a conformational change in one or more components of the transcription machinery that are bound to it and thereby stimulates RNA polymerase Il to initiate transcription.




    Each of the thousands of protein-coding genes within a eukaryotic cells competes for the limited transcription machinery that is available. The basal transcription machinery requires the assistance of a special class of transcription factors called transcription activator proteins to locate protein-coding genes that will be transcribed. Each transcription activator protein has at least two independently folding domains, a DNA-binding domain and an activation domain. The DNA binding domain makes sequence-specific contacts with control elements in a gene’s regulatory promoter or enhancer. For instance, DNA binding domains of Sp1 (selective promoter factor 1) and the C/EBP (CAAT box and enhancer binding protein) transcription activator proteins bind the GC box and the CAAT box, respectively. X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy have provided considerable information about the DNA-binding domains.
    Several different kinds of folding patterns have been observed in the DNA-binding domains, allowing us to assign most transcription factors to a structurally defined family. The activation domain recruits components of the transcription machinery to the gene and then interacts with various components of the transcription machinery to stimulate transcription. We know very little about activation domain structure at this time.
    Many transcription activator proteins also have additional structural features. Some of the most important of these are as follows. A short basic sequence containing arginine and lysine residues known as the nuclear localization signal allows transcription activator proteins to move through the nuclear pore complex from the cytoplasm to the nucleoplasm. Another signal, the nuclear export signal, permits the transcription activator proteins to move in the opposite direction. The direction of movement can be controlled by masking an important or exp......

Regulatory Promoter and Enhancer

Posted by star on 2018-12-06 21:41:06
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    Based on their knowledge of bacterial gene regulation, investigators anticipated that eukaryotic regulatory elements for protein-coding genes would be located just upstream from the transcription initiation site. Therefore, they attempted to detect these regulatory elements by first introducing mutations in this region and then determining the mutations' effects on gene expression. Deleting several base pairs (bp) at the same time might seem to offer a rapid method for locating regulatory elements within a gene, but it has a serious shortcoming. Deletion mutations not only remove the nucleotides of interest, they also alter the spacing between flanking DNA sequences. Thus, the loss of gene activity that results from deleting a DNA segment might be due to the fact that an essential segment was removed, the spacing between flanking sequences was changed, or both.
    In 1982, Stephen McKnight and Robert Kingsbury devised a new technique that eliminated the spacing problem, facilitating the search for regulatory elements. This technique, called linker-scanning mutagenesis, involves systematic replacement of short DNA segments (usually 3-10 bp) in a region of interest with a DNA linker containing a random sequence of exactly the same size. Although a linker mutation, like a deletion mutation, changes a short DNA segment,it has the advantage of preserving the spacing between nucleotide sequences on either side of the altered segment. Retention of spacing is very important because it allows us to distinguish between effects due to sequence alterations and those due to space changes between flanking sequences.
    Linker scanning mutagenesis was first used to search for the promoter of the thymidine kinase gene in the herpes simplex virus(an icosahedral, enveloped DNA virus responsible for cold sores and genital herpes). Linker mutations were introduced just upstream from the transcription initiation site of a c......


    On November 26th, Vitrakvi, an anticancer drug jointly developed by Bayer and Loxo Oncology, was officially launched in the US. Vitrakvi became the first officially approved oral TRK inhibitor, and it is the first "broad spectrum" and tumor type-agnostic anticancer drug. Applicable to patients between the ages of 4 months and 76 years. It can effectively treat 17 kinds of cancers such as lung cancer, thyroid cancer, melanoma, gastrointestinal cancer, colon cancer, soft tissue sarcoma, salivary gland, infant fibrosarcoma, appendic cancer, breast cancer, cholangiocarcinoma and pancreatic cancer. The overall response rate was 75%.
    Vitrakvi is used to treat adults and children with NTRK gene fusion, locally advanced or metastatic solid tumors, and does not produce known resistance mutations, metastatic or surgical resection may lead to serious morbidity ,there is no effective alternative treatment option.
    LOXO-101 is a targeted drug targeting tumor patients with NTRK1, NTRK2 or NTRK3 gene fusion. Simply put, this new drug does not need to consider the area where the cancer occurs. Regardless of the cancer type (tissue/cell/site), Vitkravi can be used for treatment as long as the NTRK gene is fused. So cancer patients see this gene fusion in the genetic test report, then it is very likely to be cured by the drug!
    TRK, a tropomyosin receptor kinase, is an important signaling pathway regulating cell communication and tumor growth, while NTRK is a gene encoding TRK. In rare cases, the NTRK gene fuses with other genes, resulting in an uncontrolled TRK signaling pathway that promotes tumor growth. These tumors share a common feature: they carry mutations in the TRK fusion gene and rely on this mutant gene to provide growth signals. Because they are all dependent on the TRK gene, they all respond positively to TRK-targeted drugs. According to statistics, in the United States, about 2,......

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