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    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,......

General Transcription Factors: Basal Transcription

Posted by star on 2018-11-27 18:09:34
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    RNA polymerase II requires the assistance of protein factors to bind to the core promoter. This requirement was first demonstrated by studying specific initiation at the major late promoter of adenovirus DNA, which controls highly expressed genes for structural proteins in the virus particle. RNA polymerase II cannot catalyze specific initiation at this promoter but gains the ability to do so when a soluble cell-free extract from human KB cells (cells derived from an oral epidermoid carcinoma) is added to it. In 1979, Robert G. Roeder and coworkers used classical protein fractionation techniques to isolate protein factors from the KB cell extract that assist RNA polymerase II. These protein factors, or general transcription factors (GTFs) as they are now known, were named TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH. The first two letters, TF, indicate the protein is a general transcription factor; the Roman numeral II signifies the factor supports RNA polymerase II transcription; and the final letter was assigned based on the protein fractionation scheme rather than on protein function. (The letters C and G are missing because later studies showed that the proteins originally assigned these letters afe not transcription factors for RNA polymerase II.) Subsequent studies by Roeder and other investigators demonstrated that these general transcription factors are present in all eukaryotes from yeast to humans. Moreover, archaea have similar general transcription factors. Counterparts in other eukaryotes serve the same functions.



E. coli regulates r-protein synthesis

Posted by star on 2018-11-19 22:17:58
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    A gene dosage experiment also shows that the synthesis of ribosomal proteins (r-proteins) is not regulated at the transcriptional level. The genes encoding the 52 r-proteins are organized into 20 operons. Addition of an appropriate plasmid can increase the number of copies of one of these operons in a cell, say, tenfold. This would increase the rate of synthesis of the corresponding mRNA tenfold, but the rate of production of r-proteins encoded in the mRNA remains that observed with one copy of the operon. Thus, the amount of the r-proteins that is synthesized is not proportional to the amount of the mRNA encoding them, so clearly translation and not transcription is being limited.

    An understanding of the mode of translational regulation came from in vitro translation experirnents. In these experiments, a single species of r-protein mRNA was translated and the inhibitory effect of each r-protein encoded in the mRNA was tested. It was observed that translation of each mRNA could be inhibited by the addition of one(a particular one) of the encoded r-proteins. Further analysis showed that the translational repression is a result of binding of that r-protein to a base sequence near the site at which ribosomes initially bind to mRNA. A variant of the in vitro experiment completes the story, namely, the addition of the particular rRNA (5S, 18S, or 23S) to which the r-protein binds in the ribosome prevents translational re-pression. A base sequence analysis of the mRNAs and the rRNA shows a similar sequence and a common stem-and-loop structure in the binding sites of each RNA molecule for a particular r-protein. Thus, competition exists between rRNA and r-protein mRNA for a particular r-protein. Binding studies show that each repressing r-protein species binds preferentially to the rRNA; thus, as long as rRNA is available for ribosome production, r-proteins will bind to rRNA and synthesis of r-proteins will continue. Studies with......

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