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17 Cards in this Set
- Front
- Back
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transcription factorY (?)
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specific nuclear sites at which most RNA polymerase II transcription occurs; also contain the majority of active RNA polymerase and other transcription factors
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transcription factor
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is a protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to mRNA.; can have diverse and complicated effects on transcription
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chromatin remodeling
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chromatin modification; an important step in gene regulation; the ability of the cell to alter the association of DNA with other chromatin components is essential to allow regulatory proteins to access DNA; chromatin remodeling appears to be a prerequisite for transcription of some eukaryotic genes, although it can occur simultaneously with transcription initiation and elongation of other genes; chromatin can be remodeled in two general ways: by changes to nucleosomes and modifications to DNA
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histone acetyltransferases (HATs)
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catalyzes the acetylation of the histone component of nucleosomes; when an acetate group is added to specific basic amino acids on the histone tails, the attraction bw the basic histone protein and acidic DNA is lessened; HATs are recruited to genes by specific transcription factors; the loosening of histones from DNA facilitates further chromatin remodeling catalyzed by ATP-dependent chromatin remodeling complexes. these modifications make promotor regions available for binding to transcription factors that initiate the chain of events leading to gene transcription, as well as to RNA polymerase
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histone deacetylases (HDACs)
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remove acetate groups from histone tails; like HATs, can also be recruited to genes by the presence of certain repressor proteins on regulatory regions
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insulator elements
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short DNA sequences that bind specific proteins; can act as barriers to prevent the spread of chromatin remodeling into neighboring genes
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DNA methylation
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modification of DNA after DNA replication by the enzyme-mediated addition of methyl groups to bases and sugars; often involves cytosine (in the genome of any given eukaryotic species, approx 5% of the cytosine residues are methylated; however, can be tissue-specific); the ability of base methylation to alter gene expression is known from studies on the lac operon in E. coli: methylating DNA in the operator region, even at a single cytosine residue, causes a marked change in the affinity of the repressor for the operator; methylation occurs at position 5 of cytosine, causing the methyl group to protrude into the major groove of the DNA helix, where it alters the binding of proteins to the DNA
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enhancers
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can be located on either side of a gene, at some distance from the gene, or even within the gene. They are called "cis regulators" because they function when adjacent to the structural genes they regulate, as opposed to "trans regulators" (such as DNA binding proteins), which can regulate a gene on any chromosome. Enhancers are necessary for achieving the mansimum level of transcription. Are also responsible for time- and tissue-specific gene expression. Within enhancers, binding sites are often found for positive as well as negative gene-regulatory proteins
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silencer
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another type of cis-acting transcription regulatory element; acts upon eukaryotic genes to repress the level of transcription initiation; like enhancers, are short DNA sequences elements that affect the rate of transcription initiated from an associated promoter. They often act in tissue- or temporal-specific ways to control gene expression
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cis-acting regulatory sites
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promoters, enhancers, and silencers; influence transcription initiation by acting as binding sites for specific transcription regulatory proteins
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DNA binding domain
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one domain of a transcription factor which binds to DNA sequences present in the cis-acting regulatory site
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trans-activating (or trans-repression) domain
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the other domain of a transcription factor which activates or represses transcription through protein-protein interactions
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general or basal transcription factors
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proteins needed to initiate either basal-level or enhanced levels of transcription; are not part of the RNA polymerase II molecule but assemble at the promotor in a specific order, forming a transcriptional pre-initiation complex (PIC) that in turn provides a platform where RNA polymerase is able to recognize and bind to the promoter
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DNase hypersensitive
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a constitutively open chromatin; it is free of nucleosomes; ex: structure of the UAS(G) [upstream activating sequence of GAL genes)
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GAL gene system (p. 469)
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one of the first model systems used to study eukaryotic gene regulation; involved the genes in yeast that encode enzymes that break down the sugar galactose; is composed of 4 structural genes (GAL1, GAL10, GAL2, and GAL7) and three regulatory genes (GAL4, GAL80, and GAL 3). The products of the structural genes transport galactose into the cell and metabolize the sugar. The products of the regulatory genes positively and negatively control the transcription of the structural genes.
Gal4p= encoded by the regulatory GAL4 gene of the GAL gene system; has four binding sites within the UAS(G); is negativetly regulated by the Gal80 protein (Gal80p), which is the produce of the GAL80 gene; in the absence of galactose, Gal80p is always bound to Gal4p, covering Gal4p's activation domain. Transcriptional acitivation occurs when galactose interacts with the Gal3p, encoded by the GAL3 gene. When bound to galactose, the Gal3p molecule undergoes a conformational change that allows it to interact with the UAS(G)-bound Gal4p/Gal80p complex |
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posttranscriptional regulation
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changes made to pre-mRNA molecules during conversion to mature mRNA. These include the addition of a methylated cap at the 5' end and a poly-A tail at the 3' end, excision of introns, and exon splicing.
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alternative splicing (calcitonin/calcitonin gene-related peptide)
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alternative splicing can generate different forms of mRNA from identical pre-mRNA molecules, so that expression of one gene can give rise to a number of proteins, with similar or different functions. One example is the alternative splicing of the pre-mRNA transcribed from the calcitonin/calcitonin gene-related peptide gene (CT/CGRP gene). In theyroid cells, the CT/CGRP primary transcript is spliced in such a way that the mature mRNA contains the first four exons only. In these cells, the exon 4 polyadylation signal is used to process the mRNA and add the poly-A tail. This mRNA is translated into the calcitonin peptide that regulates calcium..... p 471
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