Term
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Definition
Long stretches (100s of kb) of DNA with
uniform %GC, isochores could span >10 Mb.
High %GC = heavy isochores (H)
Low %GC = light isochores (L) |
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Term
| Traditional isochore classification of human genome |
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Definition
L1 (<37% GC), L2 (37-42%), H1 (42-47%), H2(47-52%), H3(>52%)
Often L1 and L2 are grouped together as a single L isochore |
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Term
| Where heavy/light isochores are found? |
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Definition
| Heavy isochores are found only in warm-blooded vertebrates (mammals, birds), not in cold-blooded vertebrates (fish) |
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Term
| Selectionist hypothesis about isochores |
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Definition
| GC-pairing is stronger than AT-pairing and stabilize DNA at higher temperatures. Hypothesis is supported by heavy isochores are found in warm-blooded vertebrates.Heavy isochores are gene-rich |
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Term
| Mutationist hypothesis about isochores |
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Definition
| The pool of available nucleotides changes over replication. There is more GC available early in replication, so mutations will be biased towards G or C. Over time, regions of the genome that replicate early become GC-rich. In general, GC-rich regions have been observed to replicate early. |
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Term
| GC variations on gene scale |
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Definition
| Coding regions > introns > 5’ flanking regions > 3’ flanking regions |
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Term
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Definition
| all of the synonymous codons for a particular amino acid are not used with equal frequency as would be expected at random |
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Term
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Definition
| effective number of codons, the average number of codons that are used to encode the 20 amino acids. The minimum is 20,the maximum is 61. Low ENC=high codon bias |
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Term
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Definition
Frequency of optimal codons, the frequency with which the “optimal” codon is used for each amino acid. Optimal codons are defined as those used with the highest frequency in highly expressed genes. High Fop=high codon
bias. Specie-specific |
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Term
| Observed patterns of codon bias |
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Definition
a)higher in highly-expressed genes
b)higher in short genes than in long genes
c)higher in female-expressed than in male-expressed genes |
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Term
| Selection explanation of codon bias |
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Definition
| natural selection favours the use of optimal codons (those that correspond to the most abundant tRNA) to make translation faster nd more accurate. Codon bias could be used as a way to regulate gene expression post-transcriptionally |
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Term
| Mutation explanation of codon bias |
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Definition
| There may be a bias in mutation. For example, if mutations from A or T to G or C are more frequent and there is no selection on synonymous sites, then these sites should become GC-rich. |
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Term
| Why most optimal codons end in G or C? |
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Definition
| The mutational hypothesis would require a mutational bias towards G or C, but the mutational bias is towards A or T. There is biased mismatch repair in favor of G or C,strongest in regions of high recombination. The GC content at third codon positions is correlated with local genomic GC content, suggesting an effect of mutation of codon usage. |
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Term
| What is the strength of selection acting on a particular codon? |
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Definition
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