Monday, August 29, 2022

Chapter 3: Repetitive DNA and Mobile Genetic Elements

Half of our genome is composed of highly repetitive DNA and moderately repetitive DNA. Satellite DNA. C0t curves. (pp. 57-58)
[Transcription activity in repeat regions of the human genome]
Centromeres contain highly repetitive DNA. (p. 58)
[The structures of centromeres]

Telomeres at the ends of chromosomes contain repetitive DNA. (pp. 58-59)

   Box: Dead centromeres and telomeres (pp. 59-60)

Short tandem repeats (STRs)

Short tandem repeats (STRs) are short stretches of repetitive DNA. (p. 60)

   Box: DNA fingerprints (pp. 60-61)

Mobile genetic elements
Moderately repetitive DNA consists of interspersed copies of viruses and transposons. (p. 61)
Hidden viruses in your genome
The human genome contains copies of DNA viruses and RNA viruses. Most of them are due to ancient insertions and the viral genomes have acquired inactivating mutations. Many virus-related sequences are just fragments of the original virus genome. (pp. 61-65)
What do we need to know about transposons?
The two main tpes of transposons are DNA transposons and RNA transposons (retrotransposons). (pp. 65-67)
Long interspersed elements (LINEs) are transposons that carry a gene for reverse transcriptase. Most LINE-related sequences are degenerate versions of a once-active transposons. Short interspersed elements are derived from small noncoding genes and they require exogenous reverse transcriptase to propagate. Alu elements are one example of a SINE and there are more than one million copies in the human genome. (pp. 67-70)
How much of our genome is composed of transposon-related sequences?
Most of the transposon-related sequences are inactive fragments of the original transposons. It's diffficult to get a precise estimate of the total amount of transposon-related sequences but it's probably at least 50% of the human genome.(pp. 70-72)

   BOX: What does the humped bladderwort tell us about junk DNA? (p. 72)

Selfish genes and selfish DNA
Selfish DNA refers to DNA sequences that can propagate by themselves within the genome. (p. 73)
[Junk DNA and selfish DNA] [The selfish gene vs the lucky allele]
Exaptation versus the post hoc fallacy
Some transposon-related sequences have secondarily acquired a function that contributes to the fitness of the organism. This is an example of exaptation. Some scientists believe that transposon-related sequences are retained in order to serve as a reservoir for future exaptation but this argment is related to a logical fallacy called the post hoc fallacy. (pp. 73-78)
[Peter Larsen: "There is no such thing as 'junk DNA'"]
Mitochondria are invading your genome!
The human genome contains fragments of mitochondrial DNA that have recently been incorprated by accident. (pp. 78-79)
[How much mitochondrial DNA in your genome?]
On the origin of junk DNA

A lot of junk DNA originates from ancient insertions of transposons and their subsequent degeneration by acquiring mutations. (pp. 79-80)

If it walks like a duck ...

Transposons look like junk, behave like junk, and evolve like junk, so let's just call them junk. (pp. 80-81)

Notes for Chapter 3 (pp. 320-321)

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