Chapter 3: Repetitive DNA and Mobile Genetic Elements

Introduction

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

Centromeres contain highly repetitive DNA. (p. 58)
[The structures of centromeres]

Telomeres

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)

LINES and SINES

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)

Chapter 1: Introducing Genomes

Introduction

The discovery of DNA structure and the structure of nuleotides. Defining the 5′ and 3′ ends. (pp. 7-9)

The double helix

The structure of polynucleotides and the double helix. Base pairs, stacking interactions, and hydrogen bonds. (pp. 9-13)

The goal of the human genome project was to sequence all of the base pairs

Writing DNA sequences. (pp. 13-14)

Prokaryotes and eukaryotes

Differences between prokaryotes and eukaryotes. Bacteria vs prokaryotes. The Age of Bacteria. "Higher" vs "lower." (pp. 14-16)
[We live in the age of bacteria]

How big is your genome?

Historical estimates of the weight of DNA (3.5 pg). Calculating the number of base pairs (3.2 × 10⁹ bp). Length of the genome. (pp. 16-18)
[How big is the human genome (2023)?] [Genome size confusion]

Packaging DNA: nucleosomes and chromatin

Histones, core particles, nucleosomes, and chromatin. Heterochromatin and euchromatin. Sequencing the euchromatic genome. (pp. 19-21)

Transcription

"A gene is a DNA sequence that's transcribed to produce a functional product." Transcription initiation, elongaton, termination. (pp. 21-24)

Translation

Messenger RNA. Gene orientation: template strand, coding strand. Initiation, elongation (peptide bond), termination. (pp. 24-27)

The genetic code

Aminacylated tRNA. Standard genetic code. (pp. 27-29)

Introns and exons

Protein-coding genes, noncoding genes. RNA processing, splicing, spliceosome. (pp. 29-32)

Notes for Chapter 1 (pp. 317-318)

Chapter 2: The Evolution of Sloppy Genomes

Introduction

Pufferfish, lungfish, frogs, and the C-Value Paradox. (pp. 33-34)

The complexity of genomes

Reassociation kinetics (C₀t curves). Highly repetitive DNA, moderately repetitive DNA, unique sequence DNA. (pp. 34-35)

Variation in genome size

Junk DNA explains the variations in genome size. The C-Value Enigma. You don't need new genes to explain complexity. (pp. 35-37)

Instantaneous genome doubling

Polyploidy. Brassica species. Organisms can tolerate extra DNA. (pp. 38-39)

The Onion Test

The Onion test is a way of testing your junk DNA hypotheses. (pp. 39-40)
[The Onion Test]

Modern evolutionary theory

Evolution is a change in the frequency of alleles in a population. Adaptation, fixation, postive selection, negative selection, purifying selection. (pp. 40-41)
[Is the Modern Synthesis effectively dead?] [Kevin Laland's view of "modern" evolutionary theory (again)]

Random genetic drift

Beanbag genetics and population genetics. Fixation by random genetic drift. (pp. 41-43)
[On the importance of random genetic drift in modern evolutionary theory] [Evolution by chance] [The role of chance in evolution] [One philosopher's view of random genetic drift] [A philosopher's view of random genetic drift]

Neutral Theory

Kimura and the promotion of the neutral theory. Random genetic drift as a major cause of evolution. (pp. 43-44)
[Celebrating 50 years of Neutral Theory]

Nearly neutral Theory

Ohta and the nearly neutral Theory. The fixation of slightly deleterious alleles.(pp. 44-45)

Population genetics

Population size and selection coefficients. Probability of fixation. Population size and the fixation of slightly deleterious alleles. Drift-Barrier Hypothesis. (pp. 45-49)
[Learning about modern evolutionary theory: the drift-barrier hypothesis]

   Box: Are humans are still evolving? (pp. 49-50)

On the evolution of sloppy genomes

Insertions, deletions, and random genetic drift. (pp. 50-54)
[Evolution by Accident]

   Box: Chromosome dynamics (p. 54)
   [Segmental duplications in the human genome]

Bacteria have small genomes

Why do bacteria have small genomes? (pp. 54-56)

Notes for Chapter 2 (pp. 318-320)

Five Things You Should Know if You Want to Participate in the Junk DNA Debate

Here are five things you should know if you want to engage in a legitimate scientific discussion about the amount of junk DNA in a genome.

1. Genetic Load
   Every newborn human baby has about 100 mutations not found in either parent. If most of our genome contained functional sequence information, then this would be an intolerable genetic load. Only a small percentage of our genome can contain important sequence information suggesting strongly that most of our genome is junk.
2. C-Value Paradox
   A comparison of genomes from closely related species shows that genome size can vary by a factor of ten or more. The only reasonable explanation is that most of the DNA in the larger genomes is junk.
3. Modern Evolutionary Theory
   Nothing in biology makes sense except in the light of population genetics. The modern understanding of evolution is perfectly consistent with the presence of large amounts of junk DNA in a genome.
4. Pseudogenes and broken genes are junk
   More than half of our genomes consists of pseudogenes, including broken transposons and bits and pieces of transposons. A few may have secondarily acquired a function but, to a first approximation, broken genes are junk.
5. Most of the genome is not conserved
   Most of the DNA sequences in large genomes is not conserved. These sequences diverge at a rate consistent with fixation of neutral alleles by random genetic drift. This strongly suggests that it does not have a function although one can't rule out some unknown function that doesn't depend on sequence.

If you want to argue against junk DNA then you need to refute or rationalize all five of these observations.

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This post originally appeared on Sandwalk on July 4, 2013 [Five Things You Should Know if You Want to Participate in the Junk DNA Debate]