- Junk & Jonathan: Part 1—Getting the History Correct
- Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?
- Junk & Jonathan: Part 3—The Preface: Preface
- Junk & Jonathan: Part 4—Chapter 1: The Controversy over Darwinian Evolution
- Junk & Jonathan: Part 5—Chapter 2: Junk DNA: The Last Icon of Evolution?
- Junk & Jonathan: Part 6—Chapter 3: Most DNA Is Transcribed into RNA
- Junk & Jonathan: Part 7—Chapter 4: Introns and the Splicing Code
- Junk & Jonathan: Part 8—Chapter 5: Pseudogenes—Not so Pseudo After All
- Junk & Jonathan: Part 9—Chapter 6: Jumping Genes and Repetitive DNA
The title of Chapter 7 is "Functions Independent of Exact Sequence." This is potentially the most important chapter in the book because it should address some of the serious arguments for function in the genome. We already know that sequence is not conserved in the vast majority of the genome that we call junk so in order for it to have a function it must be due to the presence of built DNA. The chapter begins with a brief description of enhancers. Enhancers are DNA binding sites required for the regulation of transcription of a gene. In many cases a protein will bind to an enhancer and also make contact with the transcription initiation complex (RNA polymerase + factors). This contact can activate or repress transcription. DNA binding sites are small (less than 10 bp) and they've already been included under regulatory sequences in calculation of genome content. Nobody thinks they're junk. However, an enhancer sequence can often be some distance away from the binding sites of other proteins and their interactions create a loop of DNA. This mode of binding is well-known and has been extensively studied in many system including the lac operon [Repression of the lac Operon] The figure shows a model of the lac repressor boud to DNA to illustrate the minimum size of a DNA loop. This DNA should be included in the amount of sequence needed for an active promoter even though the sequence is irrelevant. When binding sites are 50 bp apart, that's sufficient to allow looping. Longer stretches are okay but not necessary. Most regulatory regions lie well within 1000 bp of the transcription start site and even if you include all of this sequence—which is unreasonable—it only amounts to less than 1% of the genome. There are some famous examples of enhancer sequences that are several hundred kb (>100,000 bp) from the start site but these are exceptions, not rules. There's no reason to suspect that all of the DNA in the loop is necessary for proper transcription regulation and Wells doesn't even attempt to offer one. Theme Genomes & Junk DNAThe next section of Chapter 7 discusses chromatin and the specific example is centromeres. There's no doubt in anyone's mind that a good part of centromeric regions are essential (i.e. not junk). I've estimated that it could be a high as 2% [Centromere DNA]. Nothing new here. He forgot to mention telomeres. The last section of the chapter is truly bizarre. It's title is "Non-Protein-Coding DNA Can Function as a Lens" and it quotes a 1979 study claiming that concentrations of heterochromatin in retinal cells can function as a lens in nocturnal animals. Presumably this heterochromatin consist mostly of non-sequence-specific DNA and it may explain why we have so much of it in our genome. I don't believe it because it doesn't explain why other animals have junk DNA and it isn't a very good explanation for large plant genomes. Wells concludes the chapter with,
So at all three levels of the genomic hierarchy, there is evidence for functions that are independent of the exact DNA (or RNA) sequence. Like the evidence for sequence-dependent functions, the evidence for sequence-independent functions is almost certain to grow as scientists continue to expand their research horizon beyond the limits of the Central Dogma. There is a lot more to the genome (not to mention the living cell) than the protein-coding sequences in DNA.There certainly is more to the genome than protein coding DNA. We've known that for four decades and none of that essential DNA is called "junk." It's a shame that Wells doesn't mention this because his readers might get the false impression that Wells is on to something that scientists don't know. I'm sure he doesn't intend to deceive his readers, aren't you?