Originally posted by CuriousGene
Just to clarify some numbers here for the sciforum readership . . .
The human genome is more on the order of 50% repetitive. Even Celera's data show about ~37% repetition with the caveat that they have an underestimation. Also, clearly it's a misconception that most of the genome is junk. Media sources, like CNN and BBC, often report that only 3% of the human genome is useful and the rest is junk. The 3% is referring to only exons. But, I think it's clear that non-exonic components are quite functional. Examples of functional components outside of the 3% (and apparently living in the "junk" part of the genome) include transcription factor binding sites, introns, all types of regulatory sequences, and for all you RNA fans out there . . . there are even relatively newer classes of RNA known as micro RNA (small ~22 bps) sequences. The transcriptional terrority of polII genes alone to date (cause we haven't found them all yet) account for ~40% of the human genome.
I think what is confusing is the role the repeat component of the human genome plays. There are repeat sequences inside genic content that would preclude one from arguing that there is just "junk" in portions of the genome that contain repeats. Also of importance is the potential role that these repeat sequences themselves play in the evolution of our genome. As one of many examples of possible repeat sequence function, there is strong evidence of a repeat-driven expansion of the human genome. In addition, Alu repeats (the most ubiqitous repeat class in our human genome) have been the focus of many papers regarding their possible function . . . one of which is the linking of Alu sequences to the origin and expansion of segmental duplications which has certainly shaped our nuclear genome. Repeats in general have helped shape our genome by allowing for a dynamic medium for our genome to evolve through. Both retroposons and transposons have facilitated rearrangements, translocations, deletions, insertions, and duplications within our human genome.
When people say "junk", I wonder if they actually think they would not be any different without 97% of their own nuclear genome.