Recent revisions regarding how the genome works

Via TAMU Anthropology in the News, I found this article from the Washington Post by David Brown called How Science is Rewriting the Book on Genes that gives an update on why things that were once thought to be rules in genetics are turning out not to be so cut and dry. Many of these are pretty well known.

• A gene can code for many proteins, not just one, through alternative splicing

• The regulation of genes might contribute more than previously thought to evolutionary change than the actual content of the genes:

"Nearly 1 in 10 (genes) code for transcription factors, proteins that help turn genes on and off at the right time."

He discusses conserved, non-coding elements and says this:

"A study in the journal Science in August found that these elements are less tolerant of mutation than protein-coding genes. That means they are more likely to be identical among people, mice, fruit flies and worms than are the genes coding for proteins. It turns out that more of evolution's survival-of-the-fittest battles occurred in writing the instruction manual for running the genes than in designing the genes themselves."

However, as a side note, there was another recent study (see here) that found little effect of removing ultraconserved non-coding elements from mice, in that it did not visibly or immediately affect their viability, suggesting as the authors put it "...that extreme sequence constraint does not necessarily reflect crucial functions required for viability"

• Synonymous mutations are not as inconsequential as previously thought (see here)

• There is a premium placed on an organisms being able to quickly and efficiently mitigate the effects of an unpredictable environment:

"When a cell is translating a piece of mRNA into a protein, it stops when it reaches a three-nucleotide segment called a termination codon that causes the just-built protein chain to separate from the construction machinery -- like a car rolling off the assembly line. It now turns out that the mRNA instructions for a few proteins have a termination codon in the middle of the chain, not just at the end.

The protein-building machinery can sometimes "read through" this instruction and complete the protein. (How it does that is complicated and only partially understood). But most of the time, construction just stops. The half-finished protein is broken down, and all the effort goes for naught.

Why would an organism have an assembly line that builds a product partway and then tears it up time after time? This may be another strategy that allows the body to handle certain problems at a moment's notice."

I guess the bottom line here is that we're making slow progress towards understanding the genome,... or that "the more we know, the less we know".