Friday, December 28, 2012

Here is How Genes Are Exquisitely Timed

Ready, Set, Go

You learned in your high school biology class that genes are copied, or transcribed, and that the transcript was used by the ribosome to synthesize a protein. But how does the cell know which genes to transcribe, which form of the gene to use, and when to transcribe it? These questions are answered by various mechanisms collectively referred to as gene regulation. The DNA region upstream of a gene may have various molecules and proteins attached which influence its expression, that DNA region and the histone proteins about which it is wrapped may have methyl groups or other small groups attached to them serving as signals, once transcribed the resulting mRNA transcript may be spliced into alternate forms, the mRNA transcript can also be controlled by snippets of RNA that bind to the transcript, the speed with which the transcript is translated into a protein can be controlled at the ribosome, and so forth. It is an incredible network of signals and mechanisms controlling which genes are used, how they are used, and when they are used. Now, new research is helping to elucidate yet another mechanism which is the equivalent of a fine-control knob on the timing of the transcription process.

Gene transcription is conducted by a massive molecular machine known as RNA polymerase which, roughly translated into English, means to glue together many nucleotides to make an RNA molecule. The transcription process entails unwinding the DNA double helix, sliding along one of the strands, grabbing the correct matching nucleotide at each rung, and gluing that nucleotide to the end of the new and growing transcript.

But before this process begins the RNA polymerase machine may pause and wait for a start signal. Apparently in these cases the task at hand is not to be accomplished as soon as possible, but rather it is coordinated and synchronized with other activities. The timing of the arrival of the RNA polymerase is not sufficiently precise so it arrives a little early, and then is paused until just the right moment.

Not too surprisingly this pausing of RNA polymerase is particularly important in the embryonic development stages where the growing embryo is undergoing a massive and complex cellular choreography of events.

The new research helps to elucidate for which genes RNA polymerase is paused, and how this pausing regulation of RNA polymerase varies over time and between tissues.

It is yet another mechanism in the fantastically complex gene regulation.


  1. Related note to 'timing':

    A New Study Adds Further Depth to the Information Story - JonathanM - March 2012
    Excerpt: The conventional genetic code involves 20 different amino acids, which map to 64 different triplets of nucleotides called codons. Since there are many more codons than amino acids, this means that there is an element of redundancy because amino acids can be specified by multiple codons. As I noted before, this redundancy allows the genetic code to be exquisitely fine-tuned to minimize error. The paper explains that "redundancy in the genetic code allows the same protein to be translated at different rates." In other words, even so-called silent substitutions (that is, those mutations that exchange a nucleotide for another without changing the amino acid specified by the codon) can have an impact on the rate of translation of the protein product.

  2. If redundancy in the code is a necessary condition for timing, then that redundancy is only relatively redundant--not absolutely. The ToE is shown over and over to be littered with false, over-simplified assumptions. These in turn are used to make false deductions. When you flesh those over-simplified assumptions out to what they imply about the non-random properties of past events, they are equivalent to myriads of ad-hoc hypotheses.

    The alternative is the "tree-think" approach to explanation. But this is a species of "Platonic" thought--much like that of Nagel in his new book. That thought is, when analyzed causally, only conceivable as teleological in nature. True naturalistic explanation explains events in terms of event regularities that can be corroborated by predictions that are implied by applying the theoretical explanation to initial conditions.

    Cladistic trees, per se, don't tell us whether the large to huge phenotypical gaps are due to a lack of preservation of transitional forms, saltations or SA. The explanation for those gaps has to come from elsewhere.

  3. "The new research helps to elucidate for which genes RNA polymerase is paused, and how this pausing regulation of RNA polymerase varies over time and between tissues."

    At this rate of discovering how the cell is amazingly orchestrated, I wouldn't be surprised if they soon discover that some critical processes require simultaneous signals like when we use multiple keys to launch rockets, or require two or more witnesses to establish the truth.