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Electric DNA, Circular RNA, and Other Epigenetic Wonders

DNA

Upon completion of the Human Genome Project, scientists were baffled at the unexpectedly low number of genes. How could so few protein-coding genes (about 20,000) build a human being? It turned out that genes are only one part of the action. The old Central Dogma that viewed DNA as the master molecule, RNA as the messenger boy, and protein as the end product is long gone. Now we are beginning to see that there are three “-omes” that interact in complex ways with other molecules, including lipids and sugars. Everywhere they turn, scientists are seeing molecular wizardry at work. Here are just a few recent examples.

Another -Ome with a Code of Its Own

The Bellvitge Biomedical Research Institute (IDIBELL) of Barcelona, Spain, assumes we know about the genome and the epigenome. Now, news from IDIBELL draws our attention to another “-ome” that is rising in significance: the transcriptome, referring to the “epigenetics of RNA”:

“It is well-known that sometimes DNA produces a RNA string but then this RNA does not originate the protein. Because in these cases the alteration is neither in the genome nor the proteome, we thought it should be in the transcriptome, that is, in the RNA molecule”, Dr. Esteller explains.”In recent years, we discovered that our RNA is highly regulated and if only two or three modifications at the DNA level can control it, there may be hundreds of small changes in RNA that control its stability, its intracellular localization or its maturation in living beings”. [Emphasis added.]

For example, some non-coding RNAs are now known to be ‘guardian RNAs’ according to the modifications on their bases or sugars with methyl groups that act as tags. The field of transcriptomics is only about five years old; “It will definitely be an exciting research stage for this and the next generation of scientists,” Dr. Esteller says. See our recent article “RNA Code Surpassing DNA in Complexity” for more about this epicentric karma running over the Central Dogma.

Electric DNA

Here’s another way that DNA carries information that is rather shocking: it conducts electricity. Science Magazine describes “DNA charge transport” as an unexpected signaling system between the code and its reading machines.

DNA charge transport provides an avenue for rapid, long-range signaling between redox-active moieties coupled into the DNA duplex. Several enzymes integral to eukaryotic DNA replication contain [4Fe4S] clusters, common redox cofactors. DNA primase, the enzyme responsible for initiating replication on single-stranded DNA, is a [4Fe4S] protein. Primase synthesizes short RNA primers of a precise length before handing off the primed DNA template to DNA polymerase α, another [4Fe4S] enzyme. The [4Fe4S] cluster in primase is required for primer synthesis, but its underlying chemistry has not been established. Moreover, what orchestrates primer handoff between primase and DNA polymerase α is not well understood.

In the paper, seven researchers from Caltech and Vanderbilt tell about experiments they ran to establish the existence of electrical charge transfers between the double helix and the molecular machines that read it and duplicate it. “We demonstrate that the oxidation state of the [4Fe4S] cluster in DNA primase acts as a reversible on/off switch for DNA binding,” they conclude. And it’s not alone. Because DNA can conduct charges over long distances, “Such redox signaling by [4Fe4S] clusters may play a wider role in polymerase enzymes to coordinate eukaryotic DNA replication.”

Circular RNA

Some RNAs fold into stable loops. We have them in our brains. What do they do? When discovered, they were considered non-coding. Now, however, scientists at Hebrew University have found that they can indeed code for proteins. The paper in Molecular Cell, “Translation of CircRNAs,” opens up a new window of functional possibilities for these oddball transcripts.

Circular RNAs (circRNAs) are abundant and evolutionarily conserved RNAs of largely unknown function. Here, we show that a subset of circRNAs is translated in vivo. By performing ribosome footprinting from fly heads, we demonstrate that a group of circRNAs is associated with translating ribosomes. Many of these ribo-circRNAs use the start codon of the hosting mRNA, are bound by membrane-associated ribosomes, and have evolutionarily conserved termination codons…. Altogether, our study provides strong evidence for translation of circRNAs, revealing the existence of an unexplored layer of gene activity.

“Evolutionarily conserved,” of course, means not evolved. A layman’s account in Science Daily explains the significance of this finding.

This discovery reveals an unexplored layer of gene activity in a type of molecule not previously thought to produce proteins. It also reveals the existence of a new universe of proteins not yet characterized.

One possible function for circRNAs is stable storage of protein-coding data for regions far from the nucleus. The tips of axons, for instance, can be too far away for quick access to genes they need. “As circRNAs are extremely stable, they potentially could be stored for a long time in compartments more distant to the cell’s body like axons of neuron cells,” Science Daily says. “There, the RNA molecules could serve as a reservoir for proteins being produced at a given time.” One scientist not connected about the research expressed excitement about it. “This is a very important, promising and timely discovery that gives an important hint of the function of these abundant yet uncharacterized RNAs.”

Interdependent Modifications

As geneticists explore the universe of epigenetic modifications, they have been unable to replicate some of them in a lab dish (in vitro). Now, a reason for this is coming to light. A paper in Nature begins with surprising statistics in the number of epigenetic modifications known. Then the authors tell how they discovered a case of “interdependent” modifications:

Nucleic acids undergo naturally occurring chemical modifications. Over 100 different modifications have been described and every position in the purine and pyrimidine bases can be modified; often the sugar is also modified. Despite recent progress, the mechanism for the biosynthesis of most modifications is not fully understood, owing, in part, to the difficulty associated with reconstituting enzyme activity in vitro. Whereas some modifications can be efficiently formed with purified components, others may require more intricate pathways. A model for modification interdependence, in which one modification is a prerequisite for another, potentially explains a major hindrance in reconstituting enzymatic activity in vitro. This model was prompted by the earlier discovery of tRNA cytosine-to-uridine editing in eukaryotes, a reaction that has not been recapitulated in vitro and the mechanism of which remains unknown.

Sure enough, they found a case in a microbe where one modification was a prerequisite to another modification. The mechanism appears to provide quality control by preventing catastrophic modifications to every matching spot on a whole genome.

Here’s a case we can relate to. The human antibody response system rapidly mutates sequences looking for matches to antigens. How does activation-induced cytidine deaminase (AID) deaminate the immunoglobulin receptors (IgG) without affecting the rest of the genome? The answer may involve interdependent modifications:

In mammalian cells, AID plays a critical role in antibody class diversification by specifically targeting the IgG receptor genes, while generally leaving the rest of the genome unblemished. While the mechanism of this enzyme has been elucidated, the basis for its programmed specificity towards only a fraction of the genome is still unclear. The work presented here provides a rationale for controlling mutagenic enzymes through their interaction with other partners, as has been suggested previously. This, of course, leads to the question of how such substrate specificities evolved. Our data suggest that the answer may relate to the ability of certain protein–protein interactions to provide secondary functions based on extreme mutual dependability, as illustrated here by the interplay between TRM140a and ADAT2/3.

ID advocates are certain to catch the phrases “programmed specificity” and “extreme mutual dependency” in support of their view, while chuckling at the Darwinists’ quandary about “how such substrate specificities evolved.” Their suggested solution only appears to dig a deeper hole. They never quite get around to telling readers how “extreme mutual dependability” came up with “secondary functions” by sheer dumb luck, such that the result only gives an appearance of “programmed specificity.” ID, on the other hand, provides a common-sense answer. Programming presupposes a programmer.

Image credit: Nogas1974 (Own work) [CC BY-SA 4.0], via Wikimedia Commons.