How your chromosomes may actually be put together. Hint: Forget the text books.

Chromosomes are fascinating structures. They are dynamic and highly plastic. They break under conditions of radiation or chemotoxicity, reform into a variety of new structures, and spin off small circular chromosomes called double minutes that get randomly shuffled about in the process of cell division. According to classical genetics, chromosomes are very simple molecules of a single, continuous linear DNA wrapped up within a chemical coating of protein and other molecules called chromatin. Question is, how in the world can such a simple linear molecule undergo the fantastic rearrangements known to occur within such chromosomes?

This blog provides overviews into this problem and goes into probably more detail than the average user cares to endure. For those who want the skinny without all the details or evidence, let me say this as succinctly as possible: Your chromosomes are probably incredibly more structurally complicated than classical texts would lead you to believe. Massive amounts of chromosomal DNA don’t break apart and reunite using some kind of biological black magic. There is beauty and order in how all of this is done, even when it leads to mutations, cancer, deformities, and even death. In spite of all of this, sometimes the individual gets lucky and wins the genetic lottery, leading to increased vigor and better survival. This is the very crux of what evolution is all about.

The linear chromosome advocates would have you believe that DNA mutates gradually over long periods of time, as little as one base pair at a time. Of course, this flies in the face of overwhelming evidence that chromosomes can be broken up like shattering glass and reformed into an endless variety of “new” chromosomes. Surely, over time, some of these rearrangements can prove harmless, even beneficial to the recipient. However, such gross rearrangements may involve millions of base pairs of DNA. How can such massive rearrangements occur in a simple linear DNA model?  Imagine breaking a 50,000 micron strand in the middle within a six micron diameter cell nucleus and trying to turn one piece completely around and rejoin it with the other.

If this piques your interest and you have some time, pore over some of this blog to see what I am talking about. Skip any sections that are too involved and just go on to the next one. You can learn a lot just by doing that. You may also write me by e mail for additional information or write comments. This is an open forum and I welcome any and all constructive input:

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Circular DNA crosslinks may be the building blocks that led to your chromosomes

For 50 years, scientists have been well aware of catenated DNA circles (see sample reference link below). Catenated circles can be thought of as links in a metal chain. They are physically interlocked, but otherwise not really connected to one another.

Electron microscopy of the circular kinetoplastic DNA from Trypanosoma cruzi: Occurrence of catenated forms

However, what if there is another kind of connection between two circles? One that actually “fuses” them together. Think of two rubber bands that have been glued together at one spot. If you cut the spot where they have been glued, they become one fused circle with “dimples” marking the spot of fusion.

rubber bandfused circles

Such a fusion could be explained by tetravalent DNA strand base pairing as shown below:

Fig 40

When a portion of the hybridized region is cut out and religated, it leads to something like Fig. D. Note the dimpling effect because of continued tetravalent strand base pairing. When all four strands are cut just once and religated, the two circles remain intact and can completely fuse together as in Fig E.  If DNA isolated from the core of a chromosome is treated with DNase I for as little as 60 seconds, dimples begin to form as shown in Plate X, Fig. A below: Such a structure cannot be explained in terms of a circular DNA catenation model because it is obvious this structure has two fusion components, each preceding away from the dimpled region. When such DNA is heated to melt it in formamide, the structures break up into fragments because of the DNase damage as shown in Plate XII.

Plate X  Plate XIII

Circular DNA’s not subjected to DNase treatment but melted in formamide lead to unusual daisy-like structures like the one shown in Plate VI, Fig. A below: Compare this structure to the one in Plate X, Fig. A, surrounded by yellow arrows. Note the internal circle surrounded by this dimpled DNA that may have been damaged by DNase (red arrow).

Plate VI Plate Xb

Are these fused circular structures minor components of an otherwise linear chromosome or could they be something more? When dying mouse L-1210 cells exposed to acridine orange are treated briefly with 0.1 N HCl and photographed under UV light, the results are nothing less than spectacular (see below, pics shown elsewhere in blog):

slide 7Circles

Circles of all sizes have been released from the cells. Furthermore, these structures can be labeled with tritiated thymidine, indicating the presence of DNA (See comparison below). You will have to look very hard to find any catenated circles here, if any exist at all. It is obvious the HCl broke some very basic kinds of bonds in order to release these kinds of structures. They are quite complex and evidence shown below in Figs. 69 and 70 suggests that the “pearls” within each necklace are circular structures themselves which have not be released. In other words, circles are composed of other smaller circles.

circular arrays

69 70

Fig. 69                                                                   Fig. 70

So the obvious question is this: How can all of these circular structures be locked up inside a simple linear chromosome? How indeed! Perhaps a better explanation is in order. One that requires a considerable amount of additional investigations by many many laboratories for years and years to come.

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Follow the palindromes to see how life evolved.

You may have heard the catch phrase “follow the money” in the film, All the President’s Men.  Following the money led to an understanding of just how everything works in a money-driven social environment.

The same thing may be said about palindromes in terms of biological evolution. A palindrome occurs in DNA or RNA and results in a form of molecular mirror image symmetry. When such DNA is melted and allowed to cool quickly, it snaps back on itself, forming characteristic hairpins of DNA or RNA.

Palindromes in DNA are generally associated with regions that are involved with DNA replication, gene expression, and cellular differentiation. In other words, they seem to be involved in starting points that make DNA “tick”.

In my last post, I discussed origins of replication as not only agents of replication and localized gene amplification, but also precursors to other elements such as promoters of transcription, enhancers of transcription, and splice sites for changing the very coding of the DNA itself. In all of these structures, palindromes seem to be lurking nearby in some form or another. I have designed some models to explain how origins of replication are formed, amplified, and converted into other structures like promoters, enhancers, and splice sites. However, be warned: This is not your typical linear DNA strand model so prevalent in textbooks and scientific literature. This model is based upon hierarchical DNA circular structures which are, themselves, composed of even smaller circles that may themselves be composed of still smaller circles and so on. You will need to dive into the blog further to get a better grasp of what this all means. However, I will place one set of models here again to get you on your way.

Fig 17Fig 18fig. 23fig. 24

Fig. 1 (top left) undifferentiated DNA replicon cluster

Fig. 2 (top right) differentiated DNA replicon cluster

Fig. 3 (bottom left) RNA transcriptional pathway along the DNA

Fig. 4 (bottom right) splicing out of introns from pre-messenger RNA to generate messenger RNA

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What if an origin of replication is the origin of everything biological?

Sometimes scientists focus on their little corner of the world so intently that they fail to see the forest for the trees. Alternatively, they may be afraid to see the forest because of the ramifications. In any case, however, any biologist worth his salt understands the central dogma: DNA makes RNA which makes protein.

Here’s another “central” dogma that I believe merits further investigation: Origins of replication make origins, promoters, enhancers, and splice sites

Duplication of origins

Origins make new origins through a process of DNA amplification that generates new replicons. This is what viruses do on a regular basis. I believe this occurs when circular viruses (a form of replicon) binds to another origin on host DNA and physically attaches to it in some manner that generates a double origin of replication (see blog for details). This double origin is the mating of two different replicons, one of which may be considered as the remainder of the entire genome. They would be interlocked together into a four-strand complex in a frozen state of recombination and covalently linked together by interstrand bridges, preventing complete fusion of the two replicons. This allows the viral DNA to spin off copies of itself which are then bound up into viral particles by proteins in a cascade of events well known in virology. These viral clones make seek out other areas of the genome in which to attach as well.

Developmental gene amplification and origin regulation.

Amplification enhancers and replication origins in the autosomal chorion gene cluster of Drosophila.

Conversion of an origin of replication into a promoter of transcription

During cellular differentiation, a portion of the interior of the four-strand complex may be clipped out leaving an interior gap with exposed ends available for transcription of RNA. The ability to function as a replicon ceases to occur, resulting in a functionally larger replicon via a nearby double origin on the remaining genome. This partial fusion of the replicons makes this site more susceptible to breakage and fusion during laboratory DNA isolation.

CpG islands as genomic footprints of promoters that are associated with replication origins

Genome-wide studies highlight indirect links between human replication origins and gene regulation

Transcriptional elements as components of eukaryotic origins of DNA replication

Conversion of an origin of replication into an enhancer of transcription

The bonds holding the two replicons are split, causing the smaller replicon to be released from the genome. The single origin remaining on the genome becomes an enhancer of transcription. Unless altered further in some way, it provides a means for a new replicon to join the genome.

Development of S/MAR minicircles for enhanced and persistent transgene expression in the mouse liver

Conversion of an origin of replication into a splice site

This may happen in one of two ways, directly or indirectly: The double origin is clipped even more than what occurs to generate a promoter, or a promoter is clipped further, generating a splice site. In either case, the partial fusion of two replicons remains intact.

Origins of recently gained introns in Caenorhabditis.

Splicing of a Myosin Phosphatase Targeting Subunit 1 Alternative Exon Is Regulated by Intronic Cis-elements and a Novel Bipartite Exonic Enhancer/Silencer Element

Whether this dogma has merit or not can only be determined through rigorous scientific investigations that leave absolutely no stones unturned.

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The miracle of gastrulation or how we grow from a mass of cells into a human being.

When humans and other animals are first conceived, they are nothing more than a fertilized egg, which is simply a single cell. This cell begins to divide very rapidly into clones of itself by a process called cleavage. This stage of embryonic development is called blastulation. This one large cell begins to divide so fast that the sizes of the clones become progressively smaller and smaller.

In the case of amphibians, this original cell is divided up into as many as 4,000 smaller cells with no significant change in the original volume of the fertilized egg. This eventually results in a hollow ball of cells which look very similar to more primitive colonies of organisms like the green algae, volvox. This is a classic example of ontogeny recapitulating phylogeny, i.e., the development of the individual is based upon how it’s ancestors evolved over eons of time. Then something very remarkable begins to happen, gastrulation: The cells begin to change into three basic kinds of cells, ectoderm, mesoderm, and endoderm which interact with each other to generate even more kinds of cells in an ever more complex, progressive cascade of events.

Something else happens as well: The origins of replication that were furiously cranking out DNA for these new cells begin to be “silenced”,  resulting in origins that replicate larger pieces of DNA.

Furthermore, as these origins begin to “die off”, gene expression begins to rise dramatically at the same time. So let’s take a moment to sort all of this out:

1) Origins are furiously replicating DNA during the blastula stage at the expense of cell   size. Gene expression is essentially nonexistent.

2)  During gastrulation, origins begin to functionally “disappear”, the remaining ones take over, replicating ever larger pieces of DNA.

3) Gene expression begins to increase rapidly.

Since a replicon is a piece of DNA with an origin associated with it, it appears these replicons are somehow fusing together, resulting in the silencing of one of the two origins.

How all of this happens is the crux of this blog. I will boil it down here in just a few statements:

Origins may be silenced either by fusing with another replicon in a manner similar to lambda phage site-specific recombination, or they may be deleted entirely from the genome as a circular replicon, leaving behind a “scar”.

In the first case, this “fusion” event is only partial, opening up a free end of DNA that can be used in transcription and, therefore, gene expression.

In the second case, the “scar” left behind on the genomic DNA can function as an enhancer of transcription.

In the case of splice sites, the partial fusion of the origin to the remaining replicon may be even more complete, thus converting a potential promoter into a splice site.

How all of this can be explained with a nontraditional, circular DNA model is illustrated throughout this blog.

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Evolution, cancer, cellular differentiation, and gene expression in a complex circular DNA model

If eukaryotic chromosomes are composed of complex circular structures instead of the simple linear structures assumed by mainstream science, how are replication, tissue differentiation, and gene expression regulated?

Since this is a blog and not a scientific treatise, let me try to put this into a nutshell:

Cellular differentiation may involve two distinctly different kinds of processes:

1) Binding up of much of the pristine genome into inactive heterochromatin. This process is reversible, allowing for this portion of the genome to be recruited at some later date (partial dedifferentiation).

2) Permanent alteration of most of the remaining origins of replication in a way that either converts them into promoters of transcription, RNA splice sites, or enhancers of transcription.

Permanent alterations of origins may actually involve double origins shared by two adjacent circular DNA elements. During the course of promoter formation, the internal sequences of this double origin may be deleted out, causing a partial fusion of the two circular elements into a large circular element. A similar process could also occur with splice sites, except that additional sequences are removed. Alternatively, these circular elements may completely separate, leaving each circle with a single, simple origin. One circle is deleted from the genome, the other circle remains attached and the single origin becomes an enhancer.

In other words, at one point in time, origins, promoters, splice sites, and, enhancers may have been one and the same. You can learn more about these hypotheses by delving into the blog and looking at the models page tab.

This model also allows for enhancers of transcription to be physically much closer to their promoters even though they may appear much farther away when these circulars are ripped apart by conventional DNA analysis procedures. The larger the circular element, the further away the enhancer appears from its promoter if the circle is split between the promoter and its nearby enhancer.

Fig 17

Undifferentiated replicon cluster

Fig 184

Differentiated replicon cluster

Evolution of the chromosome using this model

Now, we can take this model a step further and consider the evolution of chromosomes over geologic spans of time. In this scenario, there would exist ancient promoters, splice sites, and enhancers that “differentiated” eons ago from ancient origins of replication. These structures would remain “static” during the differentiation process relative to origin modifications. However, they could be excised together with their circular elements during the course of differentiation.


Some heterochromatic compartments may have been locked up eons ago. Failure to do so could result in atavistic characteristics showing up, i.e., partial gene expression of the ancient ancestor.


Cancer “evolves” in the body over time by an incremental increase in DNA rearrangements. Many of these alterations may be destroyed by apoptosis or even necrosis followed by phagocytosis. However, partial clusters of actively replicating DNA circular complexes could easily be incorporated either by the host cell or nearby neighbors. Such dramatic changes in the genome would either kill the cell or corrupt its replication and transcriptional  machinery.

Implications of the model on stem cell research

Stem cells would exist as compartments of differentiated and undifferentiated DNA. Generating new tissues from stem cells of a different tissue origin would require two things:

1) The original differentiated compartments becomes locked up as heterochromatin.

2) The undifferentiated compartments required to generate the new tissue type would have to be unlocked from heterochromatin and irreversibly differentiated into the new tissue type. These kinds of “hybrid” cells could theoretically revert back to the old state under the right conditions and that would require the new tissue type to be locked back up as heterochromatin.

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Circular DNA deletions appear widespread in mammals. So what?

Circular DNA deletions appear widespread in mammals. With further inspection, this may apply throughout the animal kingdom as well and beyond. So what gives? What is this all about? How important is this phenomenon in terms of evolution, cellular differentiation, and cancer? Doesn’t this really depend upon whether these circles are merely curiosities, trivial minor alterations in the genome, or whether they are examples of something much much more? Perhaps they are not the exceptions at all, but rather the reality of how chromosomes are actually put together.


Learn more about these circular structures by reading further into this blog.

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