Somatic Recombination Part 4: Cutting up your DNA

by on Mar.06, 2011, under Immunology

So you’ve been told that all the cells in your body contain the same genetic material? I’ve seen it written as a general principle of Genetics and a quick search around the web will yield many sources indicating that all somatic cells contain the exact same DNA. I did find a few articles in science magazines which “revealed” that this may not be the case, but the general consensus that they do was prevalent.

From all I’ve read, research and texts included, the DNA contained in all somatic cells is the same with one exception; the hematopoietic cells. These cells are the cells of the blood and they all descend from a single progenitor, the Human Hematopoietic Stem cells which can be found in bone marrow. These stem cells give rise to a diverse population of progeny including erythrocytes (red blood cells), T Cells, B Cells, Macrophages, and Natural Killer cells. To be accurate, the stem cells and their immediate descendants contain “germ-line” DNA, which is DNA that was formed during the individual’s fertilization event and is shared with virtually every other somatic cell in the body. However, as the hematopoietic descendants start to specify into the progenitors of T and B cells or “lymphopoietic” progenitors, the process of Somatic Recombination which creates the antigen receptors I’ve been writing about cuts out and discards parts of certain chromosomes thus creating genetically distinct human cells within our own bodies.

In my last post I presented the gene loci on which this process acts and highlighted the first actors in the process; the Recombination Activating Gene 1 & 2 proteins (RAG1 & RAG2). The arrangement of the gene loci is very important in this discussion and the rest of what I’m about to present doesn’t make much sense without this knowledge, so you can click this link to read that post if necessary. The process is performed by the V(D)J Recombinase and the process progresses as the molecules that make it up are assembled, I will introduce them as I describe the process.

It begins with two molecules each containing one RAG1 and one RAG2. These complexes then randomly bind, one each, to two of the hundreds of Recombination Signaling Sequences (RSSs) found surrounding each gene segment in the target antigen locus. It should be noted that the selection is not random across the segment. For example, two V regions will not join; it must be a V and J, for example, in a light chain locus. After binding, the two complexes come together and bind resulting in the formation of a loop of DNA between them which contains all the gene segments that may have been between the two segments brought together.

With the loop formed, the RAG complex will cut the strand exactly at the points where the RSS ends and the coding segment begins (see diagram below). This happens because the RAG complex has an inherent ability to act as an endonuclease. This essentially means that it is a protein that can break a DNA molecule into parts. This is the action that excises a piece of our DNA which is called the signal joint (because the RSS of each segment are joined flush). At this point, because of reasons relating to the chemical properties of the structure of a molecule of DNA, the ends of each strand which are cut fuse to form hairpins.

At this point other proteins join the complex to complete the recombinase and the process. These proteins are actually ubiquitous in human cells and I believe they are present for every mitotic and meiotic event that occurs over an individual’s lifetime. The first two proteins to bind to the growing V(D)J Recombinase are named Ku70:80 and they hold together both the ends of the chromosomal DNA strand, and those of the signal joint. Note, that this is the last I will mention the signal joint as once it’s ends are fused, it is no longer part of our story.

It is here where the process becomes a little unnerving for me. The very precise cut made by the RAG1/RAG2 complex to setup the joining of gene segments is one thing, but what happens next, to me, is another. The following video presents an excellent visualization of the entire process with a voice-over by Dr. Julie Theriot; a brilliant mind. I will, however, go into a little more detail below.

A protein named DNA-PK, or DNA-dependent Protein Kinase, is formed when another protein named DNA-PKcs binds tightly with Ku after the strands are bound. And to this another protein named Artemis joins. Artemis is also an endonuclease without which we would be ending our story with a broken strand of DNA. Artemis cuts the hair pins formed after RAG1/RAG2 excised the signal joint, but the location of its cut appears to be random. It has been found that they occur anywhere along the hair pin and this is where the fun starts.

With the location being random, unequal ends are often left which must be equalized before the DNA can be rejoined. Enter another protein that is found in all our cells and has a great name; Terminal Deoxynucleotidyl Transferase (TdT). TdT randomly adds bases to the cut ends resulting in what is essentially a newly formed random sequence on each. At the same time, two more newcomers bind to each other and then the Recombinase; DNA Ligase IV and XCR44. There are ubiquitous DNA repair proteins which and as soon as they bind, they start trying to re-join the strands; the name Ligase actually comes from the Latin “ligare” meaning “to bind or tie”. With TdT inserting random bases, the repair/ligation complex may need to knock out and replace non-complementary pairings such as a Guanine to a Thiamine.

With the ligation effort winning out in the end and the chromatid now back in one piece, the process of Somatic Recombination is complete. With just a few more steps we have a complete gene which, when transcribed will form one of the two chains in an Immunoglobulin. The process, however, has left the chromatid irrevocably changed; it is unique, different from any other member of its chromosome pair in the body, including other B cells. I’d like to note again that this change is key to the efficacy of our adaptive immune response. Without the enormous diversity generated by this process, neither the B and T cell antigen receptors nor the antibodies secreted by the former would be capable of binding effectively to the diverse and ever changing peptides making up evolving pathogens. However, it also introduces a potential for a number of pathologies, including cancer.

It has been shown in research1 that if the DNA repair mechanisms like DNA Ligase IV\XCR44 and the DNA damage checkpoints are not functioning properly, Somatic Recombination can result in several pathologies. These include aneuploidy, an abnormal number of chromosomes, translocations, where one part of a chromosome is fused with another, and neoplastic transformation, cancer.

In fact, according to both Janeway’s Immuno Biology (p 312) and a paper published in Nature Immunology in 20071, translocations are found in most lymphoma tissues. What is compelling for me about these translocations is that they most often involve what are known as proto-oncogenes which are genes encoding proteins that, when not functioning properly, cause cancer.

What causes DNA checkpoints and the DNA repair proteins to malfunction? I’ve seen the research showing the obvious conclusion; mutations forming in the genes coding for the proteins which carry out the functions. However, I suspect epigenetics may play a role in at least some of the scenarios. What causes these translocations? Given the fact that many lymphomas are age onset, I would conclude that probability must be considered, but the translocations of proto-oncogenes suggest to me that epigenetic factors should be examined. There are genes such as Myc (Myelocytomatosis)that regulate the expression of up to 15% of our entire genome and do so through epigenetic factors such as HAT (Histone Acetyltransferase). It should not be surprising that Myc is an oncogene and it is, in fact, one that is involved in the translocations found in lymphoma tissues.

1. Nature Immunology 8, 801 – 808 (2007)
Published online: 19 July 2007 | doi:10.1038/

:, , , , , , , ,

Leave a Reply

You must be logged in to post a comment.

Looking for something?

Use the form below to search the site:

Still not finding what you're looking for? Drop a comment on a post or contact us so we can take care of it!


A few highly recommended websites...