Anjali Zimmer

This is the fourth and final part in a series of explainers on molecular biology topics pertinent to my recently published  PhD thesis work. See part 1 about DNA damage part 2 about damage repair, and part 3 about transcription. Unlike those posts, this last part is a little heavy on the science jargon and is intended for a scientific audience, so if this isn’t your area I suggest you check out parts 1-3!

In part 3 I left off with how RNA can invade DNA, forming a potentially dangerous RNA-DNA hybrid structure. When RNA invades duplex DNA, the resulting three-stranded structure is referred to as an R-loop. These R-loop structures have been found in the cells of many organisms, from bacteria, to yeast, to plants and humans. Cells which accumulate high levels of R-loops have high levels of DNA damage and chromosome instability. However, cells have mechanisms in place to remove and process R-loops to prevent their accumulation. All cells, from bacteria to humans, posses two enzymes that can degrade the RNA in an R-loop called RNase H1 and RNase H2. It is puzzling that cells have two enzymes that perform overlapping functions, but their evolutionary conservation indicates that they both perform indispensable jobs. Both RNase H1 and RNase H2 are each required for viability in mice and human cells, and small mutations in RNase H2 cause a neuroinflammatory autoimmune disease called Aicardi-Goutieres Syndrome in human patients.

Fortunately, RNase H1 and RNase H2 are not required for life in the simpler, single-celled organism of budding yeast, and this allowed me to study their function. I knocked out either RNase H1, H2, or both from the yeast genome and observed the effect on chromosome instability. I confirmed previous reports that cells lacking both RNase H1 and H2 had elevated levels of chromosome instability. However, I also found that the lack of only RNase H2 lead to high levels of chromosome instability, while the lack of only RNase H1 did not have elevated instability.

To add another layer of complexity, RNase H2 not only removes long molecules of RNA that form R-loops, but it also can remove single ribonucleotides that are mistakenly incorporated into the DNA strand during DNA replication. There was some controversy in the field as to which function of RNase H2 is the crucial one to prevent chromosome instability.  I determined that it was specifically the R-loop removal activity of RNase H2, not the single ribonucleotide removal activity, that was important for preventing chromosome instability. Lastly I found evidence that RNase H2 acts on hybrids genome-wide to prevent chromosome instability. In contrast, RNase H1 acts at a subset of hybrids to repress locus-restricted chromosome instability.

As R-loops have emerged as a source of DNA damage and chromosome instability, we would like to understand the systems which remove them from the genome. This study presented evidence that RNase H1 and H2 play similar yet separated roles in protecting the genome. This provided insight into why these enzymes, which have overlapping R-loop-removal activities, have been conserved throughout evolution.

This is the third in a series of explainers on molecular biology topics pertinent to my recently published  PhD thesis work. See part 1 about DNA damage and part 2 about damage repair.

As we saw in parts 1 and 2, cells work really hard to protect their DNA. But what is it all for? How is that precious information used to build cells and make entire humans? You may have heard that genes make us who we are. Well, genes are segments of DNA which instruct the assembly of proteins. Proteins are the real workhorses of the cell, they do everything including the cellular processes I talked about in parts 1 and 2. Proteins duplicate the DNA before cell division, they package up the DNA into chromosomes, and repair DNA. Parts of your body outside of the cell like your hair and the surface of your skin are also made of proteins. Proteins are everywhere doing everything!

DNA holds the information to make proteins, but it is too precious to get directly involved in the nitty gritty business of making them. It stays all safe and snug in its own section of the cell called the nucleus, and the genetic information is copied down into a molecule called RNA, which leaves the nucleus and directs the building of proteins. RNA is a molecule very similar to DNA, but it is much more disposable. Once it has done its job to make a protein, it is broken down and its parts are recycled. This process of copying DNA into RNA is called transcription.

Since transcription is so fundamental to and necessary for life, and it seems to be a process put in place to protect DNA, researchers were surprised to find that transcription itself can actually be a source of DNA damage. Over the past decade we have found that RNA can actually invade DNA forming an unstable structure. This RNA-DNA structure can lead to DNA damage, with all the potentially disastrous consequences.

Transcription is constantly happening as cells are always making new RNA and proteins. But this RNA is potentially damaging to the DNA, so what’s a cell to do? Luckily there are back-up systems in place. I studied two proteins called RNase H1 and RNase H2 which can remove the RNA from DNA and resolve the problem. We still aren’t exactly sure how RNA in the DNA causes damage, but cells that lack functional RNase H1 or RNase H2 have a lot of DNA damage, and humans cannot survive without these enzymes. For my work I studied how these two proteins act in similar and different ways to reduce DNA damage. In part 4 of this series I will go into more details about the study.

This is the second in a series of explainers on molecular biology topics pertinent to my recently published  PhD thesis work. See part 1 about DNA damage.

A quick recap of part 1: DNA can be damaged, genetic information can be lost or mutated, and this can lead to cell death or diseases including cancer. So is DNA damage always disastrous? No! Cells have ways to check-up on their DNA, find problems and fix them.

There are many cellular machines patrolling the DNA looking for things that seem amiss. You may have heard that DNA has a double helix structure. This means that it is made up of two strands (double) wrapping around each other (helix). The sequence of these two strands are perfectly matched to each other like puzzle pieces, so if something happens to one strand this matching may be disrupted. The so-called mismatch repair machinery in the cell can recognize this problem, use the partner strand to figure out what went wrong, and fix it. This is just one of several ways that cells keep tabs on their DNA and perform repairs.

As a human, you have two sets of DNA, one from your mom and one from your dad. Having these two copies can also come in handy for repairing DNA. If severe damage happens to one copy, say the copy that came from your mom, then it can use the other copy from your dad as a template for repair. This repair process involves the actions of two proteins that are pretty famous: BRCA1 and BRCA2. These little celebrities have big celebrities like Angelina Jolie talking about genetics and cancer. Mutations in BRCA1 and BRCA2 are associated with high incidences of breast and related cancers, so people who have a family history can get a genetic test to determine the status of their BRCA genes. If they have the mutation, the can elect to have preventative surgeries to remove the at-risk tissues, as Jolie did. But what exactly are BRCA1 and 2? They are both proteins that help repair DNA damage! They are involved with the process of searching for the additional copy of DNA so that the damaged DNA molecule can be repaired. With all that DNA in each cell, it is not an easy task to find just the right DNA to use as a template for repair. If you have a mutation in one of the BRCA genes, this type of DNA repair may not work. This is bad news because more mutations can start building up in the damaged DNA, which can ultimately result in cancer. Never underestimate the worth of the maintenance crew!

Avoiding DNA damage is so critical that cells go beyond just fixing the DNA once it’s broken…they also try to make sure that it never breaks in the first place. Cells can accidentally damage their own DNA. One way this can happen is during cell division. In order for a cell to divide, it has to duplicate all the DNA in its genome. For a human cell that means copying over 3 billion bases, or the individual units that encode the genetic information. With all that information, there is a lot of room for error. But the cell is prepared, and the copying machinery has proofreading capabilities to check its work.  After the DNA is duplicated, it is packaged into compact structures called chromosomes, which allows the DNA to be carefully organized and sorted into the two new cells. This packaging and sorting process is also rife with chances for error. However the cell has many checkpoints in place throughout the process to check that everything is correct, and to abort the cell division if things aren’t right. All these checks mean that DNA damage is rare and things almost always go right. However, cancer cells find ways to sneak around these checkpoints and divide uncontrollably with damaged DNA.

For my own research, I studied another cellular process that has the potential to damage DNA called transcription. This will be the subject of part 3 of this series.

I am proud to say that my paper describing some of my thesis research was published this week in the Early Edition of PNAS!

Getting my PhD in molecular biology didn’t happen overnight (more like a decade of college + grad school), so chances are if you aren’t a biologist yourself the paper might sound like gibberish written in a foreign language. So in an attempt to not bore you to death, I’m going to post a series of explainers on molecular biology ending with a summary of what I found. (Caution, that last post may contain traces of gibberish!)

I studied how DNA gets damaged, so let’s start with DNA. All of your genetic information, basically an instruction manual for how do build everything from the smallest parts of your cells to your entire body, is encoded into DNA molecules. That’s a lot of information, and if the DNA in just one of your cells was stretched out straight, it would be over 6 feet long! To pack all of that information into each microscopic cell in your body, the DNA molecules are tightly wound up and organized into structures called chromosomes. In order for organisms to grow and live, cells divide and their chromosomes are duplicated and segregated into the two new cells. In this way genetic information is passed down to the next generation, and the two new cells should be identical to the original cell.

However, this is not a perfect world. There are lots of ways that DNA can get damaged. Damage can be caused by things from outside the cell, like UV light which affects the structure of the DNA molecule. I’ll get into this in more detail, but DNA damage can ultimately lead to cancer, which is why a lot of sun exposure with all those UV rays can lead to skin cancer. In addition to UV, there are lots of chemicals, known as carcinogens, that can damage your DNA. But not all damage comes from outside the cell. Cells can accidentally damage their own DNA by doing things like making mistakes when duplicating their DNA or not segregating their chromosomes correctly during cell division.

If DNA damage does occur there are many negative outcomes. As I said, DNA encodes an instruction manual for your cells. If information is lost or mutated, the cell might not have everything it needs to live and it will die. That’s not such a big deal if the cell in question is one random skin cell on a human’s body, but if the cell is a single-celled organism like a bacterium or yeast, then that’s the end for that individual. In a less severe case, DNA mutations can lead to genetic diseases that don’t kill the cell or organism but change something about it. For example sickle cell anemia is a genetic disease in which a mutation in a single gene can cause a person’s red blood cells to be misshapen.

Another quite undesirable outcome of DNA damage is cancer. Each cell in your body is under careful control so that it adopts a certain identity and performs a specific function. However, if the cell’s DNA is damaged, these internal instructions may get jumbled. A cell that was once a skin cell doing its job to produce pigment may loose this control and instead start dividing and dividing and dividing, forming a tumor. These cells may no longer have the identity of skin cells, and they can invade other tissues of the body in a process called metastasis. This loss of cell control and cell identity is the cellular basis of cancer.

Given the potentially serious outcomes of DNA damage, molecular biologists are extremely interested in understanding it and have been studying it for decades. Luckily cells have a lot of systems in place to detect damaged DNA and repair it. Stay tuned for my next post to hear more about that!

It’s Nobel Prize season!

Beyond being a great way to recognize scientists and their achievements, the Nobel Prizes are an opportunity for everyone to learn about important discoveries and the scientific process. As a molecular biologist, I am always excited to see scientists in my field recognized for the prize in the category of Physiology and Medicine (there is no specific “Biology” category). This year’s prize is even more exciting to me personally because Yoshinori Ohsumi is being recognized for his work on autophagy, which he did by studying my favorite model organism, yeast!

Ohsumi studied how cells can break themselves down and recycle their component parts. This process is called autophagy, which literally means “self eating”. Cells can digest their various compartments and machinery before ultimately killing themselves entirely. While this may sound a little brutal, this process is very important for removing old, diseased, or damaged cells that might cause harm. This is especially important in multicellular organisms such as ourselves, but studying human cells can be very difficult. That was even more true in the late 80’s and 90’s when Ohsumi was doing these studies.

Enter in budding yeast! Yep, the same yeast that do all the hard work in brewing and baking are also on the job in biology labs around the world. Yeast are small, single-celled organisms that are easy to grow in the lab. And basic biological processes which govern how cells function are extremely similar in all organisms, so things we learn by studying yeast tell us a lot about how our own cells function.

One of the key studies that Ohsumi and his group are being recognized for is a genetic screen that identified some of the key players in the process of autophagy. To do this they treated yeast cells with a chemical that induces DNA mutations and looked for cells that had defects in the process of autophagy. A great thing about yeast is that they can be easily crossed, which is important for identifying the mutated genes. We can’t go around mating humans, and animals take months to mate, while yeast can mate and form offspring in just a few days. In doing so, Ohsumi’s group and others discovered systems in the cell that target proteins and membranes and signal the autophagy process.

While research around autophagy and the diseases that can occur in humans when it goes awry is still ongoing, the foundational insights into this process lend some thanks to the little and mighty yeast!

Hi, I’m Anjali!

To find out a little more about me and my background, check out my About page.

This blog will be a collection of my discussions of biology in the news or advances in the field of genetics. I’ll be writing for a general audience, with the goal of communicating science to the public.