Eva Dale  0:00  
From the heart of the Ohio State University on the Oval, this is Voices of Excellence from the College of Arts and Sciences with your host, David Staley. Voices focuses on the innovative work being done by faculty and staff in the College of Arts and Sciences at The Ohio State University. From departments as wide ranging as art, astronomy, chemistry and biochemistry, physics, emergent materials, mathematics and languages, among many others, the college always has something great happening. Join us to find out what's new now.

David Staley  0:31  
My guest today is Professor of Physics, Michael Poirier. He's a member of the Ohio State Biochemistry Graduate Program and the Biophysics Graduate Program and holds a courtesy appointment in the Department of Chemistry and Biochemistry. Welcome to Voices, Dr. Poirier.

Michael Poirier  0:47  
Thanks. It's great to be here.

David Staley  0:49  
So your specialty is biophysics, and I wonder if you could start by first of all telling us what biophysics is. Is it biology plus physics? Is it the biology of physics, what's biophysics?

Michael Poirier  0:59  
Well, it's a pretty big catch all phrase, right? So many, many people fall into that field. It's really about a combination of using physical approaches to study biological questions. And taking sort of tools, whether it's theory, experimental approaches, and those kinds of ideas to get at. And it could be from cell biology, biochemistry, molecular biology, even evolution, for example.

David Staley  1:28  
How does a physicist become interested in biological questions or biological issues? 

Michael Poirier  1:34  
Well, so in the world of physics, where, you know, we're developing new technologies, and using sort of more advanced newer tools, and sometimes those tools work, right to studying biological questions, what we do, and it's been sort of over the last maybe 20 years, or so where there's been this nice development of studying individual molecules, as opposed to ensemble molecules. So, you know, this is how we, you know, biochemistry people will have a tube of Avogadro's number that's, you know, 10 to the 23 molecules, right, so billions of billions of billions of molecules. And then you get an average value of some property, maybe it's binding or a structural change or some kind of interaction. But if you look at individual molecules doing that, you learn a lot more, there could be an unusual state that you wouldn't see, you can learn that there's many more states than you would see based on an average measurement. That's one of the things that we do. That's more physics-y type approaches where we manipulate and look at individual molecules.

David Staley  2:40  
Your lab in particular studies nucleosomes, and chromatin, I'm first of all going to have you define these two terms for us. 

Michael Poirier  2:47  
Sure. So both of these are involved in organizing how your DNA is inside of your cell. So, maybe in high school, one might have learned that in eukaryotic cells, so there's three life forms on Earth here, there is bacteria, there's archaeae, and there are eurkaryae.

David Staley  3:06  
And now I'm back to high school biology, I think.

Michael Poirier  3:10  
That's right. And so eukaryotes, which are like you and I, but that's also, you know, trees, and even, you know, budding yeast. So, you know, like, for example, what's great for making bread. And so they all organize their genome the same way, it's actually really beautiful, what happens is the DNA is wrapped into little coils, okay, so you know, at home in your backyard, you might have a hose, and you want to package up your hose in some convenient way where when you're ready to use it, you can pull it out, and you can put it back. And actually, we do that with our DNA, you know, the DNA inside of our cells, it depends on the organism and how much the length of your DNA is. But for humans, it's about a meter. And that's about 3 billion bases of individual units of DNA. And that has to be packaged into a very small unit cell nucleus, right? So it's sort of like taking a string that, you know, goes around a track, maybe four or five times, so maybe a mile and putting that into, I think, like a golf ball. And it's not just like you're putting it in there. And you just want to store it, right? It has all the information that makes all of your cells, so you need to make sure. So anyway, so the cell organizes the genome by wrapping into little spools, and that's a nucleosome. So in fact, about 150 base pairs, so that's about 150 individual units of the DNA is wrapped into one little spool. Okay, now, it happens over and over again, your genome is organized into about 10 million spools. 10 million, 10 million, so that's each and individual nucleosome. So that's nucleosomes. Then the chains of nucleosomes along a single chromosome, right, each chromosome has a continuous length of DNA. And so that is chromatin and in fact, There's a lot of additional components that sort of go on to the DNA, in addition to what is forming a nucleosome. Maybe the one other thing to add that's important is that the core of the nucleosome are made out of histone proteins, which we're particularly interested in. So there's actually eight proteins that the DNA wraps around to form a nucleosome. 

David Staley  5:22  
So tell us about the work of your lab, then, with nucleosomes and chromatin.

Michael Poirier  5:26  
Right. So these spools are important for basically any type of DNA processing. Okay, so just for example, now, we don't study this specifically, but just for example, when you replicate your genome, right, so you have to double the amount of DNA, it turns out the histone proteins that organize the DNA into nucleosomes, that's the same mass, you need to double the amount of histone proteins, not just the amount of DNA. So it's a key part of anything that happens on to the DNA. Okay, now, we're particularly interested in gene expression. Okay, so we want to understand how a specific gene is either being used or not being used within your cell. And the nucleosomes play a key role in that, because they can control whether a piece of another important molecule that needs to start the gene expression, whether that can bind to the beginning of a gene. So we're trying to understand how the nucleosome how the structural changes within the nucleosome, facilitate or block, basically allow or prevent a gene from being expressed? What sorts of conclusions have you reached? So there's a class of proteins called transcription factors? These are factors that bind to specific DNA sequences. Okay? Those are sort of the initial things that have to happen, right? So, you know, before all the other more complicated proteins come in, like this big motor that makes RNA, these transcription factors have to come in and bind. And what we've been trying to understand is how does the nucleosome really prevent or allow for a protein to bind into a piece of DNA? So the classic idea is that are just blocks. Okay, so, you know, your hose is wrapped or into your spool, and then, you know, you can't get to that portion of the hose. Okay. Now, what we found is, in fact, that's not the major way that nucleosomes prevent proteins from binding, they do that. But in addition, they have this massive effect of kicking proteins off, which is sort of not what you would think you think they're just a gatekeeper. They don't allow things in. So things are constantly getting into the spools. But then, because of the wrapping and the properties that it wants to rewrap it encourages things to come off. So it encourages these transcription factors to come off. 

David Staley  7:44  
What's the evolutionary necessity for that sort of behavior? Can I call it behavior?

Michael Poirier  7:50  
Yeah, that's a great question. We like to think about that. I mean, it's hard to say one of the main questions that we have is something that comes back to a chicken and the egg problem. Okay, so your genome, you don't want specific genes accessible, so things can't bind or can't get in there. But you do eventually need to get in there to say turn a gene on this happens during cell differentiation, for example. So you have stem cells that some have to become neurons, some have to become muscle cells, right. And the difference between those because all cells have the same amount of DNA, the difference is simply what genes are being used. So how was the cell going to know or figure out when to turn something on and to make it all of a sudden accessible if it can't get in there in the first place. So what we like to think is that the fact that things can still get in there just encouraged off, that means they sort of always have some access to their sights. And so they can get in there. And that allows for this regulation to work and that ultimately, a gene can be turned on, because a protein can get in there, and then maybe something changes that then allows it to stay longer. Something that we're doing now, and we're sort of very excited about is there's a class of transcription factors called pioneer factors. And these are factors that actually can circumvent nucleosomes. Completely, they don't seem to care that there's a nucleosome there most proteins that keratin, and right now we're trying to understand that. So I have a student who's just published a paper in this journal called eLife. And it's pretty exciting because he has some new insight into how that specific class of proteins work.

David Staley  9:25  
And these are described as pioneers. 

Michael Poirier  9:29  
Yeah, so they're like the first ones, like the pioneers, the first people to go out, well, I guess, at least Anglo Saxon European based people to go out west. Pioneer factors are the first proteins that come in to turn a gene on. And in fact, it's really amazing. They seem to be able to circumvent what nucleosomes are doing. We think we have some ideas on actually how they do that. 

David Staley  9:50  
Tell me more about your work with histone proteins in this context.

Michael Poirier  9:54  
I mean, so the histones form the core. These proteins are the same just like you know, DNA is basically identical in all life forms from bacteria all the way up to humans, actually, histone proteins are identical from yeast all the way up to humans. So it's highly, highly conserved. You know, again, they wrapped the DNA. So they play a main role in how DNA is a gatekeeper for what genes are turned on and what are not. But they have these antennas that stick out. So there are these portions of the molecule that kind of hang out there and can attract things. So I was talking about how a transcription factor binds to DNA sequence. But actually, many of the proteins that are recruited to a gene aren't directly interacting with the DNA. In fact, they're interacting with these histone antennas. And there's actually a code it's called a histone code that the different little units, they're called amino acids on the proteins, they can be chemically modified. You know, in DNA, you have four different bases, those are different chemical units. On the histone antennas, you have also these different chemical units. And so a gene that you want not turned on will have some combination, some type of code, where another gene that's turned off, will have a different type of code. And that is basically recruiting the right types of other molecules to either decide what's on and what's off. We're interested in how these chemical changes influenced the physical properties of the nucleosome and changing the unwrapping and changing the accessibility. So we found that at least certain ones, and certain combinations are particularly good at opening up a nucleosome and allowing for proteins to come in. One idea about these system modifications is they encode information epigenetically. What that means is basically they are encoding information that is not in the DNA, but an other levels of the organization of the genome that in fact need to be inherited.

Eva Dale  11:55  
Did you know that 23 programs in the Ohio State University College of Arts and Sciences are nationally ranked as top 25 programs with more than 10 of them in the top 10? That's why we say the College of Arts and Sciences is the intellectual and academic core of the Ohio State University. Learn more about the college at artsandsciences.osu.edu.

David Staley  12:21  
Does this work or does your work necessitate CRISPR or other kinds of gene editing technologies? 

Michael Poirier  12:28  
We haven't really worked in that area, we've thought about it. So CRISPR is an amazing tool. One thing that we've been particularly interested in other labs have already been working on this is, you know, CRISPR needs to gain access to DNA to edit a genome or to edit a base. And the nucleosome is a barrier and can influence how it functions and how it works. And of course, these are from organisms that don't know about nucleosomes, right? These are from bacteria, because it's part of the bacterial defense mechanism is how it was what CRISPR was really originally evolved to do, we do not use it. But there's a possibility later on, you know, that we might, there has been some amazing work with using what's called a dead version of CRISPR. What it does is they mutated the protein, so that it will still recognize a site in the genome. But it doesn't cut it. So regular CRISPR. What it does is it breaks the DNA. And actually, when the DNA is repaired, it's not repaired properly, and then inactivate the gene, that's the sort of standard approach for gene editing as you can target a specific gene and turn it off. Although people don't mention the fact that there's a lot of off target effects, that it's not perfect. And in fact, it's actually not at all perfect. And so there's a lot of problems with it in terms of being very precise. It's not that precise. But that said, what people have done is they've mutated what they call diecast nine, because it's a deactivated caste nine, so it will bind but it won't cut. And then you can use it to target anything you like to the genome. And what people have even done is targeted, they put onto the diecast nine, an enzyme that can modify a histone and they can target the genome. It then modifies that that specific gene. The histone doesn't do anything to the DNA, and then it turns the gene on.

David Staley  14:19  
So we're talking about tools here, sort of micro level tools, and I know that one of things you're working on is DNA nanotechnologies, and I'm curious to hear more about this sort of research. 

Michael Poirier  14:29  
Yeah, this is a more recent thing I've been doing or my my lab, I don't really do that much. It's mostly the people in my lab that doing all the work, but we have been working closely with Carlos Castro. He's a mechanical engineer, and he's an expert in making nanoscale devices using DNA origami. And so DNA origami is DNA origami, which is, well what it is, is it's an approach that you can design devices and it's devices made complete. The amount of DNA where you can isolate a fairly long piece of single strand DNA. And then you can engineer and basically, you know, you end up purchasing basically about, you know, hundreds of short pieces of DNA. And this is what Carlos is an expert at doing, he then makes these hundreds of single strand DNA is to then fold this backbone into a specific device. And so he can make hinges, we made a device together, that measures forces, we call it a nano Dine, but it can measure you know, Femto Newtons of forces Femto Newt fencing, yeah, 10 to the minus 15 Newton's, so sort of a very small fraction of what a force would be applied by an actual protein, say, inside of a cell, these devices, you know, it's basically like Legos. I mean, it's really, except the Lego self assemble, you know, like, you know, my kids at home there, it's a huge mess, like my son, he has Lego strewn all over the place. And these things, actually, they just self assemble into these very elaborate structures. And it's actually an atomic resolution. So you can really precisely place things. So we got really interested into this, because, you know, these devices could be great for studying nucleosomes, and chromatin. And so we've been working on putting nucleosomes and chromatin into devices, and then using those devices to these DNA origami devices to measure things like, you know, what it takes to open up a nucleosome. Or if we hold a nucleosome, open can then a protein bind better. And so it's been a really cool collaboration. 

David Staley  16:37  
So this all sounds like a class of devices, DNA origami, CRISPR, and it sounds like it's having really significant effects on biophysics. 

Michael Poirier  16:46  
Sure. I think, well, CRISPR, is having a massive effect, maybe less so on biophysics and just you know, in the life sciences, I mean, you see this in the news all the time, everyone knows about them. I mean, DNA nanotechnology maybe isn't as widely known. But you know, there's even the merging of these things. So for example, we recently got funded from an NSF program, to try to make devices that we can put inside of cells and then target the genome. And one of the tools were planning to use is to leverage the CRISPR, the D cast nine and put it onto an origami device, which could then go to a cell and, you know, do something mechanical or something like that.

David Staley  17:30  
And what sorts of implications do you see from all this sort of work? What is it that we're going to be able to do? 

Michael Poirier  17:36  
Yeah, okay. So, you know...

David Staley  17:38  
 We're gonna know an awful lot,  what are we gonna be able to do?

Michael Poirier  17:41  
My work... I mean, honestly, I don't have the best answer to that, because we were doing such basic science. I mean, the NIH does fund most of the work that we're doing. And the idea is that understanding the real mechanisms of how molecules work inside of a cell will ultimately allow for drug development, and very targeted precise therapy, because these are all of the proteins that are making us who we are and what we do follow physical and chemical rules, but you need to understand them. If you don't understand them. There's just no way you're just in the dark.

David Staley  18:18  
There are no applications. 

Michael Poirier  18:19  
So, well...

David Staley  18:21  
 We don't know.

Michael Poirier  18:22  
Yeah, I mean, exactly. The types of devices that we're working on. And I think in this field, there's applications in terms of using them as tools to do more basic science. Beyond that, I would be hesitant to predict, I should say that for the engineers. 

David Staley  18:38  
Tell us about the classes that you teach undergraduate and graduate classes. 

Michael Poirier  18:42  
Yeah, I teach, you know, one of the entry level engineering physics classes. So that's physics 1250. You know, it's I think it's technically 226 students, oh, good nurse section, because that's the number of seats in the room. And it's great, you know, you know, we cover a range of mechanics and a little bit of thermodynamics. You I work with freshmen and sophomores, mostly. And it's really fun. They're very motivated, a lot of them come by my office, but it's it's sort of a big, massive effort to manage that class, and you're working as a team, because there's many sections and they need to be coordinated. It's really a lot of fun to interact with that many students. Now, in addition to that, like another class that I teach is a graduate level biophysics course, where then we really get into the sort of the advanced topics of what are sort of not only current technologies, but the current, you know, approaches ideas on what's happening in biophysics. I focus a lot on applications of statistical mechanics and thermodynamics that we use to understand biology. So it you know, it cycles back to biophysics, so using biophysical ideas and tools to understand biology. And then actually right now what I'm teaching I did this this morning, as I'm teaching the The Advanced undergrad class and stat mech and thermodynamics. And that's a neat in between the, you know, the senior level physics students are super curious. They ask awesome questions that you usually don't know the answer to in the class, and you have to like, think about it, and maybe you'll come up with it, or maybe you have to come back the next day. It's, again, close to the physical tools that we use. And the ideas from physics for biology are often coming from statistical mechanics and thermodynamics. So, you know, it mixes well with my interests. So the whole range, and all of them are a lot of fun. It's a lot of work. But it's great.

David Staley  20:37  
Tell us what's next for your research.

Michael Poirier  20:40  
One of the things we're really excited about in the near term are pioneer factors. I think I mentioned this earlier in our discussions, these are the proteins that literally first target a genome to turn a gene on, they're not understood how they work. So there's a few ideas about how they function. And we recently did some single molecule experiments. And we I should say, you know, Ben Donovan, in my lab, he's about done, he's probably going to finish up his PhD this semester, he discovered that actually, these pioneer factors, at least a certain class of them, so there's probably different strategies that they will use to get into a nucleosome is that even though they can bind to a nucleosome, as well to just naked DNA, so they don't seem to care about them, they do this, they actually are inhibited by the nucleosome. So they have a harder time getting on. But they're pretty smart, they actually have figured out how to stay around a long time. So in the end, even though they take longer to get on, they take a lot longer to get often from DNA. And so they end up actually still having the same efficiency of targeting a site. So that's really neat and exciting. So we're trying to understand actually how they do that. So you know, probably over the next, you know, five years or so we'll probably work on designing experiments, looking at different similar proteins, but not the same one, and do comparative studies to try to understand that. And then after that, it's you know, it's hard to say, what I like to tell my students, and this comes from my postdoc advisor is that, you know, when you're doing good science, it always raises more questions than you answer. You know, one of the exciting things about doing science and answering new questions and approaching things that people don't understand yet, is that when you discover something, you're gonna have a whole bunch of new stuff to work on, because now you found something new. But you don't understand how that works, which is an example with this pioneer factor. So you know, who knows what will happen next. But I imagine it'll be more questions than we can even answer.

David Staley  22:43  
And it sounds like a lot of your work is highly collaborative. 

Michael Poirier  22:48  
Oh yeah. I find probably one of the most fun things about science, at least, the way that we do it, is that you get to work with so many different people from different areas. I mean, we talked about working with Carlos Castro, but I have a whole range of different collaborators and colleagues. You know, in the physics department, I collaborate closely with Ralph boonchu. He's a theorist. And we even have joint group meetings together, which is a delight. Because you, you know, the theory perspective and experimental perspective is very different. And it's great for the students. I have a number of collaborations with people in the chemistry department. And it's great, you learn new things, you get different perspectives. The science is a collaborative effort, you don't do things in a vacuum, you read papers, that based on those papers, you figure out new things that you might want to work on. You know, Ben and I were just talking about a paper from the 90s, that actually provides us a whole bunch of insight into some of the experiments that we're now designing on Pioneer factor. So I mean, working with people is key. And it's probably one of the best parts of doing research. 

David Staley  23:52  
Is this where science is going, you think? More and more kind of collaboration? 

Michael Poirier  23:55  
Oh yeah, for sure. You know, more and more of the grant opportunities are team grants. In fact, Carlos and I, and he was pi on both of them. We just got two new NSF team grants from different programs that they're, you know, collaborations with three or five people. And I think this is key. I mean, there are other areas in science, which had been doing this for a long time. So like high energy, physics, astrophysics, large teams to attack, you know, really challenging problems. And I think this is happening more and more in the life sciences is that larger team efforts are needed to attack, you know, important problems. And so if you're open to working as a team and not get all of the credit, but just share all the credit. I think it's a great way to go.

David Staley  24:42  
Michael Poirier. Thank you.

Michael Poirier  24:43  
Well, thank you. It's been a delight.

Eva Dale  24:45  
Voices from the Arts and Sciences is produced and recorded at The Ohio State University College of Arts and Sciences Technology Services studio. Sound engineering by Scott Sprague. Produced by Doug dangler Hi,

Transcribed by https://otter.ai