Remodeling talking about is really just changes in chromatin structure we talk earlier in the semester we talked about how May is wrapped up really tightly as heterochromatin sounds more loosely active euchromatin Anna loosely packed stuff is generally believed to be transcriptionally active and this does appear to be the case from last week all the euchromatin loosely packed open chromatin confirmation this is not the same thing is open promoters right open promoters that are specifically referring to the promoters themselves this is overall the chromatin around and around a particular gene chromatin on the other hand is tightly packed and is associated with with the repression or the inactivity in active transcription of a particular region of the genome but this is also known as the closed chromatin confirmation in regulated regions of the genome for regulated teams that the packing can go back and forth between heterochromatin and euchromatin so when we say when we're talking about remodeling what we're really talking about is shifting between heterochromatic DNA and euchromatic DNA so from transcription only inactive actually active so these changes in chromatin structure that we're talking about here are primarily bought brought on by biochemical modifications to the history are not Alteration of the histone tails so remember the histones this with this is here these old curlicues are histone tails so remember the histones are linear proteins and they have these most of them you know within the nucleosome that has the histone proteins are all folded up on it on themselves but they have these linear tails that are negatively charged help hold the nucleus sound together but we can change those positively charged I just said that backwards DNA is negatively charged positively charged so we can change the relationship between the histones and the DNA that their soci ated with chemically altering miss stone tails this these chemical alterations include things like metalation groups Salvation adding acetyl groups and and other like things like phosphorylation which I don't think I have on this slide so adding these chemical groups to histone tail tails change the Association between the DNA and histone these chemical modifications often result in remodeling so moving the nucleosomes around so that we go from either heterochromatin euchromatin or euchromatin to heterochromatin this remodeling if we're talking about turning genes on and then becoming transcriptionally active remodeling ultimately results in the altered Accessibility properties like transcription factors and RNA polymerase to the DNA to the elements of the promoter other regulatory elements that are necessary to have proteins bound to in order for transcription to occur these chemical modifications signal in some way chromatin remodeling that can result in either the chromatin becoming more loosely packed or more tightly packed depending on the specific chemical modifications and we'll talk about those some more and these modifications ultimately result in a change in the chromatin structure can allow things like transcription factors to find through their binding elements because they're more accessible when the DNA is less packed OK so we're gonna keep talking about transcription factors most transcription factors needed to access the there's important DNA elements for transcription to be activated and but their proteins their DNA providing proteins as well and so they have to access their binding sequences in the in the DNA and The FDA is tightly packed around nucleosomes that those transcription factors that may signal a loosening of the chromosomes elucidating of the chromatin to upregulate transcription those don't really have anymore access to the DNA then then so in order for the transcription factors to get in there something has to initiate the loosening the chromatin and there's an idea that there might be these special transcription factors called pioneer factors that may be because of their shape are capable of sort of getting themselves into the nucleosome even when it's tightly packed and binding to the DNA by its DNA binding sites and causing a remodeling of the chromatin to to euchromatin to allow for transcription so this pioneer factor would be an activator because because it's overall action is to initiate transcription or aid in the initiation of transcription remember there's for almost all eukaryotic genes there are many transcription factors that are necessary and they may be causing different things so some transcription factors may be pioneer factors that result in a changing chromatin structure to allow other transcription factors to buy into their DNA binding elements so that they can interact with the promoter and transfer and initiate transcription that way so there's a lot of different ways that these transcription factors can can be involved in regulating transcription one potential one is as a pioneer factor this is again this special maybe extra small or specially shaped protein that can wedge itself into a tightly packed nucleosome into tightly packed chromatin interact with its DNA binding site and cause some downstream effects that is DNA unpacking or euchromatin creation these are just extra figures of the same thing talking Rainier factors than that there just allowed for they are capable of accessing heterochromatic binding sites and heterochromatic DNA so that they can signal or maybe cause you chromatin formation and then other proteins would be involved in this and we'll come back and talk about the proteins that are involved in this in just a few minutes so what is hopefully becoming kind of clear is that nucleosomes are dynamic they're not static that is they don't stay in one place all the time the nucleosomes are moving around because in order to loosen or tighten the chromatin you have to move those nucleus sounds around so there's nucleosomes their positions in a chromosome when in a piece of DNA can change they can move around remodeling is the process of really moving those chromosomes Crump nucleosomes around changing their position and there are a few different mechanisms that cells can use in order to to remodel the chromosomes one of those is by changing that the histone structure of the nucleosomes and this is this H2 AC is come up for last time 8 two AZ is a special AlterNet histone H2 a histone so it's different from our normal age to a it's chemically different so some remodelers which are proteins that actually move and it already actually move turns around for cause systems to be moved around some remodelers that the histone composition of the nucleosome to include this age to Etsy and what is thought to be the case here is that H2 AZ is aleister affinity for the DNA so it doesn't bind to DNA as tightly and it's so it's easy to move an H2 AZ histone through the DNA and so one and H2 azs were were one of the elements that we find an open promoters so those promoters that are consecutively active tend to be associated with change traceys but other choices are also associated with regulated genes when they are in the on position and it's believed it because it's crazy nucleosomes are easier to move around and the remodelers the proteins that change out the histones are possibly recruited by regulatory factors by chemical signaling petition of steel groups or methyl groups or phosphates on the of his stops so there's a whole lot going on here so we might have some regulatory protein changed the To allow for remodeling of chromatin isn't an alteration of the nucleosome structure by replacing H two ways with HTC is done a second way that the modifications can occur is also through these addition of these different groups these different chemical groups to the histone tails so it's fairly well substantiated although not completely understood that the addition of acetyl groups to histone tails and these are just normal histone tails actually reduces the tight relationship between histones in the DNA so remember histones are positively charged and DNA is negatively charged and these negatively positively charged tails kind of attracted to and stick to the negatively charged DNA an when acetyl groups are added the acetyl groups actually reduced the positive charge of the histone tails because they are negatively charged groups and this loses the Association between the histones and the negatively charged DNA so chemically modifying the histone tails can more directly influence the relationship the binding relationship between positively charged histones and negatively charged DNA which allow the histones to be moved off of the promoter more easily allows for euchromatin formation and so suddenly is generally associated with chromatin formation will be coming back to match the little while I third kind up so we can you know we can change the the type of nucleus down we can chemically alter the histone tails ultimately we want our our remodelers to change the positions of our nucleosomes to move them ouf up importantly in elements so positioning so we can change the composition of the histone we can modify the his socks and we can move those histones around and all of these things all of these mechanisms for modeling occur simultaneously and are tightly linked to each other the end goal of remodeling is to move the nucleosomes loosen the nucleosomes up loosen the chromatin app so that these DNA elements where regulatory factors things that other transcription factors can bind to they're important DNA elements and help regulate the transcription of those genes in that area anybody have any questions OK so technique used to identify open versus closed chromatin that is loosely packed versus tightly packed chromatin euchromatin 1st is heterochromatin The DNA sensitivity assay dnas is an enzyme that cuts up DNA cannot access tightly packed DNA any better than any of the other proteins that might be involved in transcription can't can't because it's a big old enzyme so it can't cut up DNA that is very heterochromatic and so we can identify regions that are euchromatic by doing this DNA sensitivity assay where we basically we basically take regions of DNA we take parts of the genome and apply the NAC this enzyme to it an if the dnas can cut so if it can cut that DNA that suggests that that is incorrect because the DNA is loose enough that the DNA's can get in there and cut and cut the DNA app and so when regions are sensitive to DNA that is they get cut out by DNA then those regions are probably being actively transcribed because those are euchromatic regions of DNA in nucleosomes have been moved off of that region of DNA so that RNA polymerase and all the necessary transcription factors can get in there and transcribe that DNA so we use these DNA sensitivity assays to determine whether or not transcription is occurring in a region of the genome and this is a figure of an agros gel basically showing a sensitive region of rather insensitive DNA here to sensitive DNA so here the DNA is largely uncut by dnas is very big and as that DNA becomes more euchromatic and more or less tightly packed it becomes more and more sensitive to the DNA and so smaller and smaller pieces of DNA are present in the gel because DNA is cut back at the dnas has cut that DNA up into little bitty pieces and it can only do that if that DNA is more and more euchromatic that makes sense everybody so the regions of the genome become DNA sensitive or hypersensitive after nucleosomes have been displaced opening up regions of egeno an is that hyper hyper sensitivity persists that is you know we have we have that monitor that you keep testing the cells to see if their DNA the DNA is DNA sensitive in this region if that DNA sensitivity were for longer periods of time Davis suggested this region may be consecutively expressed or is being expressed for a specific a specific time frame in the cells life which can be detected by this this relatively simple assay called out jealous red one more time I understand that smaller pieces but what is exactly the top indicating compared to the side I'm aware of based pairs going up and down but so this big watch label that you can see it because it's labeled DNA is uncut and that's why it's way up here it's really big and there's relatively little this streak is not spray these are all smaller pieces and as the genome that region of the genome becomes more and more DNA sensitive more and more of this why is being broken up as being kind happen is running further down the job which is why we have this smear and over here where it's most sensitive the big big pieces are all on because they've all been cut up and we're seeing many many many many different sized fragments in this in this big smear thank you so much the top number the amount of dnase that's being outed is that what that is yes OK I just couldn't read that it was little small thank you leader anything else yeah micro milliliter I know that that actually says permits per mil that's in the entire DNA assay OK realistically figure it's very bad for awhile but usually it's microlitre when we're doing things like this I'm sorry I just yeah yeah yeah it doesn't matter too much just that there's more being here than there is here basically is more is a more important part of this thank you doctor you're welcome OK So what we're talking about is remodeling chromatin right we're modeling the chromatin so that we can turn genes on we can make them constraints with transcriptionally active and there are several different types of proteins that are specifically involved in chromatin remodeling so we're getting a little bit more specific I've been talking about remodeling a bit more generally these are all ATP dependent so they require energy that's all that means in order for remodeling to occur so these are specific protein complexes their enzymes movement Imitation switch don't ask me where that name comes from I've looked it up before but it doesn't make any kind of sense so it's just called imitation imitation switch I ask WI stands for imitation switch and this is a chromatin remodeling complex that specifically spaces nucleosomes at regular intervals so if it went isw I is active it moves nucleus comes around irrespective of DNA sequences so that those chromatis goes a nucleosomes are equally distant apart this is generally associated with inactivity inactivity transcriptional inactivity Cortana sing off in that region because imitation switch when it moves these nucleosomes around and makes them equidistant apart it has a tendency to cover Chrome elements so imitation switch is associated with gene inactivity this these two others one called sweet sniff which dance for switch sucrose non fermentable again you don't really have to know that sweet sniff is another family of protein complexes that are remodelers their remodeling proteins and these either move nucleus comes around or eject them from the DNA so sweet Smith proteins in response to an activator maybe this is a pioneer crew did to the nucleus sound an actually move the nucleus comes around 2 open up the important elements of the promoter so these guys either move them around or eject nucleosomes entirely which has to open the chromatin up and so these guys are associated with activity gene activity so genes being turned on so sweet step associated with activity and the last one is SW R1 which stands for switch remodeling complex and this is a protein that actually replaces H2 a histones with H2 AZ histones and again there's 8 two azs are easier to move and so too so if if SWR comes in and replaces the histone in a region with H2 AZ this nucleosome is more easily movable off of this particular element so both of these are associated with gene activity activity so sheated with turning Jesus these two are associated with turning jeans on because these tend to expose promoter elements cover them up and these are all of these guys are are generally acting in response to different kinds of transcription factors either activators or repressors so the activator maybe is a pioneer and it comes in an it recruits we sniff to move the Chrome with the nucleus comes around to expose the elements of the promoter may recruit SWRSWRV R1 to insert H2 azs so that we can easily move that nucleosome off the promoter at the appropriate times whereas imitation switch might be recruited by some kind of oppressor that causes that causes irritation switch to regularly spaced in nucleosomes thereby covering up in promoter elements and preventing the activator from binding to its from his DNA binding elements these proteins may also berecruited an act in response to those histone modifications like acetylation isolation it will come back to these in just a few minutes I should mention she mentioned earlier these kinds of modifications histone tails are what are known as epigenetic modifications and we'll come back and talk about those more in just a few minutes OK so we've got these kinds of commentator modeling complexes they're actually moving nucleosomes around or changing out nucleosome histones for more easily movable histones chromatin modifiers chemically modified histones by adding removing those chemical groups from their histone tails these affect the happy genetic modifications so these modifiers can add or remove acetyl groups they can add or remove methyl groups or phosphate groups for two and from the histone tails so there are three general types covered in modifyers modelers they're modifyers the action of the modifyers may recruit remodelers OK so these chromatin remodeler modifiers are just adding or removing chemical groups from this step tails and there are three very general types are quite simple erasers remove epigenetic marks or tax so those chemical groups that are added and removed from histone tails are known as epigenetic marks or epigenetic tags features are modifiers that remove epigenetic tags writers are modifyers that epigenetic tags and readers are enzymes that can identify the tags Anne kasama fact like for modeling so are remodelers may also happy genetic readers because if the remodelers act in response to these different types of epigenetic tags then they can read those epigenetic tags and cause some effect which is usually the moving of nucleosomes around don't worry about all this detail and we will be coming back and talking about these things in just a minute not all of them every genetic readers chromatin modifiers that are I'm sorry every genetic writers chromatin modifiers to add any genetic tags we have epigenetic racers hires that remove every genetic tags and then we have readers that can identify the what kind of tags are on those histone tails and has some effect to the nucleus to neither loosening the nucleus doped up or listening the chromatin up or making it get tighter OK thank you so much OK so these kinds of chromatin modifications adding and removing the chemical groups on the histone tails meaning to the South through the readers there is or patterns these different chemical groups on histone tails so here is my histone an age 3 is done three is one of the ones that has been fairly well studied and here is its tail and the letters are the different amino acids in that polypeptide strand that his detail about his dumb and and so this particular histone has a whole bunch of marks at the genetic markson's phosphate group on this amino acid and there is both an acetyl Anna methyl group on this aceto acet amino acid and there's a methyl group on this amino acid so there's lots of different modifications that are occurring to the same tail what is believed is that the pattern of modifications has the kind of information that the proteins of the cell can decode to cast the the the nucleosomes to move around the movement of the nucleosomes by the remodelers so this pattern of chemical modification it was known as the epigenetic code so remember with the genetic code you know we've got aced he's Jesus season those and the order of those days he's Jesus sees how meaning they mean in codons they mean different amino acids in the origin of replication this sequence of those nucleotides means this is where our name player DNA polymerase binds in promoters the sequence of those of those nucleotides means this is where party polymerase binds and transcription starts so that is all information this is also a form of information that the cell uses in order to determine whether or not these histones will be packed really tightly close together or rather than nucleosomes will react really closely together or far apart so the plan is the cumulative effect of lots of these different epigenetic marks that contain the information is the pattern of epigenetic marks on the specific amino acids in these histone tails that contain information about how tightly packed the chromosomes should be the chromatin should be rather and this is what epigenetics really is is the study of the pattern of chemical modifications to the histones that contain information about nucleosome packing this is all information that is also related to transcriptional activity because transcriptional activity is directly related to how tightly packed chromatin ESTs so the epigenetic code regulatory into the information in it maybe there's some epigenetic code that dictates this and the cell understands it we don't we know that this exists there's lots of evidence for it but it is not very well understood exactly how the epigenetic code works but there are some things that have been fairly well substantiated that we can generalize about so using Pepsi that is that neat that allows us to determine when proteins are bound to two regions of the genome it has been identified that when the 4th play scene K is lysine when IV lysine on histones 3 is methyl lated 3 * 3 means so when his dad 3 fourth wife scene is methyl lated three times that is associated with active promoters ship seekers identified that RNA polymerase is there OK so genetic mark is associated with transcriptional activity transcription factors tend to be bad at distal and cancers are distal elements control elements when 8 three K forest methylating one his still that that epigenetic mark is generally associated with an enhancer that has transcription factors bound to it which is also associated with gene activity or transcriptional activity when hyster 3K20 Lacey #27 is acetylated that tends to be associated with both active promoters and enhancers OK so these these epigenetic marks these are very specific marks and this data simply suggests that these specific marks these experiences only these ones have been found associated with these that this kind of activity different elements within the genome bye never are these he's in isolation there are other epigenetic marks along the length of the histone three tail it's just that this is one that we have managed to identify is associated with active promoters 83K27 when methylating three times is associated with inactive chromatin when are two is on the chromatin is being transcribed that's what we would expect we had a scribe some generalities to the effect of acetylation and metalation in particular in terms of what they mean for transcriptional activity these are very broad generalities in reality it is the cumulative effect of all of these different types of chemical modifications that determines whether or not genes are active or not whether or not the promoters are closed or opened OK so in reality it's the cumulative effects of all of these different kinds of chemical modifications on histone tails in a particular gene region that is informational we don't understand this very well but we can make some general conclusions based on what is currently known the addition of fetal groups in general when acetyl groups are found on his details this is associated with euchromatin with uncondensed chromatin with loosely packed chromatin acetylation so remember the histones are positively charged DNA is negatively charged and this is believed to help keep nucleosomes and chromatin nice and tight positively charged tales of the nucleosome of the history of the nucleosome probably interact with the negatively charged fast state of DNA that make DNA negatively charged they hang on tight to each other when you add acetyl groups to those histone tails it makes the histone tails a little less positive and may we the interaction between those histone tails and the DNA allowing for it's become looser and allowing for things like transcription factors to find to that now loosely associated DNA so is saturation The proteins that are called histone attempt to settle transferases or how for short these acedo groups so when these enzymes enzymes are active air region of the genome that means that that region of the genome that histones there are being acetylated and that region of the genome is probably being activated again is Seattle groups don't act in isolation but there is a general Association with acetylation and gene activation if that is true then the action of these histone acetylation sis is to activate genes to turn them on because what they do is add acetyl groups to these histone tails Alternatively Ajax which stands for histone DSM alesis are associated with don't put it up here Kim inactivity he studies thoroughly remove his settle groups from the histone tails which caused the histones and the DNA to be more tightly associated with each other thereby preventing other transcription factors and proteins from accessing the DNA and this causes the jeans to be inactive so Ajax are associated with gene inactivity pastor associated with gene activation because has acetol groups and Ajax removes them anybody have any questions so these are the erasers and writers that we were talking about riders these are erasers exactly good observation another quick question is each each histone has the tail or is this just for ease of illustration or is there only one per histone so there's eight particular so there are there are possible tails that can be modified three particularly important role that's not necessarily true that's just the one that is more well studied so this stuff is this epigenetic stuff is is still kind of a black box we don't know a whole lot about how heavy genetic function epigenetics functions indeed gene regulation except you know that it does play it doesn't regulate through to chromatin modeling through chromatin structure but we don't know that much about how epigenetics works so that's why we're where we're working with these broad generalities but acknowledging that these are generalities and things are much much more complicated than this OK doctor Christopher I have to ask like why particularly like things I'm looking at the structure and I was just wondering if you is that just like another black box thing or I mean so it seems I mean I mean it you know it could be that like things are more easily modifiable and then again I mean there are other so here there are other amino acids here's a couple that are modified it's just that these are the ones that have been studied thank you I think is on going I mean it's not like this is what's been studied in that's it there's newer information than this out there I'm sure on epigenetics I just haven't updated my my lectures to include all the most recent information and and you should probably thank me for that because it's it there's a lot of it and so we're just trying to keep things much more general with what has been well established because this is it is a very it is largely black box actually can spend their whole life just studying the histone tail of H3 and still not even begin to scratch the surface of everything that's going on yeah yeah and The thing is that this stuff is incredibly hard to study right like getting that kind of information you know first of all determining first of all this stuff changes right like so so you mean the genome in comparison is easy right the nucleotide sequences don't change except through mutation which is relatively rare so you could take any cell from my body and it's gonna have the same Gino it's not gonna have the same epigenetic code code is going to change during the lifetime of cells in response to environmental factors that cause changes in transcription so it's and it is extremely complex and so it's very difficult to tell like what the you know what marks are in the 1st place and then what they mean is extraordinary extraordinarily complicated things to study thank you doctor see her like you know sidetracking a little bit on this 'cause I'm really interested POV on it so I can kind of grasp my mind perfectly honest I don't know what kind about epigenetics it is it is fascinating because it is a brand new code that we simply don't understand but is extremely important because it's regulatory which which really matters let's get back on topic is obviously we can add his guns in reverse and remove his stuff so through the addition of his sorry we can add that histones at a set of groups and remove a settled groups to and from histone tails by the actions of hats and eight each decks convenient mechanism through ranch can **** chromosomes, tank can be caused to condense Andy condense and so go back and forth between euchromatic and heterochromatic states through the action of things like hats and each tax so high activity would tend to cause convention condensed chromatin to become more loosely packed and then Ajax can come in and remove those acetyl groups and cause the chromatin to recondense so complexity the action of the house the assembly sis and the Ajax are mediated by transcription factors so there are proteins that can find who let's see where your proteins that bind to their elements in the DNA that then recruit family says so maybe this is a pioneer again that recruit a steadily systor histone acetylation sis that region of the Gina the hat that adds a bunch of acetyl groups causes the listening of the DNA may be directly but maybe also through the recruitment of chromatin remodelers like sweetness for example or as WR these that loosen up the chromatin in that region and allow for our gigantic RNA polymerase and all the transcription factors that are needed to initiate transcription in that region it is sort of begun by the by the transcription factor at that is a pioneer maybe that recruits the hat that then makes adds a bunch of acetyl groups that maybe gets with chromatin remodelers going they loosen up that whole region of the genome transcription can be turned on transcription occurs we've got our gene being expressed week then we end up we get enough of affecting product whatever the protein is an a difference maybe repressor protein comes in recruits ajax the H dash Z In activate transcription so there is a whole lot going on here and transcription factors are believed to play a central role through recruitment of things like hats in Ajax OK so hot the situation is that regulated by the remodelers or by regulatory proteins Ajax are we call it recruiting so the assembly controlled by the transcription factors so the the transplant again again transcription factors are very broad thing if any protein that binds to some element in the DNA the result in transcription either being activated or inactivated so transcription factors are any kind of protein that binds DNA and has some effects on transcription so that can be they can act through very very large variety of the mechanisms so here it is a transcription factor that when it binds to its element in the DNA and again maybe it's a pioneer transcription factor because the DNA is the chromatin is tightly packed so this activator squeezes its way in there and when it's present its presence causes the past come in and the action of the hat through acetylation results in the loosening of the chromatin this may involve the recruitment of remodelers probably involves the recruitment of the remodelers so they have come in they cause acetylation the acetylation Ruth is the chromatin itself a little bit because of the reduction of positive charge of them histone tails but may also recruit these remodelers likes we sniff that move the nucleosomes around exposing the promoter to proteins like the RNA polymerase is an additional transcription factors the general transcription factors that are played that play a role in getting RNA polymerase active so it's really the transcription factors that are doing the ultimate regulation but they're regulating through the action of hats and Ajax anra modelers so there's a lot of layers of regulation occurring in in in eukaryotes which is why it's so poorly understood is just incredibly complex and then it starts with the situation is that an all histones or is that just one way that they can be I guess the word would not be regulated but in HVAC service to modifyers and so not all his stones are where is it be modified with the simulation are necessarily modified so for example we have regions of the remember we have regions of the genome that are situated Lee heterochromatic there always tightly packed like the kilometers those are always tightly packed there never transcriptionally active what this try to but i'm suggests is that there never acetylated and there is lots of evidence to suggest that so all histones can be modified but not all his sounds are modified some regions of the genome are always oph and some regions of the genome are always on African secretively active housekeeping genes don't go through this kind of remodeling so they may be you know those regions that are always on maybe always acetylated so that makes sense yes thank you I just wanted to know if the if the histones if all of them were acetylated but they can be but not all of them are that means that they can be but not all of them are because the hitters are all the same so right because in less they get in less than stones get replaced by that age too lazy the histones in the nucleus sounds are all the same which is why it's believed that it has to be some kind of an activator that is capable of specifically recognizing a sequence of DNA that causes that happen H dex to alter that the simulation state of the histones in that region because it can't be anything about the histones themselves they're all the same that information that causes the action that hasn't aged X has to be within the genome itself did that make sense yes thank you that really helps