lecture 5 - 9/29 so tired grandpa

chromaton modification and histone n terminal tail and how thatimpacts change in chromatin structure, lysins that are postively charge interact with negative charges with dna and other chormsomses and then it will compact the chromtin more. acetylation neutralizes the charge and lead to decompaction . methylation of the tails like mono, di, tri, of the lusins will make the chromatin make it more condensed because it recruits reader proteins.

modifications happen on the histone tail can have a direct impact but it can recruit other factors to those nucleosomes and they have a direct role. specific proteins with the domains help to recognize these marks like HP1 proteins that binds to the H3K9 tri methylated nucleosome region will bind. the hp1 has the chormodomain that binds to the mark of the nucleosome and chormoshadow interacts with other proteins with the chormsooshadow proteins. two hp1 proteins can interct with eachother through the chormsooshaodow and other proteins that have it to. the boromo domains proteins being to the aceytlated regions which are also present, active chroamtin regions .

how these modifications influcnece gene gtrancirptions. how they are loaded andhow they change the chormatin structure. moving from a highly condensed to open chromtin structure is assoicated with trancirptional acivity. how a specific region could change to a more opent structure.

the top poart of the chormin is a protmoer or enhancer sequence but when closed it is slient. with a specific singling evben the cell opens the choromin to allow pol2 to bind. Like NFKB is a TF and bind to enahncer of psecific genes, NFKB enhancer sequence could be closed , even if u have enough NFKB in the cell and the chromin is closed no matter what it is not going to cause trancipriton, it has to open. or when a singla happens the cell will clos the chormin. so specific singla can turn on or off the gene . it is bidrectional system. . .

nucelusosomes that are part of the chormin can have negative impat on trancirption. particular chormin structure has nucelsoomes attached it inhibits tranciprion of the gene. cell jas to remove the nucleosomes. naked dna is better in tranciprion . yeast was a model system. a group of proetins called switch SWI2 or SNF2 proteins. some mutation on the gnenes SNF or SWI.

a gene called swi2/SNF2 - in yeast. if you make mutation on this gene, loss of funciton mtuation will reduce tranciprion of some unrelated genes.

loss of funciton mtuation on gene a gene be tranciprion is impacted on gene b. so like gene a is the swi/snif it will lead to tranciprion to be impacted in gene b.

study two - when mutation on swi gene has an impact on C as well. B and C is two different independent pathways and unrelated genes so swi/snf has an impact on these unrelated genes.

HO genes = the product protein is a dna endonucleuase thats essential for process in yeast called. mating type swithcing. In absence of the switch two gene the HO gene tracnription is inhibtied.

sugar fermatnation in yeast. mutation in switch two loss of fucntion mtuation leads to losso foecpression of SUC2 which is an invertase needed for fermantitonin yeast, these geens are indenpendent and unrelated.

if you take this yeast strain losso fo funciton with SNf2 and cross it with another strain that has a reduced activity of histone four, that is part of the nucleosome core. the histone four reduced activity means it ocntians less amount of histone four, s id doesnt make funcitonal nculosomes that efficiently. when cross they could reactivate the expression of HO gene or SUC2 gene. H four activity reduceds core histone formaiton, nucelsome formation. and when crossing these two it will lead to the reactivation of the HO gene back to normal level.

Epistasis.

there is a relationship between the switch two gene and histone four. switch two mtuation losso fo fucntion ho gene is abolished.

when swtihc two gene is mutated the nuclsoems on the HO gene is not changed, or remjoved. IF HO gene to get activated you need to remove the nuclsoems to beocme naked dna to enhance the region of the HO gene that has to be removed. TF and other proteins can come in and bind. In the losso f fucntion of switch two that remodleing is not taking place. So when you bring back the H4 hsitone losso fo fucntion in the backgroun there are less nucleosomes to start with ebcause the H4 core losso f fucniton. H4 is a core nculeosme proteins, so less nucleosmes when there is loss of function h4 . so les sncuelsomes means less amount of nucleosomes on the HO gene so we dont even need the SWTICH 2 protein anymore. because SWTICH2 main job is to remove the nucleosomes on the promoter so we dont even need it.

a = swithc 2.. so gene A’s product is to remove nucelosmes from specifc genes. so without gene A it cant remove the nucleosomes of a specific gene and lead to inactivation of this said specific gene. NOw if we cross this gene A loss of fucntion and cross it with loss of fucntion H4 core . then that means there are less nucleosomes and therefore the dna is less compaxted and the specific gene can be activated without the help of the gene A regardless if its loss of fucntion or not.

either overactive switthc two gene so it removes more nucleosomes or reduce the amount of core histones to resuce to losso fo fucntion of switch 2. there are speicif protein compelxs that change the nculsooems structure on a chromin and imjpact the tranciprioal actitiy of a gene. Swithc two protein is part of a complex called swithc snf compexl and swf2/snf2 is one of them. this si a conscerved structure. this si a chormaitn remodleing factor complex. the swithc snf two protein is a atpase enzyme, it has atpase activity to change the chormin structure with the help of atp hydrolysis and is part of the swf.snf compex.

it is an important family of protiens. chormin remodling factor function?

dna is wraped aorund the core nucleosome strucutre the red line is a binding site for a tf and in order to inhibti or activate a gene the tf has to acess the dna binding sequence. if that sequence is inside the ncuelsome region then that region isnt accessible. however if the sequence is outside the nucleosome maybe the tf can bind and activate the trancirption of the gene. chromin remodling factors can change the postiion of the nucelosmes to the sequence is accessibel to a tf of interest.

chromoin remodling factors or atp dependingt chormin remdoling factors can achieve this process . the first process is called cotamer sliding . this si nothign but a nucleosme made of eight proteins. octamer sliding or ctamer transport so this is different ype of chormin remodling factors that the cell can do/changes. singlig even happens and so then the nucelosme is slide out of the way to free the enhancer. atp depending chorming remodling factors will bing to the sequence and push the ncuesomes on either side. in octamer transfer they phsycially remove the nucleomes form ther egion of interest. you need to bring the atp depending chormin remdoling factors needs to be rbough to the region and either push octamers to either side or transfer it . atp dependin remcokign facots resultsin either activation or inhibitiron of tranciprion. because it depends on where the chormin remoldin factor is recruited. it can push the nucleosme on top of an enyhancer and keep it inhibited even more. in order to happen on specific chromin the chormin remodling factors needs to be brought, the chormin remodling does not have a dna binding domain meaning that it cannot by itself come to and bind to the dna sequence so it needs assisance form other factors so it can ber ecruited to a specific strettch of dna.

octomer is a nucleosome structure its the same thing.

based on what we elearnd look at the sitation, closed chormin and tranciprioally off, and the structure needs to be changed. in order for that to happen we need the chromatin remolding atp dependt factor. it needs help ebcause it doesnt have a dna binding domain. in order for this to happen, some protiens in the cell will have to recruit the remodling factor to a specific region. this function is done by a group of tranciprion factors that has the ability to bind to dna sequence which are masked by nculeosmes, a small group not all and these are called pioneer trancirpioin factors. these pioneer tranciprion factors can recruit other fracvtors to that region including the atp depending chormin remodling factors. every tfc should have a dna binding domain and a activation or repssor domain. so the acttivation domain of the pioneer tranciorion facto is the domain in which specifally bidn to an atp dendtn chromin remjodling factor and recruit it. inside the cell there is no naked dna na dall dna is present in form of chromtain.

you need all these factors to activate tranciprion. normal tf dont have the ability to bind to dna that is part of a closed dna/chormatin. if its withing the linker dna it can but if its part of the nculeosoem it cannot in normal TF’s. so pioneer tf it can bind even if its tighly bound dna around nucleosome it can recruit the other factors.

lets look at yeast model swithc two will activate HO gene.

HO gene enhancer is tighly bound. in swtihc five is a prioneer tranciprion factor and it will bind to those enhancer sequences within the HO gene , and once it binds it has a activation domain and recruits the SWI/SNF complex which is the chormin remodling factor complex, and then it recuirts other ocmplexs like HAT complex. HAT is histone acetylation transferarse. Hat’s main job is to add aceyl groups to the tail of hsitone lysin 9,4, or 27. acetylation happen it helps reduce the charge and crease the chormin opening. so the swithc snif complex will change the compaction and reduces, the hat comeplex in yeast are called SAGA. both together funciton to change the strucuter to open stucture. that means it removes it first it modifies the ncuelsome by neutralizing the charge, it opnes the neucleoms further but then the swtihc sytwm of complex will rmeove or tranfer the ncueolme to make it ferrer on the nehancer of the ho gene. that open chormin will recruit further tranciprion factors that are non piooner tranciroion facts that are requied to activate the gene. its a stepwsie proces that a pionner facto comes recuirts these factors, addional cofactors because thos histone actyltranferase compex,, saga complex or the swithc snf complex they dont have a direct dna bidnign activity . so it requires the assitance of a priooner tranciprion factor there and change the chorminst ructure loosen, the chromin structure now recuirts further tf and ultimluy recruit the GTfs and pol two.

in order for poly to trancribe the gene the complete gene structure should have a ncuelsome free,3?

so whena. gene peolymerase is passing thorugh in one direction if the gene is there it has to remal all the nucleomes out of the way. this process happens the entire lenght of the entire gene. that complete gene cannot be naked the entire time, the cells are endo nuclease, nucleases which can cleave and break the dna sequence, so when polmerase is moving through this free DNA, the surrounding, the region behind the poly the nucelomes will be added back in a highly dynamic process. the pol poasses this directio, the new closome is added going this way. the new poly it has to be removed so its high active enregy consuming process. thats only where cell knows how to activate tracnripoin or controll the chromins tructure and reults in tranciprioal activation of a gene.

• go back and watch the last ten mins cuz im tired.

complete gene cannot be naked the entier time becuase cells have nedocnuelause that can break an cleavge the dna seuqnece. so as the polymerase moves thorugh the ncuelsoms will be added back. so the region isnt exposed to the enodnucleus. its energy consuming process.

if something goes wrong those open dna the dna could break by endonucleus. if it happens on a tumor supressor gene its. aproblem. we use the work coactivator that are protiens like chorming remoding factors, hstione acetyltranfe, histone methyl tranfases that inflcunce the chormtin structure but do not have a direct dna bidngin domain itself. so it requies the help of other proritne s like pioneer tf’s that do have that dna binding domain . or co repressors.

many of Tf’s are activators that bind to dna and rectuirs HAts, Mediators, gtfs, chormain remdolign complex to change the chromatin structure. THIS I activation.

if its repression its h3k9 methyl tranferase. no mediators, no gtfs , yes to chormatin remodling.

Hat will aceytl nucleomses that increase te decompation of chormtin. but we can change and make it more comact by histone deactyalse, HDAC. will remove the acetyl from the lysin and make the ncuelomes more code.

The code reade rhyptothesseis - the hy

Histone code reader wrtier hypothesis -

hp1 is a reader, because it recognizes the code of methylation site on the lysine 9 or 27.

methyl trafnerase is the writer. Hat and HDAc are writers because they add or erase modficiations.

all about hsitoen fmodication - talk about speicif exmple - histone tail modifiation infleunce the chormin structure and that has a direct impatn on tranciptions. its a very imprtoa essiential process -

other type of modication on the dna can ifnelucne the chormin strucutre. so one modifucation is the dna seuqnce . dna modifation is that dna can modified by the cytosine methayltion. methyatlion of the cytosine resideue on the dna sequence . this happens on the dna nuceltodies not PROTEINS .

if you have a dna sequence chromtin bound , if the cytositne resideues gets methyalted it infleucne structure. methylation of cytosin recruits proteincs called methyaltion bidngin protein MeCP2. and these proteins chang ethe chormtin strucutre. if a chroomin is cytositne methyalted it can change the chromtin into more highly chormtin compaction, it is a repressor mof the gene. methyaltion site recruit proteins liek MECP2 that are methyl bdingin protein MBPs and chang ehte chormign structure.

so now MECP2 can recruit enzyme like HDAC(histone de acetyaltion) to change the ncueome structure. it can also recruit hsitone tranfease to ad dmethyaltion ot o the nucelomse. if a region is methylated it recruits protein complex that results in further compaction. cytosine methyaltion impacts compaction is a type of protmoer. what tyep of core promtoer where we can have cytosien methaytlion? CPG, large numebr of CPG cor epromtoers are vulnerable to the cytosien methyatlion and results in repression .