AMB: III Transcriptional regulation

describe nuclear homone receptor type I

its a ligan activated TF, in absence of a hormone it’s located in the cytosplams, when a hormone binds it undergoes conformational change, localizes to the nucleus where it forms a dimer with another NHR, and binds response elements at the inverted repeat sequence, which activates transcription. NHR can also repress transcription, but in this case they bind to other TF rather than to the DNA

describe nuclear homone receptor type II

Is already localized in the nucleus, it functions as a heterodimer, but in absene of a ligand (hormone) it represses a gene due to corepressor complex (histone deacetylase) which leads to heterochromatin production. when a hormone binds and NHR undergoes conformational change the corepressor complex is released and a coactivator complex is recruited, histone acetyl transferase, leads to euchromatin, and transcription

most signal transduction pathways regulate TF, what is the affect of post translation modifications (acetylation, ubiquitylation, P) on TF

they modify the DNA binding domain, influencing the TF-TF or TF-mediator protein interactions, ultimately changing the DNA binding state or localization. These are mostly reversible so it can return to the default state after the signal is over

how do heat shock factors work

HSF is kept in the cytoplasm as monomer but repressed by heat shock proteins, upon stress, when proteins unfold, the heat chock proteins that chaperon other protein release HSF1 from the complex and it trimerizes. HSF1 is then transported to the nucleus where it is hyperphosphorylated and activates expression of heat shock genes (binds to their promoter), as these heat shock proteins are expressed, number of unfolded proteins decrease and so do the heat schock proteins (negative feedback loop)

How come heat schok proteins can be expressed so quickly (tip dit is regulation at elongation level)

promoter is in a transcription competent state, but RNA pol is stalled (CTD Ser5 only partly P). RNA pol is on the initiation complex and ready to go, however in absence of HSF, elongation is stalled by negative elongation factor (NELF) and DRB sensitivity inducing factor (DSIF), when HSF enters nucleus it P Ser2 of CTD and NELF & DSIF → transcription

what is targeted during chromatin regulation

the N erminal tail of the nucleosome (nucleosome = compartment of DNA wrapped around histones), can be acetylated, ubiquitylaed, methylated, sumoylated or phosphorylated

what is the effect of chromatin regulation (3)

SN: modifications zijn reversible

1. chnage chromatin structure

2. change nucleosome stability

3. change recruitment of effector proteins

effect of histone acetylene transferase

(SN: most histone modifying complex work with both ac and deac in 1 go, both active)

acetylene lowers the positive charge, decreasing affinity for the N terminal (+) of histones with DNA (-) → loosely packed → euchromatin

heterochromatin formation in S.cerevisiae

Near telomeres:

1. Rap 1 recognizes silencer and recruits Sir 3 and 4

2. Sir 3 and 4 cofer nucleation of the silencer domain and recruit Sir2

3. Sir 2 deactelyases adjacent histone tails which recruit more Sir3 and 4, contributing to further spreading

how can chromatin spreading be stopped

boundary elements

heterochromatin formation in S.Pombe

1. Suv39 trimethylates H3K9

2. HP1 binds with its chromodomain and oligomerizes (multiple HP1 interact together through oligodomain), leading to heterochromatin formation

Heterochromatin formation in higher eukaryotes (eg drosophilia)

1. PRC2 trimethylates H3K27

2. this recruits PRC1, leads to permanent silencing of hox (=homeotic) genes

heterochromatin formaion at centromeres

guided by small interfering RNAs, thee load onto RITS complex by binding complementary RNA, recruits histone deacetylase and methyl transferases (leading to heterochromatin)

what effect does trimethylation of H3K4 have (tip: trithorax genes)

leads to activation of nearby genes