HC8 histone modifications and genome regulation

Question 1

TADs

Answer 1

topologically associated domains.
genomic DNA is well organised: into active and inactive departments.
TADs are regions where chromatin with similiar epigenetic marks are clustered together,

Question 2

Histone modifications: where on the histone?

Answer 2

mostly at N-terminal histone tail. modifications result in the recruitment of effector proteins –> change chromatin structure –> stimulating or hampering transcription by RNA polymerase

Question 3

Chromatin immunoprecipitation (ChIP-seq)

Answer 3

sonication of genomic DNA –> incubate with antibody against histone modification –> precipitation of target DNA by incubating with beads against ab –> sequence the DNA bound beads

Question 4

Cross talk between modifications example SET1

Answer 4

SET1 methylates H3K4 –> H3K4me3 facilitates binding of NuA3 HAT complex –> acetylation of H3K14ac

Question 5

H3K4me3 presence and its role

Answer 5

present at transcription start sites –> recruites histone acetylases (HATs) –> prevents 5mC, since DNMT3 cannot bind

Question 6

acetylation

Answer 6

removes positive charge from lysine –> less strong binding between DNA (- charged) and histones.

TF binds –> HAT –> histone acetylation –> remodelling proteins open up chromatin –> RNA pol and factors bind –> transcription

Question 7

H3K36me

Answer 7

prevents cryptic initiation of transcription. is added behind RNAPII during transcription.

Question 8

bivalent/poised chromatin structure

Answer 8

presence of H3K4me and H3K27me. upon differentiation cells will loose one mark en will become either active/inactive

Question 9

writers

Answer 9

acetyl/methyltransferases, kinases, ubiquitin ligases etc.
Get recruited by sequence specific TFs.

Question 10

readers

Answer 10

proteins that interprate the histone modifications. different protein domains can recognise different histone modifications. also different protein domains can bind to the same histone modification.

Question 11

erasers

Answer 11

deacetylases/demethyales/protein phosphatases

Question 12

phase separtion

Answer 12

molecules with intrinsically disorganised regions (IDR) can intereract with each other. you get supramolecular assemblies of protein, nucleic acids and other molecules.