Application structural biology

Question 1

genome folding

Answer 1

nucleossome - chromatin fiber folds into loops (upstream gene regulatory elements close to promoter to control transcription) - chromatin domains (TADs) - chromatin components

Question 2

condensin, cohesin, CTCF, SMCs

Answer 2

condensin: compacts DNA into mitotic chr (catalyses folding)

cohesin: holds sister chromatids

CTCF: helps estabilishing organization, transcription factor (activator, repressor, insulator) - interacts with SA2 - most important tyrosine and phenylanine without them doesn´t bind and there are no loops in chromatin - counterinterats Wapl release - can isolate or activate gene expression blocking or joining together the enhancer and promoter in the loops; can block the Wapl-C the cohesin doesn´t get remove

Wapl - releases arms- also has phenylanine - competes with CTCF - M and C bind to SA and C is essential for removal of cohesin

SMCs: homo or heterodimer (eukaryotes) - 2 proteins connected at the hinge, heads possess ATPase activity with kleisin ligating

SCC1 P355L mutation hotspot
protection factors also bind of SA

Question 3

Removal of cohesin - mitosis

Answer 3

prophase - arms removal by WapI (antagonist):
1- phosphorilation by mitotic kinases (CDK1 and PLK1) and aurora B
2- WapI is able to remove cohesin
3- centromeric cohesin is protected by SG01 + PP2A that counter interacts with phosphorilation and prevents WapI binding

metaphase to anaphase - centromeric removal with separase: separase removes cohesin (cleaves Scc1 subunit) and triggers separation to opposite poles of the cell

Question 4

regulation by acetylation

Answer 4

ESCO1- acetylates and pauses the looping process
HDAC8 - reverses

Question 5

VDJ recombination

Answer 5

loops formed by loop extrusion by CTCF you can induce proximity of RAG to the V gene and can lead to somatic recombination
Ab made by VDJ recombination almost every gene has CTCF poiting to interior of nucleus, cohesin folds locus and RAG scans