eukaryotic gene regulation-7 long range chromatin interactions

Question 1

where are LCRs located

Answer 1

upstream or down stream

Question 2

how is the specificity of enhancers mediated

Answer 2

by transcription factors

Question 3

what are the 4 models of enhancer action

Answer 3

looping
tracking
facilitated tracking
linking

Question 4

describe the looping model

Answer 4

cross links formed between proteins or protein and DNA
restriction enzymes break DNA
DNA is ligated
removal of cross links by heat treatment and proteolysis
PCR used to see if distant regions interact with nucleus

Question 5

what has been used mostly in studies relating to LCR interactions

Answer 5

human beta globin locus

Question 6

when LCR loop together what do they form

Answer 6

active chromatin hub

Question 7

what interacts with this active chromatin hub

Answer 7

globin genes from the locus

Question 8

in foetal development what interacts with the LCR

Answer 8

gamma globin genes

Question 9

after birth what interacts with the LCR

Answer 9

delta and beta globin genes

Question 10

what do mouse beta globin LCR interact with

Answer 10

3’ end of locus

Question 11

what delineates the 3’ end of the locus

Answer 11

3’ HS1 hypersensitive site which is downstream of the beta globin gene

Question 12

what mediates the long range looping

Answer 12

CTCF binds to 5’ and 3’ hypersensitive sites

Question 13

what does the Th2 locus coordinate

Answer 13

IL-4,IL5,IL-13
LCR at end of Rad50 gene

Question 14

are Rad50 and Kif3a regulated by LCR

Answer 14

no

Question 15

what can naïve T cells differentiate in to

Answer 15

Th1 which expresses interferon gamma
Th2 expressing IL-4 IL-5 IL-13

Question 16

before differentiation what did the interferon gamma promoter interact with

Answer 16

Th2 LCR

Question 17

what evidence is there for tracking/facilitated tracking

Answer 17

insulator placed between the enhancer and a globin gene promoter prevented enhancer from activating and also prevented histone acetylation between enhancer and promoter

Question 18

how are chromosomes arranged

Answer 18

in topologically associating domains

Question 19

where does CTCF usual sit

Answer 19

at boundaries of TAD

Question 20

what does CTCF interact with

Answer 20

cohesin

Question 21

what are the sub domains with TADs

Answer 21

loop extrusion forms
cohesin mediates the formation of these loops

Question 22

what is the difference between an LCR and enhancer

Answer 22

enhancer-defined in transient transfection assays
defined by specific chromatin signatures H3K4me1 and p300 binding
LCR-position independent

Question 23

some LCR hypersensitive sites have enhancer function what function do other have

Answer 23

some function only when integrated into the genome

Question 24

what is 3C

Answer 24

chromosome conformation capture

Question 25

what are the 2 functions of insulators

Answer 25

block enhancer heterochromatin barrier

Question 26

where was insulator function found in chicken beta globin locus

Answer 26

5' HS4 3' HS1

Question 27

what are the 3 models for how insulators acts as enhancer blockers

Answer 27

1- promoter decoy model-enhancer +insulator 2- tracking-can block enhancer when it tracks along chromosome 3-structural-organises chromosome into topologically constrained loops

Question 28

purification of factors that bind to enhancer blocking insulators showed what

Answer 28

showed that CTCF binds

Question 29

how does CTCF/cohesin complex help with the functioning of insulators

Answer 29

it forms loops that acts as obstacle in tracking and prevents outside promoters from interacting

Question 30

where are CTCF sites found and what are they needed for

Answer 30

adjacent to nuclear laminar associated domains enhancer blocking

Question 31

apart from CTCF acting as barrier what other mechanism is there for enhancer blocking

Answer 31

tethering to nuclear structures

Question 32

what does the barrier function in insulators lead to

Answer 32

stops spread of heterochromatin

Question 33

what mediates the barrier function of the cHS4 insulator

Answer 33

USF1 and 2 recruit histone acetyltransferases as barrier HP1 bind to H3K9me3 recruits H3K9 methyltransferase

Question 34

what happens when USF sites are mutated

Answer 34

usually there is a peak in acetylation at cHS4 which is now lost

Question 35

what are transcription factories

Answer 35

region in nucleus with high RNA pol II concentration gene transcription takes place here DNA spooled through immobile polymerase

Question 36

give evidence that polymerase stay immobile

Answer 36

early-nascent transcripts in the distinct foci later-antibodies against pol II show it's present at distinct foci

Question 37

explain the relaxed transcription factory model

Answer 37

high concentration of RNA pol II and machinery within nucleus genes move here for transcription dynamic not rigid pol II can move along gene

Question 38

what is an advantage of these factories

Answer 38

splicing and transcription efficiency

Question 39

what are some dangers of the factories

Answer 39

risk of trans splicing chromosome translocation-burkitt's lymphoma