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BIOC2306 > eukaryotic gene regulation-7 long range chromatin interactions > Flashcards

eukaryotic gene regulation-7 long range chromatin interactions Flashcards

1
Q

where are LCRs located

A

upstream or down stream

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2
Q

how is the specificity of enhancers mediated

A

by transcription factors

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3
Q

what are the 4 models of enhancer action

A

looping
tracking
facilitated tracking
linking

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4
Q

describe the looping model

A

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

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5
Q

what has been used mostly in studies relating to LCR interactions

A

human beta globin locus

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6
Q

when LCR loop together what do they form

A

active chromatin hub

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7
Q

what interacts with this active chromatin hub

A

globin genes from the locus

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8
Q

in foetal development what interacts with the LCR

A

gamma globin genes

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9
Q

after birth what interacts with the LCR

A

delta and beta globin genes

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10
Q

what do mouse beta globin LCR interact with

A

3’ end of locus

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11
Q

what delineates the 3’ end of the locus

A

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

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12
Q

what mediates the long range looping

A

CTCF binds to 5’ and 3’ hypersensitive sites

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13
Q

what does the Th2 locus coordinate

A

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

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14
Q

are Rad50 and Kif3a regulated by LCR

A

no

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15
Q

what can naïve T cells differentiate in to

A

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

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16
Q

before differentiation what did the interferon gamma promoter interact with

A

Th2 LCR

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17
Q

what evidence is there for tracking/facilitated tracking

A

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

18
Q

how are chromosomes arranged

A

in topologically associating domains

19
Q

where does CTCF usual sit

A

at boundaries of TAD

20
Q

what does CTCF interact with

A

cohesin

21
Q

what are the sub domains with TADs

A

loop extrusion forms
cohesin mediates the formation of these loops

22
Q

what is the difference between an LCR and enhancer

A

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

23
Q

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

A

some function only when integrated into the genome

24
Q

what is 3C

A

chromosome conformation capture

25
Q

what are the 2 functions of insulators

A

block enhancer
heterochromatin barrier

26
Q

where was insulator function found in chicken beta globin locus

A

5’ HS4
3’ HS1

27
Q

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

A

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

28
Q

purification of factors that bind to enhancer blocking insulators showed what

A

showed that CTCF binds

29
Q

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

A

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

30
Q

where are CTCF sites found and what are they needed for

A

adjacent to nuclear laminar associated domains
enhancer blocking

31
Q

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

A

tethering to nuclear structures

32
Q

what does the barrier function in insulators lead to

A

stops spread of heterochromatin

33
Q

what mediates the barrier function of the cHS4 insulator

A

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

34
Q

what happens when USF sites are mutated

A

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

35
Q

what are transcription factories

A

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

36
Q

give evidence that polymerase stay immobile

A

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

37
Q

explain the relaxed transcription factory model

A

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

38
Q

what is an advantage of these factories

A

splicing and transcription efficiency

39
Q

what are some dangers of the factories

A

risk of trans splicing
chromosome translocation-burkitt’s lymphoma

40
Q
A

BIOC2306 (10 decks)

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