PhD Molecular Genetics- Brainson

chemical composition of chromatin?

DNA, RNA, proteins (histones)

large domain of chromatin?

topologically associating domain (TAD)

subunits of histone octamer?

2x H2A, H2B, H3, H4

what is H1? Where located?

linker histone subjected to PTM; outside of core nucleosome

4 different histone variants?

H3.3, MacroH2A, H2A.X, H2A.Z

H2A.Z function

flags transcription marks

MacroH2A function

X chromosome inactivation

H2A.X function

flags for damage

H3.3 function

flags transcription marks

2 histone remodelers?

SNF/RSC

2 histone chaperones?

HIRA and FACT

examples of modifications to histone tails?

ubiquination, methylation, phosphorylation, acetylation

what complexes change the pattern of histone modifications?

writers and erasers

types of readers?

bromo and chromo

types of writers

HAT and HMT/KMT

types of erasers

HDAC and HDM/KDM

what is used to visualize histone marks?

Chip seq

what is used to visualize histone marks in a few cells?

ATAC seq

database that collects histone modification pattern data?

encode

where can DNA methylation only occur?

on C next to G

DNMT1=

maintenance methyl

DNMT3A/B=

de novo methyl

how can DNA be demethyl?

TET proteins

open chromatin → ___methylated → active/silent

hypo, active

closed chromatin → ___methylated → active/silent

hyper, silent

open chromatin=

euchchromatinc

closed chromatin=

heterochromatin

how do histone variants get incorporated?

chaperons and remodelers

how wide is a basic chromatin fiber?

30 nm

names for transcribed strand of DNA

template, antisense, non coding

names of the not transcribed strand of DNA

coding, sense, non template

what type of RNA does each RNA polymerase make

pol 1- rRNA, pol 2- mRNA, pol 3- tRNA

different channels formed in RNA pol complex?

T strand, entrance, RNA exit, rNTP

6 stages of transcription

1. promoter recognition

2. PIC: closed to open

3. initiation

4. pause

5. elongation

6. termination

def of core promoter

site PIC forms around TSS

major function of TFIIH

unwinds DNA and kinase domain

2 protein complexes that stabilize PIC

mediator and cohesion

how many nucleotides transcribed before pausing

30-50

proteins that initiate the pause

DSIF and NELF

2 complexes that break the pause

SEC and PTEFb

what protein stabilizes the pause

7SK

2 models of how RNA pol knows it reached the end of the gene

torpedo and allosteric

difference between general and specific transcription factor

general- assembles PIC, seq specific- binds other proteins/DNA

2 domains of TF

activation domain and DNA binding domain

2 classes of TF based on DNA binding motifs

winged helix and zinc fingers

3 regions of DNA involved in transcription control

enhances, silencers, insulators

how can transcriptional states be propogated through mitosis

bookmarking TF

assay that shows chromatin topology

chromatin conformation capture

how can a silenced gene be able to turn on by changing chromatin state

heterochrom→euchrom by acetylation or demethylation

how can an expressed gene be able to turn off by changing chromatin state

euchrom→heterochrom by methylation or deacetylation

what is a super-enhancer

many enhancers

what is the role of a super-enhancer

controls gene expression by recruiting lots of TF

how is the extra X chromosome turned off

long noncoding RNA coats X chromosome with methylation

what happens during active to inactive X chromosome

1) Xist lncRNA is bound

2) It recruits RRC2 and 1 to methylate and ubiquitinate chromatin

3) chaperones removed H2A.Z and H3.3

4) chaperones swap in macroH2A

5) DNA becomes methylated

active forms of chromatin 

H3K27ac,  H3K36me3, H3K4me3

inactive forms of chromatin

H3K27me3

ChIP seq

cross link, sonicate, immunoprecipitated, de cross link, purify DNA, sequence, align, wiggle plot

what proteins can be found at enhancers

mediator complex, RNA pol II, specific TF

functions of general TF

bind TATA, helicase activity