Epigenetics II: Histone Modifications Flashcards
Position effect variegation in Drosophila is heritable gene silencing by (euchromatin/heterochromatin)
Heterochromatin
Antennapedia is the loss of silencing of ________ genes at the wrong time in development
Hox
True or false: There is DNA methylation in Drosophila
False
What is the fundamental unit of chromatin structure?
Nucleosome
H3K4, H3K36 and H3K79 methylation are markers for (on/off) chromatin states
On
H3K9 and H3K27 methylation are markers for (on/off) chromatin states
Off
What is the function of histone modifications?
Acetylation of lysine side-chains
What is the benefit of acetylation of the lysine side-chains?
Neutralizes positive charge and abrogates interaction with DNA
Histone acetylation correlates with what events?
Transcriptional activity and dynamic chromatin structure
(HDAC/HAT) enzymes are involved in transcriptional activity and (HDAC/HAT) is involved in repression
HAT; HDAC
What domains bind to acetylated histones?
Bromodomains
Histone lysine methylation is catalyzed by enzymes containing a __________ domain
SET
How is histone lysine de-methylated?
Oxidation of methyl lysine by LSD and JMJC enzymes
H3K9 methylation characterizes (facultative/constitutive) heterochromatin
Constitutive
H3K27 methylation characterizes (facultative/constitutive) heterochromatin
Facultative
SUV39H1, SETDB1 and GLP are histone methyltransferases that methylate (H3K9/H3K27)
H3K9
EZH1 and EZH2 are histone methyltransferases that methylate (H3K9/H3K27)
H3K27
Which heterochromatin protein bind to methylated K9?
HP1
Which heterochromatin protein binds to methylated K27?
Polycomb
Heterochromatin proteins share a domain. What is the domain?
Chromodomain
What technique is used to map histone modifications and chromatin proteins on chromosomes?
ChIP-seq
Endoderm specification depends on the (gain/loss) of H3K9me
Gain
H3K9me3-dependent (facultative/constitutive) heterochromatin is essential for proper differentiation
Facultative
Which family of proteins bind to H3K9me and mediate transcriptional repression?
HP1
What properties of HP1 help create heterochromatin “foci” in cells?
Biophysical properties
Silencing of which protein requires H3K27 methylation and is a specialized facultative heterochromatin system?
Polycomb
In flies, what does a loss of PcG silencing cause?
Developmental transformations
In mammals, loss of Polycomb proteins causes what?
Developmental phenotypes like gastrulation defects and neurological defects
__________ is a H3K27 methyltransferase complex, with catalytic subunit EZH1/2, AEBP2 and JARID2 that bind to ubiquitylated H2A
PRC2
___________ contains Cbx chromodomain proteins that bind to H3K27me mark, also contains RNF2 H2A monoubiquitylation enzyme
PRC1
Repression function of H3K27me resides in (PRC1/PRC2)
PRC1
Why is the Polycomb system important for oligodendrocyte differentiation?
PRC2 is important to repress signaling pathways that cause cell fate switch and allow myelination by oligodendrocytes
Knockout of Eed in OPCs prevent myelination and induce cell fate switch of OPCs to astrocytes
Which of the following are ways for DNA/H3K9/HeK27 methyltransferases get to their target genes?
a. Interaction with other chromatin factors
b. Interaction with site-specific DNA-binding proteins
c. Polycomb interaction with coding RNA
a and b
How is loop linking DNA methylation to H3K9me formed?
UHRF1 TTD domain binds to H3K9me and UHRF1 SRA domain binds to methyl CpG
UHRF1 and DNMT1 interact
Methyl-DNA binding proteins like _________ form complexes with HDAC enzymes
MeCP1, MeCP2, MBD
