Epigenetic regulators

Question 1

Cytosine modification chemistry

Answer 1

Question 2

AID/APOBEC polynucleotide cytidine deaminases

Answer 2

Class of nucleoside editors that may catalyze C-to-U edits in DNA only (specialist) or in both DNA and RNA (generalist). The family contains APOBEC1-4 and AID.

Question 3

APOBEC1

Answer 3

Expressed exclusively in the small intestine. Generalist.

Editing of a CAA in APOB mRNA to UAA by APOBEC1 produces the stop codon that truncates the protein (from APOB-100) and creates the APOB-48 variant.

Question 4

AID

Answer 4

Expressed exclusively in maturing lymphocytes. Specialist (ssDNA only).

AID is responsible for somatic hypermutation of the Ig genes, specifically the V gene.

Question 5

APOBEC2

Answer 5

Expressed in cardiac and skeletal muscle.

Strongly conserved and thought to have an as yet undiscovered essential molecular function.

Does not have deaminase activity in DNA or RNA, but does bind DNA at specific promotter regions and is thought to act as a transcriptional repressor.

Question 6

APOBEC3

Answer 6

In primates, divided into a seven gene subfamily (A3A, A3B, A3C, A3D, A3F, A3G, and A3H) which all act in the restriction of viruses and genomic mobile elements.

Functionally a part of ther innate immune system.

Deaminates obligatory single standed cDNA intermediates of viruses/transposons, which can then be cleaved and degraded. If the DNA is not degraded, it may however facilitate mutations which contribute to viral evolution.

Question 7

APOBEC4

Answer 7

Expressed in mammalial testis.

Thought to have a role in promoter modulation in mammals, but is poorly understood.

Question 8

Generalist AID/APOBEC enzymes

Answer 8

APOBEC1
A3A
A3G

Question 9

Specialist AID/APOBEC enzymes

Answer 9

AID
A3B
A3C
A3F
A3H

Question 10

Cytidine deaminase domain

Answer 10

Domain of AID/APOBEC family proteins that catalyzes deamination.

Note that it is a zinc-dependent deaminase.

Question 11

In mammalian genomes, 5mC exists mostly in the ___ context and about 70-80% of ___ are methylated

Answer 11

In mammalian genomes, 5mC exists mostly in the CpG context and about 70-80% of CpGs are methylated

Question 12

Passive DNA demethylation

Answer 12

Loss of 5mC during successive rounds of replication in the absence of functional DNA methylation maintenance machinery.

Question 13

TETs

Answer 13

TET1/2/3. TET = Ten eleven translocation

A family of epigenetic regulators which oxygenate 5-methyl-cytosine (5mC) to 5-hydroxymethyl-cytosine (5hmC). It is capable of further iterative oxidation to 5-formyl-cytosine (5fC) and 5-carboxyl-cytosine (5caC) as well.

TETs utilize iron as a cofactor. They use molecular oxygen to catalyse oxidative decarboxylation of alpha-ketoglutarate, generating a reactive high-valent, enzyme-bound Fe(IV)-oxo intermediate, which then reacts with 5mC to create 5hmC.

Question 14

TDG

Answer 14

Thymine DNA glycosylase

Has two important functions:
* Repairs T-G and hmU-G mismatches by glycosylating T and hmU in these situations to initiate base-excision repair.
* Recognizes 5hmC-G after the action of TET and initiates base-excision repair to remove the 5hm, acting as an epigenetic eraser

Question 15

Tet dioxygenase diagrams

Answer 15

Question 16

TET1

Answer 16

Two isoforms:

Full length is virtually restricted to early embryonic states and primordial germ cells.

The shorter TET1 isoform is expressed in most somatic tissues.

Question 17

TET mechanism

Answer 17

The His-His-Asp motif is highly conserved and is necessary for iron(II) interaction and catalysis

Question 18

TET2

Answer 18

Three isoforms, all of which arise from different promoters. Expressed in early embryogenesis as well as in hematopoietic cells, where they are important for differentiation.

Question 19

TET3

Answer 19

Three isoforms, one of which occurs only in oocytes and the one cell stage of the zygote and disappears by the two cell stage.