dna modification stuff

hyperacetylated histones

associated with _ transcribed genes

_ is responsible

actively, histone acetyltransferase

acetylation modifes _ residues of the histone, which is a positively charged on the negatively charged DNA backbone

lysine

_ can function over long distances on chromatin

enhancers

_ specifically block such promiscuous enhancer behavior

insulator proteins

promiscuous enhancement is blocked by _

insulator proteins

enhancer-blocking insulators prevent _

enhancer activation

_ prevent enhancer activation

enhancer-blocking insulators

insulator proteins insulate various _ from the activation by various enhancers

promoters

enhancer with enhancer binding protein bound to it

evolved to control promoter 2, but other nearby promoters like promoter 1 can be activated by that enhancer

_ prevents promiscuous activation of promoters by an enhancer - prevents folding so the enhancer can’t activate another promoter

enhancer blocking insulator

enhancers interact with proteins that promote assembly of the _

transcription initiation complex

_ interact with proteins that promote assembly of the transcription initiation complex

enhancers

enhancer activity can be blocked by _

insulators

_ activity can be blocked by insulators

enhancer

enhancers can also recruit proteins that modify _ structure

chromatin

_ can also recruit proteins that modify chromatin structure

enhancers

enhancers can also recruit proteins that modify chromatin structure:

_ of histones

_ of histones

_ of DNA

acetylation, methylation, methylation

enhancers can also recruit proteins that modify chromatin structure:

acetylation of _

methylation of _

methylation of _

histones, histones, DNA

_ fundamental regulatory modifications of histones - fundamental because we understand best because they were the first discovered:

_ and _ of histones

two, acetylation, methylation

_ are the fundamental proteins of nucleosomes and fundamental to the formation of chromatin

histones

histones are the fundamental proteins of _ and fundamental to the formation of _

nucleosomes, chromatin

_ and _ have direct impact on the activation of genes

acetylation of histones, methylation of histones

methylated DNA tends to be _

inactive

methylation of DNA drives the chromatin into an _ structure (_ instead of _)

inactive, heterochromatin, euchromatin

the histones form the nucleosome complex, DNA is wound around, the _ of the different histones projects out away from core of histones, makes the _ region available for modification

amino terminus, amino terminal

_ of the different histones are critical for methylation and acetylation

amino terminal tails

modified _ protrude from the nucleosome

histone tails

the beads on a string represent _ wound around nucleosomes

DNA

chromatin remodeling exposes _

regulatory sequences

_ exposes regulatory sequences

chromatin remodeling

_ modifies histone lysine residues which are positively charged

acetylation

acetylation modifies histone _ residues which are positively charged

lysine

acetylation modifies histone lysine residues which are _ charged

positively

DNA is _ charged

negatively

modifications either increase the affinity of the histones to DNA, in which case they _ the activity of genes in that region

or _ the interaction of histones with the DNA - allows nucleosomes to be shoved around by enzymes

inhibit, loosen

a promoter element wound tightly around the nucleosome complex is _

modifications of nucleosome complex can allow nucleosome to be pushed out of way/become exposed so it can become _

inactive, active

one of the first modifications observed was acetylation of the _ residues in the amino terminal tail of the histones

lysine

one of the first modifications observed was acetylation of the lysine residues in the _ of the histones

amino terminal tail

acetylation of DNA drives the _ of the chromatin - drives into a _ formation, which is _

relaxation, euchromatin, active

_ of DNA drives the relaxation of the chromatin - drives into a euchromatin formation, which is active

acetylation

acetylation means lysine is no longer _, it _ the hold of that particular nucleosome on the DNA, makes it able to form _ structure and accessible to _

charged, relaxes, euchromatin, transcription

_ means lysine is no longer charged, it relaxes the hold of that particular nucleosome on the DNA, makes it able to form euchromatin structure and accessible to transcription

acetylation

_ allows DNA to pack tightly and prevents transcription

deacetylation

deacetylation allows DNA to pack tightly and prevents _

transcription

_ lysine binds tightly to the negatively charged DNA backbone

unmodified

_ histones

associated with actively transcribed genes

histone acetyltransferases responsible

hyperacetylated

_ histones

associated with inactive genes

histone deacetylases

hypoacetylated

hypoacetylated histones

associated with _ genes

uses _

inactive, histone deacetylase

_ neutralizes the positive charge of lysine, reducing the affinity for the negatively charged DNA backbone

acetylation

acetylationn eutralizes the positive charge of _, reducing the affinity for the negatively charged DNA backbone

lysine

histone _ uses histone acetyltransferase (HAT) and produces open chromatin or euchromatin

acetylation

histone acetylation uses _ and produces _ chromatin or _

histone acetyltransferase (HAT), open, euchromatin

histone _ uses histone deacetylases and produces closed chromatin or heterochromatin

deacetylation

histone deacetylation uses _ and produces _ chromatin or _

histone deacetylases, closed, heterochromatin

depending upon which _ you modify in histones, can either have methylation inhibit transcription or active transcription

amino acid

methylation of lysine _ on histone _ correlates with active transcription

4, 3

methylation of lysine 4 on histone 3 correlates with _ transcription

active

methylation of lysine _ of histone _ correlates with inactive regions of chromatin

9, 3

methylation of lysine 9 of histone 3 correlates with _ regions of chromatin

inactive

methylated cytosine is associated with _ chromatin

inactive

association of lysine 9 methylated histones with DNA promotes recruits enzymes that methylate _, which locks down the chromatin into heterochromatin state

cytosine

the methylation of _ locks down the chromatin into a heterochromatin state

cytosine

without methylation of cytosine, histones and DNA are _ accessible to transcription, the chromatin is _ or _, and the gene is switched _

more, active, open, on

with methylation of cytosine, the DNA and histone are _ accessible to transcription, the chromatin is _ or _, and the gene is switched _

less, condensed, closed, off

the function of the _ is to recruit RNA polymerase and drive expression of the gene

promoter

_ drive local concentration of cytosine residues

CpG islands

local runs of CpG dinucleotides are frequently found in the _ of eukaryotic genes

promoters

local runs of _ are frequently found in the promoters of eukaryotic genes

CpG dinucleotides

local runs of CpG dinucleotides are frequently found in the promoters of _ genes

eukaryotic

CpG islands:

the _ residues are a frequent target of methylation - to silence genes

cytosine

CpG islands:

the cytosine residues are a frequent target of _ - to silence genes

methylation

eukaryotes _

sequence on one strange that is C followed by G with phosphate in between

on other strand, have C followed by a G with phosphate in between

drives a local concentration of cytosine residues

CpG islands

there is a mechanism to maintain methylated DNA during replication - maintain methylation states from _ to _ cell

important in development during first trimester where a single cell becomes an embryo through cell division

parent, daughter

the two big phases of pregnancy:

first trimester - rapid cell _ with development, lay down tissues and organs

rest of pregnancy - _

division, growth

during replication of methylated DNA, the new chromatin _ methylated because can’t incorporate methylated C into DNA

is not

if the chromatin in the cell undergoes changes in methylation of the DNA during development, it _ maintained

applies to Dutch famine embryos

is

when the cell undergoes division, new chromatin _ methylated because can’t incorporate methylated cytosine into DNA

is not

in cell division, the parent strand has a _ that recruits enzymes to methylate the daughter strand cytosine

methyl signal

histones in the nucleosomes:

histone modifications can be _ using a similar mechanism to DNA methylation replication - modifications in the parent cell _ passed on in the daughter cell

maintained, can be

dna methylation across generations

_ gene - affects coat color

mixture of yellow and black pigment (gray color) = _ gene

yellow mice w/o black pigment, obese mice = _ gene

agouti, wild type, dominant mutated

dominant mutation of agouti gene has significant effect on _ and _

coat color, energy storage

dominant mutated agouti gene mice become particularly obese if feed a _ diet - if provide this as control diet to mother, progeny are _ and _

if add _ to the diet, drives synthesis of _ which is a methyl donor, in the mutant mice, reverts to the wild-type phenotype

high fat, obese, yellow, folate, adenosylmethionine

agouti gene in wild type form, end up with a _ mouse

normal gray

agouti gene plays a large role in establishing hair follicle pigments and typically becomes _ in the adult (wild-type)

develop coat color properly, but they don’t become obese unless agouti gene continues to be _

inactivated, expressed

if provide mother with plenty of folate in diet, drives the synthesis of _

the promoter of the agouti gene in developing embryos becomes _, preventing the development of _

adenosylmethionine, methylated, obesity

need of the male for reproduction is to

pass on genome to next generation

need for female for reproduction:

pass on genome to next generation

has to _ to pass genome to next generation

survive

conflict between male and female during reproduction:

both male and female want to pass genome onto the next generation, but the female has to _

survive

insulin like growth factor 2 is the expressed allele inherited from the _ side

paternal

_ is the expressed allele inherited from the paternal side

insulin like growth factor 2

H19 is the expressed allele inherited from the _ side

maternal

_ is the expressed allele inherited from the maternal side

H19

insulin like growth factor 2 promotes _

growth

for insulin like growth factor 2 to be expressed in the developing embryo, has to be inherited from _, because the allele in _ is inactivated in the gametes

dad, mom

H19 is essential for _ of the embryo

survival

for H19 to be expressed in the developing embryo, it has to be inherited from _, because the allele in _ is inactivated in the gametes

mom, dad

imprinted genes

which of the two alleles that are inherited from mom and dad at fertilization is expressed is a function of _

which parent donated the allele

with imprinted genes, inherit both genes from mom and dad, they are not _, they are on _

sex linked, autosomes

for _ genes, which of the two alleles that are inherited from mom and dad at fertilization is expressed is a function of which parent donated the allele

imprinted