chromosome structure: epigenetics

prokaryote DNA packaging levels

2 levels

2 levels of prokaryote DNA packaging

1. looped domains

2. supercoiling

looped domains

each loop is held together by DNA binding proteins

related genes are usually located in the same loop so they are usually expressed together

supercoiling

happens in loops

more condensed DNA fits into smaller space

topoisomerase active here

topoisomerase

relax/increase supercoiling

DNA girase

a type of topoisomerase

eukaryote number of levels of DNA packaging

4 levels

4 levels of DNA packaging in eukaryotes

1. DNA double helix

2. nucleosome core of 8 histone molecules → beads on a string

3. chromatosome

4. chromatin = DNA + proteins

   1. chromosomes are condensed chromatin → contains DNA and proteins

specific steps to eukaryote DNA packaging

double stranded DNA → wraps around histones → nucleosomes → chromatin folding → 300 nm fiber wrapping/folding → 250 nm fiber → folding → chromosome

2 types of chromosomes

1. heterochromatin

2. euchromatin

heterochromatin

highly condensed throughout the cell cycle

• no gene expression → tightly packed DNA

• can be consticulative or facultative

consticulative

always condensed → centromeres/telomeres

faculative

condensed at certain times → activation and inactivation

euchromatin

less condensed when gene expression happens

• packaging changes during cell cycle

• when more loosely packed it allows x inactivation

centromeres

heterochromatin

• part of chromosome that attaches to spindle fibers

• required for proper segregation

• protein binding sites

• tightly packed → no gene expression

• highly repetitive DNA

telomeres

heterochromatin

• binding site for POT proteins

• single stranded overhang

• provide stability

• tightly packed → no gene expression

POT proteins

POT = protection of telomeres

prevents ends from degrading/sticking to other molecules

metaphase

where chromosomes are the most compact

histones

beads on a string → observable in low salt conditions

nucleosome

8 histones each with DNA wrapped around twice

linker DNA

the “string” between nucleosomes

nuclease

can only destroy linker DNA because histone proteins protect DNA wrapped around it

histones are positively charged

bind tightly with negatively charged DNA

• positive charge comes from amino acids

5 types of histones

H1

H2A

H2B

H3

H4

linker histone

H1

formation of a histone

2 of each type of H2A, H2B, H3, and H4

epigenetics

a recently developed field to study phenotypic variation because of differences in gene expression

heritable in body cells and offspring

influenced by the environment

chromatin structure is altered by chemical modifications on DNA and histones in epigenetics

modifications are reversible

level of packaging regulates expression

DNA modification

add a methyl group to cytosine to produce methyl cytosine

• adds to CPG island

• modifies both DNA strands

• ALWAYS CAUSES A DECREASE IN EXPRESSION

CPG island

sequence of C and G nucleotides

4 different types of histone modification

1. phosphorilation

2. methylation

3. acetalation

4. ubiquitin

3 steps to make methylated DNA heritable

1. methylated DNA is replicated

2. DNA molecules are hemimethylated and DNA methyltransferase brings new methyl groups

3. both strands are methylated

hemimethylation

methylated template strand and unmethylated new strand

DNA methyltransferase

enzyme in G2 of cell cycle that sees unmethylated DNA as a mistake and transfers methyl groups to the unmethylated new strand

DNA methylation decreases expression 2 ways

1. methyl groups bind to the major grove and prevent transcription factors from binding

2. methyl groups create binding sites for histone deacetylase enzyme

transcription factors

important for gene expression

histone deacetylase enzyme

removes acetyl groups from histones and leads to tighter histone-DNA interactions and a more condensed structure so less gene expression

histone acetylation

adds acetyl groups to DNA → less condensed structure → increased expression

histone methylation

creates binding sites for transcription factors

• creates marks for increase or decrease in expression

• increase vs decrease depends on which histone the mark shows up on

histone modification is heritable

less understood than DNA epigenetic inheritance but we know that we need these proteins throughout the cell cycle so the packaging proteins must also be replicated in S phase

honey bees epigenetics

queen/worker bees come from identical eggs

• queens: bigger size, fertile, job is to reproduce

• workers: smaller size, sterile, job is to take care of the hive

differences come from their diet → queen bees eat royal jelly → less DNA methylation

x inactivation epigenetics

example of facultative heterochromatin

• caused by histone modification → creates differences in x inactivation center

  • xist

  • tsix

  • jpx

  • xite

x inactivation center

where x inactivation begins

xist and tsix

complementary m RNA

x-ist

controls inactivation of one x chromosome

codes for long RNA strand

• binds to where it was synthesized

• attracts proteins that methylate histones to decrease expression

tsix jpx xite

control keeping one x chromosome active

tsix

codes for RNA

complementary with x-ist

prevents x-ist binding on one chromosome

jpx

functions as RNA

xite

sustains tsix expression

genomic imprinting epigenetics

expression is determined by which parent the gene comes from

• gives different phenotypes in reciprocal crosses

• clusters of 3-2: some code for protein, others code for noncoding RNA

• we think this process is similar to x inactivation

• genetic conflict hypothesis

genetic conflict hypothesis

parents benefit from different expression