Lecture 24

Front 1

Chromatin

Back 1

DNA-protein (histone) complex

core histones

Hint 1

H2A, H2B, H3 and H4

Front 2

Describe the 10-nm fiber/nucleosome

Back 2

DNA helix is wrapped around an octamer of core histones (2 of each)

nucleosome fiber is colied into a thicker structure

Hint 2

30-nm fiber

Front 3

Higher order structures

Back 3

additional levels of packaging

Front 4

Cis-acting elements

Back 4

1. promoter
2. Promoter proximal elements
3. enhancers

Hint 4

1. has TATA box, which is binding site for TBP (TATA binding protein)
2. found upstream TATA box
3. distance-independent; upstream of downstream; orientation independent

Front 5

UAS

Back 5

In yeast, enhancers are referred to as upstream activation sequences (UAS)

Front 6

Trans-acting factors

Back 6

FUNCTION: assist RNA polymerase with initiation of transcription
1. Basal (or general) transcription factors
2. regulatory transcription factors
3. Mediator
4. Coactivators
5. Corepressors

Hint 6

1. Part of the holoenzyme that bind the promoter (TFII is their abbreviation)
2. bind to enhancers away from the promoter region. Much more specific than basal TFII and they regulate a smaller subset of genes
3. large protein complex that links regulatory TFII to enhancers and basal TFII/RNA poly complex to the promoter (helps to regulate transcription factors)
4. Unlike TFIIs, have no DNA binding domain, but like TFIIs help to enhancer transcription. Bind to reg. TFII that are bound to enhancer to facilitate transcription
5. Like coactivator, but serve opposite function: they have a negative affect on transcription once they bind to a bound reg. TFII

Front 7

eurochromatin

Back 7

more loosely packed and active portions of chromatin; accessible transcription factors; Less DNA methylation; activation modifications of histones (H4 acetylation, H3 lysine 4 methylation)

heterochromatin

Hint 7

more tightly/densely packed and inactive portions; inaccessible to transcription factors; More DNA methylation; Inactivating modifications of histones (H3 lysine 9 methylation)

Front 8

Yeast Gal system (genes)

Back 8

1. Galactose present
2. Galactose not present
3. Coordinate control

Hint 8

1. Gal 7, 10, 1 and 2 expressed
2. Gal 7, 10, 1 and 2 not expressed
3. Use shared enhancers and UAS

Front 9

Yeast Gal system (proteins)

Back 9

1. Galactose present
2. Galactose not present
2.5. Galactose interaction...
3. Activator is bound to...

Hint 9

1. Gal 4 (activator) can activate genes
2. Gal 80 blocks Gal 4 and prevents activation of genes
2.5. Gal3 binds galactose and this complex binds gal80, removing it from gal4
3. UAS sites

Front 10

Compare activators in Euk. (yeast) and Prok.

Back 10

1. CAP
2. Gal4

Hint 10

1. cannot bind to DNA without cAMP. Its regulated step: DNA binding (to allow RNA poly to bind and transcribe)
2. always bound to DNA. Regulated step: exposing the activation site (because gal80 is bound to it so it cannot activate transcription)

Front 11

Regulatory Transcription Factors (General)

Back 11

1. DNA binding domain
2. Activation domain
3. Optional: hormone receptor domain; dimerization domain

Hint 11

1. Bind enhancer

Front 12

Regulatory Transcription Factors (as dimers)

Back 12

1. Myc and Max
2. Myc/Max
3. Max/Max

Hint 12

1. Always act as dimer to regulate
2. HETERODIMER: Activator because Myc has activator domain
3. HOMODIMER: Repressor because no activation domain

Front 13

How do transcription factors activate transcription? (part one)

Back 13

Direct interaction with basal transcription apparatus

Front 14

How do transcription factors activate transcription? (part two)

Back 14

Open up chromatin to make it more accessible to RNA Poly II homoenzyme

Front 15

How do transcription factors activate transcription? (part two.one)

Back 15

1. Chromatin remodeling

Hint 15

1. "Chromatin remodeling complex"-pushes/slides nucleasome and exposes promoter

Front 16

How do transcription factors activate transcription? (part two.two)

Back 16

2. Post-translational histone modifications

Hint 16

2. Change way the histones interact by loosening and tightening chromatin (Methylation, acetylation, phosphorylation). Do this for each of the histones in the octamer

Front 17

How do transcription factors activate transcription? (part two.three)

Back 17

3. Histone variants

Hint 17

3. Replace core histone with a variant and therefore the properties of the histone and octamer (like charge), and how it interacts

Front 18

Regulation of gene expression on the DNA level (example one)

Back 18

DNA methylation, acetylation, Phosphorylation

Hint 18

example 1: DNA is negative, acetylation (adding negative acetyl groups) yields repulsion of octamers, which loosens or tightens packaging

Front 19

Regulation of gene expression on the DNA level (example two)

Back 19

DNA methylation, acetylation, Phosphorylation

Hint 19

example 2: Acetylation creates binding sites for other proteins (other regulatory proteins that can repress or activate)

Front 20

Regulation of gene expression on the DNA level (example three)

Back 20

Insulators

Hint 20

example 3: Enhancer-blocking insulator (insulator blocks access to some genes)

Front 21

Regulation of gene expression on the DNA level (example four)

Back 21

Insulators

Hint 21

example 4: Barrier insulators (inactivity of heterochromatin can spread unless in the presence of insulator, which stops the spread)

Front 22

Regulation of gene expression on the translational level (example five)

Back 22

Inhibition of translaion by MicroRNAs (miRNAs)

Hint 22

miRNA gene-->txn-->hairpin loop of RNA transcript--> dicer-->~22nts miRNA-->bind 3'-UTR of target gene and imperfectly base pairing--> inhibits translation

Front 23

Regulation of gene expression on the translational level (example six)

Back 23

Inhibition of translaion by Silencing./ Short interfering RNAs (siRNAs)

Hint 23

siRNA ds RNA transcript-->dicer-->siRNAs-->one side of ds siRNA binds to RNA induced silencing complex (RISC)-->this complex binds to target mRNA with perfect base pairing--> induced degradation of mRNA

Front 24

Regulation of gene expression on the translational level (example six)

Back 24

Inhibition of translaion by Silencing./ Short interfering RNAs (siRNAs)

Hint 24

siRNA mediate transcriptional gene silencing by directing heterochromatin formation to silence genes (USED TO SILENCE REPETITIVE GENES)