Lecture 7 - Transcription in Eukaryotes, Regulation, and Epigenetics

Question 1

what are the differences of eukaryotic transcription compared to prokaryotes?

Answer 1

bacteria have 1 RNA Pol while eukary have 3; bacterial RNA Pol can initiate without anything while eukary needs transcription factors; eukary DNA is packed into histones and chromatin; regulatory proteins can act on a gene many nucleotides away

Question 2

what genes does RNA Pol 1 transcribe?

Answer 2

most rRNA genes

Question 3

what genes does RNA Pol 2 transcribe?

Answer 3

protein coding genes

Question 4

what genes does RNA Pol 3 transcribe?

Answer 4

tRNA, 5S rRNA, structural genes for RNA

Question 5

what else does RNA Pol require for mRNA transcription?

Answer 5

transcription factors unlike transcription in prokaryotes

Question 6

what is TBP?

Answer 6

used in initiation; TBP is TATA binding protein which recognizes the TATA box

Question 7

what is TF2A?

Answer 7

initiation; stabilizes binding of TBP and TF2B to promoter

Question 8

what is TF2B?

Answer 8

initiation; binds to TBP, then recruits TF2F-Pol 2 complex

Question 9

what is TF2E?

Answer 9

initiation; recruits TF2H; has ATPase and helicase properties

Question 10

what is TF2F?

Answer 10

initiation; binds to Pol 2 and binds to TF2B, it prevents binding of Pol 2 to other sequences

Question 11

what is TF2H?

Answer 11

initiation; has protein kinase activity = phosphorylates Pol 2 at CTD by adding phosphate groups that allow Pol 2 to separate from transcription factors, helicase activity = unwinding;recruits nucleotide excision repair proteins

Question 12

what happens during the assembly of RNA polymerase at promoter? which enzymes involved?

Answer 12

TBP along with other proteins bind to the TATA box to form a multiprotein complex, then TF2H acts as helicase and unwinds the DNA at the promoter

Question 13

what is CTD?

Answer 13

CTD is the carboxyl terminal domain which is were RNA Pol2 starts transcribing after it is phosphorylated by TF2H

Question 14

What happens to RNA Pol 2 during elongation?

Answer 14

elongation factors bind to RNA Pol2 which helps it proceed with transcription

Question 15

what happens at termination of RNA Pol2?

Answer 15

Termination occurs by binding of termination factors that remove elongation factors from RNA Pol 2; also it gets dephosphorylated

Question 16

Do transcribed genes or silent genes get repaired more often?

Answer 16

transcribed genes repaired more often because they are useful

Question 17

How is TF2H part of the repair process?

Answer 17

TF2H can recruit the NER or nucleotide excision repair complex at a lesion. genetic repair defects are associated with TF2H defects

Question 18

How is DNA packed?

Answer 18

DNA is packed into nucleosomes and chromatin using histones which are positively charged.

Question 19

how can nucleosomes regulate gene expression?

Answer 19

nucleosomes on top of a promoter site prevents transcription

Question 20

in what ways can activator proteins influence unpacking or packing (transcription) of DNA?

Answer 20

activator proteins such as chromatin remodeling complexes and histone modifying proteins (acetylase) regulate access to DNA

Question 21

What can repressor proteins do for unpacking and packing DNA?

Answer 21

repressor proteins can attract histone modifying proteins such as deacetylases.

Question 22

how does histone acetylation affect binding to DNA?

Answer 22

non acetylated histones have a positive charge that have a high affinity to the negatively charged DNA, but when the histones are acetylated then it weakens the interactions between DNA

Question 23

what happens when a phosphate group is added to an acetylated histone tail?

Answer 23

gene expression occurs because the negative charge from the histone will weaken the histones interaction with negatively charged DNA

Question 24

what is the function of histone deacetylase and methyltransferase?

Answer 24

gene silencing and acts as a repressor for gene expression

Question 25

what is combinatorial control and how does this play a role in eukaryotic gene expression?

Answer 25

combinatorial control is a group of proteins working together to determine gene regulation

Question 26

How do you get differnet types of cells?

Answer 26

add a regulatory protein. 2^n = # of different types of cells

Question 27

how can expression of many genes be activated at the same time?

Answer 27

glucocorticoid receptors bind to the promoter of many genes and when glucocorticoid hormone binds to the receptor, it activates all those genes; similar to an operon, but genes are located everywhere

Question 28

what are the different forms of post-transcriptional regulation?

Answer 28

alternative splicing (splicing same gene different ways); riboswitches (short sequences of RNA that change shape when interacting with metabolites); regulation of translation initiation by untranslated mRNA regions; repressors can bind to the 5' CAP to prevent translation; miRNA

Question 29

what is a riboswitch?

Answer 29

riboswitch is a short sequence of RNA that change shape when interacting with metabolites which can regulate translation or transcription; EX - guanine binds to riboswitch and it changes shape to turn off transcription

Question 30

how can untranslated mRNA regions regulate translation?

Answer 30

RNA binding proteins can bind to the promoter region and act as a repressor to prevent the ribosome from attaching; some can also act as thermal sensors that change shape to allow protein to be made; binding of a small molecule to a riboswitch can also activate a sequence for translation; complementary or anti-sense RNA made by another gene can bind to the binding site

Question 31

what are microRNAs?

Answer 31

miRNAs are noncoding RNA. They regulate protein coding genes by binding to mRNAs and can degrade them; joins with RISCs so that they can degrade RNA or reduce translation of the specific mRNA

Question 32

what are RISCs?

Answer 32

RISCs are RNA-induced silencing complex proteins that join with miRNA to silence mRNA translation

Question 33

what is RNA interference?

Answer 33

RNA interference is a mechanism to prevent the translation of foreign DNA. When ds RNA is detected, a protein called Dicer is attracted and cuts it up into 23 NT pieces called siRNAs, then it's incorporated into the RISC protein and then it searches for complementary mRNA to degrade

Question 34

what is siRNA?

Answer 34

siRNAs are small interfering RNAs that bind with RISCs to find other mRNAs to degrade

Question 35

what does epigenetics mean?

Answer 35

epigenetics mean that they are heritable genetic modifications that doesn't affect the sequence

Question 36

how is regulation of gene expression passed to the offspring?

Answer 36

changes to DNA sequence affecting the promoters and chemical modifications that dont change the sequences; can be reversible

Question 37

what the 3 mechanisms that are involved in epigenetic gene expression?

Answer 37

DNA methylation, modification of histones, non protein coding RNAs

Question 38

what is DNA methylation?

Answer 38

repression of near by genes and can also mediate genomic imprinting

Question 39

what is epigenetic histone modification?

Answer 39

modification of histones in chromatin to allow or not allow access to DNA that is to be transcribed

Question 40

what do non coding proteins have to do with epigenetics?

Answer 40

ncRNAs can inhibit gene expression such as miRNAs

Question 41

what creates a yellow mouse in terms of methylation and its DNA?

Answer 41

if the gene is methylated then it will be black, if not then it will be yellow

Question 42

Can the environment affect epigenetics?

Answer 42

Yes it can, mice given supplements were darker in color so they were methylated

Question 43

does methylation change over time?

Answer 43

yes, in twins it has been shown. this is why twins can have same genetic code but not the same features

Question 44

what else can methylation affect?

Answer 44

memory, materal behavior of rats (no methylation = higher care mothers; methylation = lower care)

Question 45

what is the correlation between maternal care and methylation?

Answer 45

more maternal care means less methylation and vice versa; however, if mice who had high care and switched to low care ended up losing methylation of the glucocorticoid receptor gene