Lecture 7 - Transcription in Eukaryotes, Regulation, and Epigenetics Flashcards
what are the differences of eukaryotic transcription compared to prokaryotes?
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
what genes does RNA Pol 1 transcribe?
most rRNA genes
what genes does RNA Pol 2 transcribe?
protein coding genes
what genes does RNA Pol 3 transcribe?
tRNA, 5S rRNA, structural genes for RNA
what else does RNA Pol require for mRNA transcription?
transcription factors unlike transcription in prokaryotes
what is TBP?
used in initiation; TBP is TATA binding protein which recognizes the TATA box
what is TF2A?
initiation; stabilizes binding of TBP and TF2B to promoter
what is TF2B?
initiation; binds to TBP, then recruits TF2F-Pol 2 complex
what is TF2E?
initiation; recruits TF2H; has ATPase and helicase properties
what is TF2F?
initiation; binds to Pol 2 and binds to TF2B, it prevents binding of Pol 2 to other sequences
what is TF2H?
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
what happens during the assembly of RNA polymerase at promoter? which enzymes involved?
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
what is CTD?
CTD is the carboxyl terminal domain which is were RNA Pol2 starts transcribing after it is phosphorylated by TF2H
What happens to RNA Pol 2 during elongation?
elongation factors bind to RNA Pol2 which helps it proceed with transcription
what happens at termination of RNA Pol2?
Termination occurs by binding of termination factors that remove elongation factors from RNA Pol 2; also it gets dephosphorylated
Do transcribed genes or silent genes get repaired more often?
transcribed genes repaired more often because they are useful
How is TF2H part of the repair process?
TF2H can recruit the NER or nucleotide excision repair complex at a lesion. genetic repair defects are associated with TF2H defects
How is DNA packed?
DNA is packed into nucleosomes and chromatin using histones which are positively charged.
how can nucleosomes regulate gene expression?
nucleosomes on top of a promoter site prevents transcription
in what ways can activator proteins influence unpacking or packing (transcription) of DNA?
activator proteins such as chromatin remodeling complexes and histone modifying proteins (acetylase) regulate access to DNA
What can repressor proteins do for unpacking and packing DNA?
repressor proteins can attract histone modifying proteins such as deacetylases.
how does histone acetylation affect binding to DNA?
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
what happens when a phosphate group is added to an acetylated histone tail?
gene expression occurs because the negative charge from the histone will weaken the histones interaction with negatively charged DNA
what is the function of histone deacetylase and methyltransferase?
gene silencing and acts as a repressor for gene expression
what is combinatorial control and how does this play a role in eukaryotic gene expression?
combinatorial control is a group of proteins working together to determine gene regulation
How do you get differnet types of cells?
add a regulatory protein. 2^n = # of different types of cells
how can expression of many genes be activated at the same time?
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
what are the different forms of post-transcriptional regulation?
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
what is a riboswitch?
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
how can untranslated mRNA regions regulate translation?
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
what are microRNAs?
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
what are RISCs?
RISCs are RNA-induced silencing complex proteins that join with miRNA to silence mRNA translation
what is RNA interference?
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
what is siRNA?
siRNAs are small interfering RNAs that bind with RISCs to find other mRNAs to degrade
what does epigenetics mean?
epigenetics mean that they are heritable genetic modifications that doesn’t affect the sequence
how is regulation of gene expression passed to the offspring?
changes to DNA sequence affecting the promoters and chemical modifications that dont change the sequences; can be reversible
what the 3 mechanisms that are involved in epigenetic gene expression?
DNA methylation, modification of histones, non protein coding RNAs
what is DNA methylation?
repression of near by genes and can also mediate genomic imprinting
what is epigenetic histone modification?
modification of histones in chromatin to allow or not allow access to DNA that is to be transcribed
what do non coding proteins have to do with epigenetics?
ncRNAs can inhibit gene expression such as miRNAs
what creates a yellow mouse in terms of methylation and its DNA?
if the gene is methylated then it will be black, if not then it will be yellow
Can the environment affect epigenetics?
Yes it can, mice given supplements were darker in color so they were methylated
does methylation change over time?
yes, in twins it has been shown. this is why twins can have same genetic code but not the same features
what else can methylation affect?
memory, materal behavior of rats (no methylation = higher care mothers; methylation = lower care)
what is the correlation between maternal care and methylation?
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
