Transcriptional Regulation Eukaryotes

In addition to promoter sequences, eukaryotes also require _____ and _____ for initiation of transcription

Enhancers
Silencers

cis-acting sequence that increases level of transcription of specific genes

enhancer

cis-acting sequence that represses transcription of specific genes

silencer

Enhancer sequences can be bound by

activator proteins
repressor proteins
cofactors

Silencer sequences can be bound by

repressor proteins

What competes with activators and repressors for binding at enhancers?

cofactors and corepressors

Enhancers in yeast are called

upstream activator sequences (UAS)

Increases transcription rates by interacting directly or indirectly (from an enhancer) with basal factors at the promoter, responsible for much of the high levels of transcription of different genes

Activator protein (specific transcription factors)

What are three mechanisms how the activator proteins promote transcription

Stimulate recruitment of basal factors and RNA pol II to promoters
Stimulate activity of basal factors already assembled on promoters
Facilitate changes in chromatin structure

Sequence-specific domain of an activator protein that binds to the enhancer sequence

DNA binding domain

Domain of an activator protein that interacts with other transcriptional regulatory proteins/molecules

Activator domain

What are three mechanisms how transcriptional repressors reduce transcription

Bind to enhancer sequence

Binds to either domain of activator protein
Interfere with the basal transcription apparatus

GAL genes are not expressed until the presence of

galactose

What are the three regulatory proteins in GAL system

GAL4
GAL80
GAL3

Which regulatory protein in GAL system is a transcriptional regulator that binds to UAS sequence (enhancer)

GAL4

Maximal transcription of GAL genes happens when _____ is bound to a UASg

GAL4

Which GAL regulatory protein is a repressor that binds to the activation domain of GAL4

GAL80

When GAL80 is bound to GAL4, GAL4 does or does not activate transcription

Does not

Which GAL regulatory protein binds to GAL80 and and inhibits it’s interaction with GAL4?

GAL3

GAL3 binding to GAL80 is regulated by what total effector molecule?

Galactose

No galactose present:
GAL3 (active/inactive)
GAL80 (active/inactive)
GAL4 (active/inactive)
Transcription of GAL structural genes (on/off)

inactive
active
inactive
off

Galactose present:
GAL3 (active/inactive)
GAL80 (active/inactive)
GAL4 (active/inactive)
Transcription of GAL structural genes (on/off)

active
inactive
active
on

Galactose binds to which regulatory GAL protein

GAL3

The GAL system is an example of what level of gene expression regulation in eukaryotes

Transcriptional

Alternative splicing/Drosophila sex-determination is an example of eukaryotic gene expression at what levle?

Post-transcriptional

_____ ______ results in the generation of different isoforms (proteins) from a single gene

Alternative splicing

Four types of alternative splicing

Exon skipping
Alternative 3’ splice site
alternative 5’ splice site

Mutually exclusive exons

Protein in Drosophila sex-determination that is present and functional in males and females, but as separate isoforms. Alternatively spliced by Tra protein

Dsx (double-sex)

Protein in Drosophila sex-determination that is functional in females and non-functional in males. Alternatively spliced by Sxl and alternatively splices Dsx

Tra (transformer)

The signal of X-to-A ratio determines when the Drosophila will transcribe the _____ gene, and the late transcription makes it inactive in males.

Sxl (sex lethal)

If the Sxl and Tra genes lose function, flies develop into phenotypic

males

If the Dsx gene loses function, flies develop into phenotypic

intersex

Order of the genes in sex determination of Drosophila

Sxl
Tra
Dsx

The reason Sxl in males alternatively splices Tra in a non-functional way is a

Premature stop codon

The reason Tra in males alternatively splices Dsx in a non-functional way is a

Skipped exon

Posttranscriptional regulation that is triggered by double-stranded RNA (dsRNA) but mediated by small noncoding RNAs

RNA interference (RNAi)

Two classes of RNAi to know about

miRNA
siRNA

What protein recognizes and cleaves dsRNA into smaller fragments

Dicer

RISC stands for

RNA-Induced Silencing Complex

Once paired with RISC, (siRNA/miRNA) will make imperfect base pairing?

miRNA

Once paired with RISC (siRNA/miRNA) will make perfect base pairing?

siRNA

Imperfect base pairing with the target mRNA caused by miRNA causes

Silenced translation

Perfect base pairing with target mRNA by siRNA causes

Cleavage and degradation of mRNA

The base-pairing part of RNAi is usually in what region of target mRNAs

3’-UTR

Once paired with RISC, what happens to one strand of the two dsRNA strands?

Degraded

does miRNA or siRNA also have a pathway including RITS

siRNA

lncRNA stands for

long non-coding RNA

is miRNA or siRNA formed from single-stranded RNA that forms short hairpins of dsRNA?

miRNA

does miRNA or siRNA come from “it’s own distinct gene”

miRNA

does miRNA or siRNA come from cleavage of an RNA duplex (dsRNA)

siRNA

Combined effects of rate of transcription and the reate of mRNA degradation leads to mRNA having

steady state levels

What is the timer for mRNA in transport

shortening of polyA tail by exonuclease

All reasons for WHAT?
1.) less energy needed

2.) prevent activity in the wrong place
3.) facilitate macromolecules correctly
4.) fine-tuning of expression in space and time

Localize mRNA and not protein

does siRNA or miRNA target mRNA of the gene it came from

siRNA

Which comes first, slicer or dicer

Dicer

Is slicer or dicer part of the RISC complex

slicer

Which alternate splicing site would affect where the exon starts (may start too early or too late). May have a downstream frame effect that makes it end early as well

Alternate 5’ splice

Which alternate splicing affects where the codon stops? (Starts at the correct spot, but exon may be shorter or longer than usual)

Alternate 3’ splice

Activator proteins are also called

Specific transcription factors