Chapter Nineteen: Gene Regulation in Eukaryotes Flashcards
what are at least five ways to regulate gene expression in a eukaryote
- transcription initiation
- transcription processing
- mRNA export from the nucleus
- translation of mRNA
- protein localization
- protein modification
compared to prokaryotes, eukaryotes have additional levels of complexity for controlling ___
gene expression
___ in eukaryotes often makes DNA unavailable to transcription machinery
chromatin structure
additional ___ processing events occur in eukaryotes
RNA
in eukaryotes, transcription occurs in the ___ and translation occurs in the ___
nucleus
cytoplasm
gene regulation controls ___ into hundreds of specialized cell types
cell differentiation
RNA pol I transcribes ___
RNA pol II transcribes ___
RNA pol III transcribes ___
rRNA genes
genes that encode proteins
tRNA genes and some small RNAs
DNA sequence that is usually directly adjacent to the gene, where RNA polymerase binds
promoter
promoters in eukaryotes often have a ___
TATA box
genes that are expressed at low levels all the time
housekeeping genes
genes that make cells unique, expression is cell or time specific
luxury genes
there are ___ cell types in humans
200
a regulatory site that can be far away from the gene
enhancer
enhancers are binding sites for ___
transcription factors
enhancers still function when moved to different positions relative to promoter because of ___
flexibility of DNA
a ___ can tell you the location and time of gene expression
reporter gene
three general reporter genes
- GFP
- LacZ
- luciferase
GFP is ___ and has ___ sensitivity
fluorescent
high
lacZ is ___ and has ___ sensitivity
chromatogenic
medium
luciferase is ___ and has ___ sensitivity
luminescent
low
transcription factors are ___ that act in ___ to control ___
proteins
trans
transcription initiation
transcription factors bind to ___ and ___
promoters and enhancers
transcription factors recruit ___ to influence transcription
other types of proteins
three types of transcription factors
- basal factors
- activators
- repressors
basal factors bind to ___ of protein-encoding genes
promoters
a complex of more than 20 proteins needed most of the time for transcription of eukaryotic genes
mediator complex
mediator complex bridges ___ and ___
RNA pol II and enhancer
activators are responsible for much of the ___ in levels of transcription of different genes
variation
activators stimulate recruitment of ___ and ___ to promoters
basal factors and RNA pol II
activators recruit ___ to open chromatin structure
coactivators
activator proteins have at least ___ functional domains
two
most DNA binding proteins are dimers
true/false
true
domain that binds to a specific enhancer
DNA binding domain
domain that binds to other proteins
activation domain
domain that allows an activator to interact with other proteins
dimerization domain
two domains that every activator has
DNA binding domain
activation domain
two examples of a DNA binding domain
- helix-turn-helix
- zinc finger
DNA binding domains fit within the ___ of DNA
major groove
dimerization domains are specialized for ___ interactions
polypeptide-polypeptide
multimeric proteins made of identical subunits
homodimers
multimeric proteins made of nonidentical subunits
heterodimers
repressor proteins suppress transcription initiation by recruiting ___
corepressors
two alternate functions of corepressors
- prevent RNA pol II complex from binding to promoter
- modify histones to close chromatin structure
the same transcription factor can play ___ roles in different cells
different
repressor proteins can act through competition with an ___
activator protein
interferes with the function of an activator
indirect repressor
histone ___ affects transcription
modifications
___ acetylate histone tails
histone acetyl transferase (HAT)
many transcription factor ___ are HATs
coactivators
histone acetylation ___ chromatin, which ___ gene expression
opens
favors
___ methylate histone tails
histone methyltransferase (HMT)
HMT can ___ or ___ transcription, some are ___ some are ___
activate or repress
coactivators
corepressors
modifications made by HATs and HMTs can be taken off by ___ or ___
histone deacetylases ot histone demethylases
in humans, ___ genes code for transcriptional regulatory proteins
2000, 10%
each regulatory protein can act on ___
many genes
each enhancer has binding sites with ___ affinities for activators and repressors
varying
call-type specific transcription is achieved by changes in ___
transcription factors
the function of trans acting proteins changes by ___, ___, or ___
allosteric interactions, modification of transcription factors, or transcription factor cascades
tool for finding all target gens of a particular transcription factor within the entire genome of a. particular cell
chromatin immunoprecipitation-sequencing (ChIP-Seq)
two methods to see if a protein binds to DNA
DNA foot printing
ChIP-Seq
sequences located between an enhancer and a promoter that block access to the promoter
insulators
insulators organize genomic DNA into ___
loops
human insulators bind ___ to form loops called ___
CTCF proteins
topologically associating domains (TADs)
enhancers activate promoters located in the ___ loop
same
scientists detect TADs through ___
chromatin conformation capture
correct enhancer promoter reactions require specific TAD ___
boundaries
mutations that disrupt TAD boundaries can alter ___
genes expression
one form of ___ is due to deletion of TAD boundary between EPH4A and IHH genes
polydactyly
post transcriptional regulation can occur at the level of ___ and ___
RNA and protein
three mechanisms of RNA regulation
splicing, stability, and localization
three mechanisms of protein regulation
synthesis, stability, modification, localization
sex-specific courting behavior is controlled by male-specific ___
Fru-M
Fru-M and Fru-F are produced by ___ of the ___ primary transcript
alternative splicing
same
___ and ___ are expressed in females and clock use of a splice acceptor site, so the use of different ___ leads different Fruits proteins in males and females
Tra and Tra2
exons
control of translation often occurs at ___
initiation
the small subunit of the ribosome recognizes a complex structure built around the ___ of the mRNA
5’ cap
eIFG protein binds to ___ at the poly-A tail to circularize mRNA
poly-A binding protein (PABP)
mRNA translation can be regulated in response to ___ in the environment
nutrients
presence of nutrients and growth factors int he environment leads to ___ of 4E-NP1
phosphorylation
translation can also be controlled through ___ length
poly-A tail
longer poly-A tails bind PABP ___ efficiently than shorter tails, so the translation initiation complex forms ___ efficiently
more
more
upstream ORFs that begin with a decoy AUG and encode small peptides that have no function
decoy ORF
the decoy ORF mechanism is used in the drosophila ___ pathway
sex differentiation
ribosomal profiling measures translation ___
efficiency
the amount of gene product does not always correlate with the amount of ___
mRNA
ribosome profiling allows researchers to observe ___ of ribosomes on mRNA
positions
specialized RNAs that prevent expression of specific genes through complementary base pairing, 21-30 nt long
small RNAs
small RNAs regulate mRNA ___ and ___
stability and translation
three classes of small RNAs
- micro-RNAs (miRNAs)
- small interfering RNAs (siRNAs)
- piwi-interacting RNAs (piRNAs)
miRNAs target ___; function to ___ translation and ___ mRNAs
mRNA
block
destabilize
siRNAs target ___ and ___; function to ___ translation/___ mRNA and recruit histone modifying enzymes to DNA resulting in ___
mRNA and nascent transcripts of chromosomal regions destined to become heterochromatin
block
destabilize
heterochromatin formation
piRNAs target ___; function to ___ TE mRNA and facilitate histone modifications that inhibit ___
transposable element transcripts and promoters
degrade
transposable element transcription
most miRNA are transcribed by ___
RNA pol II
two ways miRNAs can down regulate expression of target genes
- when complementary is perfect, target mRNA is degraded
- when complementary is imperfect, translation of mRNA target is repressed
siRNAs are useful experimental tools to selectively ___ of target genes through ___ interference
known down expression
RNA
piRNAs minimize ___
transposable element mobilization
the ___ of X chromosomes determines sex in drosophila
number
maleness is brought about by the present of ___ X chromosome
one
two X chromosomes are required to activate transcription of the ___ gene in early drosophila embryogenesis
Sxl
Sxl transcription influences sex through these three pathways
- male vs. female appearance and behavior
- development of germ cells as eggs or sperm
- dosage compensation
sex lethal (Sxl) gene encodes an RNA binding protein that controls the ___ of RNA targets
alternative splicing
Sxl transcription is necessary for ___ development
female
