16.4 eukaryotic regulation Flashcards
What are the two major differences from prokaryotes?
- Eukaryotes have DNA organized into chromatin (complicates protein-DNA interaction)
- Eukaryotic transcription occurs in nucleus while translation occurs in the cytoplasm
- amount of DNA involved in regulating eukaryotic genes much larger
general transcription factors
necessary for the assembly of a transcription apparatus and recruitment of RNA polymerase 2 to a promoter
TFIID recognizes ______ sequences
After TFIID binds, what 5 TF’s bind? (along wth many TADs)
This initiation complex can initiate synthesis and what level?
TATA box sequences
TFIIE, TFIIF, TFIIA, TFIIB, and TFIIH
basal
specific transcription factors
act in a tissue- or time-dependent manner to stimulate higher levels of transcription than the basal level
What does each specific transcription factor consist of?
a DNA binding domain and a separate activating domain
What does the activating domain interact with?
The transcription apparatus; these domains are independent in the protein
Promoters
Form the binding sites for general transcription
what do promoters mediate?
the binding of RNA polymerase 2 to the promoter
enhancers
the binding site of the specific transcription factors
How do enhancers work?
act over large distances by bending DNA to form loop to position enhancer closer to promoter
What doe coactivators and mediators do?
bind to transcription factors and bind to other parts of the transcription apparatus
Are mediators essential to all transcription factors?
Some, not all
The number of coactivators is ____ compared to number of transcription factors because …
small; the same coactivator can be used with multiple TF
Virtually all genes that are transcribed by RNA polymerase 2 need the same or different suite of general factors to assemble an initiation complex?
the same
Ultimate level or transcription depend on what?
specific transcription factors that together make up the transcription complex
What is the eukaryotic chromatin structure?
DNA wound around histone proteins to form nucleosomes
How do nucleosomes and histones complicate the process of transcription?
restricts access of the transcription machinery to the DNA
Chromatin structure is ______ modulated to allow transcription
selectively
epigenetic alterations
alterations in chromatin structure are thought to be the basis - heritable changes in phenotype not due to changes in DNA sequence
Epigenetic alterations must persist in the absence of the ____ ______, and must be ____ through cell division
invading stimulus, inherited
What are the two chromatin modifications?
DNA methylation and X chromosome inactivation
DNA methylation
high levels of DNA methylation correlate with inactive genes
allele specific gene expression seen in genomic imprinting is at least partially due to DNA methylation
X chromosome inactivation
mammalian females inactivate one X chromosome as a form of dosage compensation
Long noncoding RNA called ______ coats the entire inactive x chromosome, leading to histone modification
X inactivation specific transcript (Xist)
How many histones can be modified?
4
(histone modification)
in general ____ is correlated with active sites of transcription
acetylation
Some transcription coactivators have been shown to be ______ . Transcription is increased by…
histone acetylases (HATs); removing higher order chromatin structure that would prevent transcription
Histone deacetylases (HDACs)
remove acetyl groups from histones
Gene expression can be controlled after transcription with:
-small rnas
-alternative splicing
rna editing
mrna degradation
lin 4 alters ___ ____ in C. elegans
developmental timing
lin 4 does not encode a protein product, instead, it encodes…
two small RNA molecules
miRNA production begins with RNA pol ___ producing a transcript called ______
2; pri-miRNA
lin 4 RNA acts as a ____ ____ of an mRNA
transcriptional repressor
miRNA folds back on itself to form a stem and loop structure which is cleaved by Drosha to form ____
pre-miRNA
pre miRNA exported from the nucleus and cleaved by ______ to produce a short double stranded RNA containing the miRNA
Dicer
(RNA induced silencing complex)
miRNA loaded into a protein complex called an _____
RNA induced silencing complex (RISC)
(RNA induced silencing complex)
RISC includes the RNA binding protein ___, which interacts with the miRNA
Ago
(RNA induced silencing complex)
RISC is targeted to _____ the expression of genes based on sequence complementarity to the miRNA
- complementary region usually in ___ untranslated region of genes
repress; 3’
siRNA
