1-15 Eukaryotic Transcription I Flashcards
With regard to medical application, what does transcription help us understand?
- Normal development (how the same DNA results in differentiation)
- How cells respond to signals and their environment
- The molecular basis of disease
- How to develop effective therapies and better diagnostics
In mRNA synthesis, what forms the phosphodiester bonds?
Ribonucleoside triphosphate (rNTP) precursors, NOT dNTP precursors.
How many different kinds of RNA polymerase do eukaryotes possess, and which one is most significant for eukaryotic transcription?
Three.
RNA polymerase II.
Does all RNA encode protein?
No. Many types of RNA are non-coding and involved in gene regulation.
How is transcription initiated?
- TATA-Binding Protein (TBP) binds to the TATA box, bending DNA
- TBP and other basal factors recruit RNA pol II to the promoter sequence to form the pre-initiation complex
- RNA pol II is phosphorylated, leaves promoter, and starts transcribing mRNA
What are the major steps in regulated eukaryotic transcription?
- TFs bind to enhancers, open chromatin, and/or recruit mediator
- Mediator stabilizes pre-initiation complex
- RNA pol II starts, then pauses, then begins elongation
What are transcription factors, and what do they do?
TFs are a proteins made of modular domains; they bind to enhancers and stimulate RNA pol II. The activation/repression domain provides function, while the DNA-binding domain (including dimerization and ligand-binding) provides specificity.
They can control the transcription of multiple genes, which may explain why some treatments have seemingly unrelated side effects.
What is an enhancer?
An enhancer is a cis-acting regulatory sequence that can be located far upstream or downstream of the gene on which it acts. Activators/repressors (transcription regulatory proteins, often just called TFs) can bind to them to stimulate/repress transcription.
How do TFs recognize and make contact with specific DNA sequences?
They form a recognition α-helix, usu. H bonds, in the major groove, using specific amino acid sequences. Several side chain contacts are required.
TFs can also make use of different motifs, such as zinc fingers and leucine zippers.
Why is the expression of different TFs important?
It underlies the development of different cell types.
What is a mediator?
A protein complex that bridges activators to RNA pol II and basal factors. It is required to activate transcription and may stabilize the pre-initiation complex and promote elongation.
What are epigenetic changes, and how do they occur?
Epigenetic changes are heritable changes in gene function that DO NOT involve changes in DNA sequence.
They occur when TFs recruit chromatin modifiers while loosening chromatin for transcription. Chromatin modifiers target histone N-terminal tails, adding covalent histone modifications, performing ATP-dependent nucleosome remodeling, or carrying out DNA modification.
What are the three modes of epigenetic modification on histones and DNA?
- Reading: proteins with specialized binding domains that recognize and bind to covalent modifications
- Writing: enzymes responsible for the addition of covalent modifications
- Erasing: enzymes that catalyze the removal of covalent modifications
How are TFs themselves regulated?
TF synthesis and activity is regulated by MANY external signals, including cell-cell interaction, nurtrients, hormones, and stress.
Why does the RNA pol II complex pause after initiation?
Most human genes are regulated at the elongation step as well as initiation. Negative elongation factors (NELFs) pause the complex, which can be activated by positive elongation factors (P-TEFb).
Over-recruitment of P-TEFb can upregulate many genes, which occurs in some cancers.
