transcription elongation Flashcards
what are the 2 productive alternatives after promoter clearance?
elongation and termination
what is the challenge of termination?
destabilizing the elongation complex because it is extremely stable
when does termination occur?
at a given position only if RNA polymerase enters the termination pathway faster than nucleotide addition moves the DNA template to the next position
what are the 2 non-productive alternatives after promoter clearance?
backtracking and arrest
RNA synthesis is….
slow
processive
efficient
what is proximal promoter pausing?
occurs in many eukaryotic genes due to RNA polymerase 2 stalling after 35-50 nucleotides have been synthesized
what causes the rate of synthesis to not be uniform?
Hairpin formation in the new RNA, instability in the DNA-RNA hybrid inside the transcription bubble (AU rich, incorrect nucleotide = possible backtracked pause)
describe the characteristics of hairpin formation pausing;
Stabilized pause
Occurs whenever an RNA hairpin forms in the RNA exit channel
describe the characteristics of the instability in the RNA-DNA hybrid (backtracked) pause;
Backtracked pause
Stabilized pause
Occurs when RNA polymerase reverse-translocates to a more stable RNA-DNA hybrid, displacing the RNA 3’ end from the active site
Allows for proofreading of misincorporated bases
describe transcriptional arrest;
Occurs when RNA polymerase encounters an obstacle or forms a backtracked complex and cannot resume RNA synthesis on its own
Serious rescue is needed
Paused complexes:
what is the role of gating tyrosine?
prevent further backtracking of not so serious cases of pausing
describe how paused complexs resume;
RNA polymerase backtracks by one position
Further backtracking is prevented by a tyrosine residue
Backtracked complexes: polymerase-intrinsic cleavage of a dinucleotide from the 3’ end of the RNA occurs and then elongation resumes
describe how arrested complexes attempt to resume;
The RNA is forced to backtrack beyond the gating tyrosine
Extensive backtracking traps RNA and the trigger loop in the pore of the enzyme inhibiting any further elongation
Special elongation factors are required for revival - TFIIS
what are elongation factors?
Proteins or protein complexes that associate with RNA polymerase during elongation that are essential to maintain transcription and to restart paused complexes. They are important for maintaining transcription in eukaryotes.
describe the role of TFIIS;
needed to overcome transcriptional arrest.. Add NTPs to start reaction, add heparin to bind free RNAP2 and then add TFIIS. Transcription cleavage factor in eukaryotes
