Regulation of Gene Expression Flashcards
Chapter 3
AMPK
AMP-activated protein kinases
5’-capping
Addition of a 7-methlguanosine cap to the 5’ end of the nascent pre-mRNA while elongation is in progress. The 5’ cap protects the nascent transcript from degradation from its 5’ end and assist in ribosome binding during translation.
Carboxy terminal domain (CTD)
The carboxylic terminal domain of the RNA polymerase II largest subunit, consisting in tandem repeats of a heptad sequence (consensus: Tyr1Ser2Pro3Thr4Ser5Pro6Ser7,52 repeats in humans), changes the CTD phosphorylation status through the transcription cycle to allow its progression and the cotranscriptional processing of the nascent mRNA through the recruitment of protein factors involved.
Chromatin
A complex of DNA and proteins that forms chromosomes within the nucleus of eukaryotic cells.
Chromatin looping
A chromatin loop occurs when stretches of genomic sequence that lie on the same chromosome are in closer physical proximity to each other than to intervening sequences.
Chromatin remodeling
Dynamic modification of chromatin architecture to allow or suppress the access of regulatory machineries.
Cohesin
A protein complex that holds sister chromatids together after DNA replication until anaphase, when removal of cohesin leads to separation of sister chromatids, and which also functions as a chromatin looping factor.
Core promoter
a minimal stretch of contiguous DNA sequence that is sufficient to direct the accurate initiation of transcription by the RNA polymerase II machinery; it encompasses the transcription start site (s)
Coregulators
Proteins with which sequence-specific DNA-bound transcription factors interact to exert their effect on target gene transcription but that do not bind themselves to the DNA in a sequence-specific manner. In the group of coregulators, activator transcription factors need coactivators to work, and repressive transcription factors need co-repressors to work.
Enhancer
A short (50-1500 bp) DNA stretch containing multiple activators and/or repressor binding sites, to which a complex of transcription factors binds to affect the transcription from related core promoters. A promoter can be controlled by multiple enhancers, and a given enhancer can control more than one promoter.
Enhancer-derived RNA (eRNA)
Noncoding RNA transcripts produced from genomic regions that are presumed enhancer DNA elements; eRNA interacts with looping factors and facilitates / stabilizes chromosomal looping between the enhancer and promoters of cognate target genes.
General (or basal) transcription factors (GTFs)
Proteins that are not part of RNA polymerase but are needed for accurate initiation of transcription and are part of the transcription preinitiation complex.
Mediator
A Mult subunit assembly that appears to be required for regulating expression of most RNA polymerase II transcripts, activating both GTF and coactivators.
Nucleosome
Any of the subunits that repeat in chromatin consist of a length of DNA (147 bp) coiled around an octamer of histone proteins consisting of an H3-H4 tetramer flanked by two H2A-H2B dimers.
Poly A tail
A stretch of adenine nucleotides that is sequentially added to the mRNA molecule following 3’ -specific cleavage, as part of pre-mRNA processing; the poly A tail increases the stability of the mRNA molecule and facilitates translation. 3’-clevage and polyadenylation of the mRNA transcript is cotranscriptional and is required for termination of transcription by RNA Pol II.
