Gene Regulation in Eukaryotes

Flashcards from Eukaryotic Gene Regulation Lecture Notes

Enhancer

DNA sequence that can be far away from gene; improves or represses the basal level of transcription; may be located either 5′ or 3′ to the transcription start site; still function when moved to different positions relative to the promoter.

Transcription Factors

Sequence specific DNA binding proteins that bind to promoters and enhancers to recruit other proteins to influence transcription; three types: basal factors, activators, repressors.

Chromatin Immunoprecipitation-Sequencing (ChIP-Seq)

Allows the identification of transcription factor binding sites by crosslinking DNA and protein, fragmenting DNA, using an antibody specific to the protein of interest to bind, purifying complexes and sequencing DNA.

GAL4

A transcriptional activator which aides in recruiting the transcription complex to the start of the gene by binding to an Upstream Activating sequence (Enhancer) close to the promoter of the GAL genes.

GAL80

Is bound by GAL3 which does not allow it to enter the nucleus in the presence of Galactose.

RNA Sequencing

Determines the relative number of mRNAs per gene in a cell; RNA is isolated, reverse transcribed, and fragmented; adapter sequences are ligated to fragment ends for hybridization, PCR, sequencing, and bioinformatic analyses.

Nucleosomes

Approximately 160 bp of DNA wrap twice around core of eight histones; 40 bp of linker DNA connects adjacent nucleosomes; Histone H1 associates with linker DNA.

Chromatin Remodeling Complexes

Can unwind the DNA around nucleosomes and place the promoter or enhancer sequences into the area of the linker DNA and make it available for binding.

Histone Acetyltransferases

Add acetyl groups to histone tails, preventing close packing of nucleosomes and favoring expression of genes in euchromatin; reversed by histone deacetylases.

Histone Methyltransferases

Add methyl groups to histone tails, with the effect depending on the specific amino acid modified; Adding methyl group to H3 lysine 9 favors heterochromatin formation; reversed by histone demethylases.

Micro RNAs (miRNAs)

Small RNA molecules that affect gene expression; form double stranded stem loops; Drosha excises stem-loop from primary miRNA (pri-miRNA) to generate pre-miRNA; Dicer processes pre-miRNA to a mature duplex miRNA.

miRNA Influence on Gene Expression

Target mRNA is degraded when complementarity is perfect; translation of mRNA target is repressed when complementarity is imperfect.

RNA Interference

Artificially expressing short double stranded RNA molecules that can be processed similarly to the miRNAs and hence get incorporated into the RISK complex to degrade mRNA molecules.

Ribosome Profiling

Allows researchers to observe positions of ribosomes on mRNAs, determining the rate of translation of specific genes.