Eukaryotic Gene Expression Managing the Complexities of Controlling Eukaryotic Genes

Prokaryotes vs. Eukaryotes Closely related genes are clustered together Related genes are located on different chromosomes Largely transcriptional control Significant transcriptional control; other levels of control possible Larger number of larger-sized genes Trans-acting sequence-specific DNA binding proteins Proximal Cis-acting sequences Cis-acting sequences can be located at significant distances

Control Points for Gene Expression in Eukaryotes DNA transcription Transcriptional Control RNA Post-Transcriptional Control translation Translational Control Protein Post-Translational Control

Levels of Eukaryotic Chromatin Structure First level of chromatin coiling Nucleosome = DNA + histone proteins Variations in chromatin condensation affect gene activity.

Transcriptional Regulation: Effects of Chromatin Structure Decompaction of chromatin: Transcription factors unwind nucleosomes in the area where transcription will begin, creating DNAse I hypersensitive sites RNA polymerase unwinds more nucleosomes as transcription proceeds

Transcriptional Regulation: Effects of Chromatin Structure Acetylation of histone proteins (adding -CH3CO) reduces DNA-histone interaction, permitting transcription factors to bind.

Transcriptional Regulation: Effects of Chromatin Structure DNA Methylation DNA Methylation (adding -CH3) can occur on cytosines at CpG groupings near transcription start sites Inactive genes have methylated cytosines Active genes have demethylated cytosines Acetylation of histones is associated with cytosine demethylation

Transcriptional Regulation: Control of Initiation Transcriptional Activator Proteins assist in the formation or action of the basal transcription apparatus

Transcriptional Regulation: Control of Initiation Transcriptional Activator Proteins bind to Enhancer sequences that increase transcription Enhancers can influence promoters at distances of 50 kb or greater due to DNA looping mechanism Insulators control the direction of enhancer action

Transcriptional Regulation: Control of Initiation Transcriptional Repressor Proteins have three possible modes of action compete with activators for DNA binding sites bind to sites near activator site and inhibit activator contact with basal transcription apparatus interfere with assembly of basal transcription apparatus

Post-Transcriptional Regulation: Alternative RNA Splicing

Post-Transcriptional Regulation: RNA Editing Base substitution after transcription =

Translational Regulation: RNA Stability Degradation of mRNA can occur from the 5’ or 3’ end Stability of mRNA depends on 5’ cap 3’ poly-A tail 5’ and 3’ UTRs: serve as binding sites for regulatory factors Coding region Example: Hormone prolactin increases the longevity of casein mRNA coding for milk protein in lactating mammals

Translational Regulation Masking of mRNAs Many species store mRNAs in the cytoplasm of the egg. These mRNAs are inactive due to masking by proteins. Fertilization of the egg initiates unmasking and translation of these mRNAs. Availability of specific tRNAs In the embryonic development of a hornworm, an mRNA is present from day 1 but a specific tRNA needed for its translation is not produced until day 6.

Translational Regulation: RNA Silencing Small interfering RNAs microRNAs RNA-induced silencing complex

Post-Translational Modification: Phosphorylation Addition or removal of a phosphate group is a common way to change protein activity.

Post-Translational Modification: Peptide cleavage Proteins that have an inactive form after synthesis are activated by removal of a small number of amino acids. Prothrombin Thrombin Cleavage Fibrinogen Fibrin Cleavage Fibrin polymer (blood clot) Activation of blood clotting factors by cleavage