Gene Expression and RNA Splicing

Gene Expression in Prokaryotes vs Eukaryotes

• Eukaryotes possess separate cellular compartments for transcription and translation, allowing for posttranscriptional regulation.
• Prokaryotes lack this compartmentalization, resulting in coupled transcription and translation.
• Eukaryotes have complex gene structures with longer introns, contrasting with prokaryotic genes.
• Regulatory RNA-binding proteins are predominantly found in eukaryotic cells, playing crucial roles in gene expression modulation.

Pre-mRNA Splicing Core Elements

• Core cis-elements crucial for pre-mRNA splicing include 5' splice site, 3' splice site, branch point sequence, and polypyrimidine tract.
• Exonic splicing enhancers are not considered core cis-elements required for pre-mRNA splicing.

Role of RNA-Binding Proteins in Splicing

• The influence of regulatory RNA-binding proteins (like SR proteins and hnRNPs) on splicing is context-dependent, based on their binding positions relative to regulated exons.
• These proteins can both promote and repress splicing through their interaction with various cis-elements.

Function of the Spliceosome

• The spliceosome identifies 5' and 3' splice sites and facilitates the removal of introns while ligating exons.
• It plays a role in alternative splicing by interacting with splicing enhancers and silencers.

Eukaryotic Splicing Mechanisms

• Eukaryotic cells use additional cis-elements and trans-acting factors to ensure accurate splicing, despite longer and more complicated splice sites compared to prokaryotes.

mRNA Editing in Eukaryotes

• RNA editing by ADAR enzymes involves converting adenosine to inosine within mRNA transcripts.
• APOBEC1 carries out RNA editing that converts cytidine to uridine.

mRNA Localization and its Functions

• The primary role of mRNA localization is to control the development of multicellular organisms and ensure efficient translation.
• Dysregulation of mRNA localization can lead to disease.

IRE-IRE-BP System in mRNA Stability

• This system stabilizes transferrin receptor mRNA when iron levels are low, thereby regulating iron homeostasis.

Alternative Splicing and Its Impact

• Alternative splicing allows a single gene to produce multiple mRNA isoforms, enhancing protein diversity.
• Splicing enhancers and silencers modulate alternative splicing through RNA-binding protein interactions.

Drosophila Sex Determination

• Proteins like Sxl, Tra, and Dsx are vital in regulating alternative splicing of key genes essential for determining sex in Drosophila.
• Specifically, Tra produces a functional protein only in females, while Dsx generates transcription factors crucial for male or female development.

Dysregulation of RNA-Based Mechanisms

• Dysregulation in splicing or mRNA editing can lead to various diseases, including neurological disorders and metabolic issues.

Modern Experimental Approaches

• Reporter assays measure the activity of splicing enhancers and silencers to understand splicing regulation.
• RNA immunoprecipitation and crosslinking-mass spectrometry are techniques used to identify RNA-binding proteins interacting with specific cis-elements.
• High-throughput sequencing allows researchers to analyze alternative splicing patterns on a genome-wide scale.
• Biochemical approaches help identify RNA-binding proteins interacting with specific cis-elements.
• Genetic approaches are vital for revealing novel regulatory mechanisms and discovering RNA-binding proteins.