Ch. 9: Post-Transcriptional Control of Gene Expression
Chapter 9: Post-transcriptional Gene Control: RNA Processing, Post-transcriptional Regulation and Nuclear-Cytoplasmic Transport
Introduction to Gene Expression Control
The most significant control over gene expression often initiates at the level of gene transcription, particularly the rates of transcription initiation.
However, primary transcripts (such as mRNAs, tRNAs, and rRNAs) are not immediately functional.
Their maturation, occurring in the nucleus before export to the cytoplasm, represents a critical level of regulation for gene expression, known as post-transcriptional control.
Post-transcriptional Gene Control
This broad concept encompasses all mechanisms that regulate gene expression following transcription.
Major players include mRNA and associated ribonucleoproteins (RNPs), which perform various protective and functional roles.
RNA Nomenclature and Types
Key RNA types involved in gene expression and its regulation include:
mRNA: The fully processed, mature messenger RNA.
pre-mRNA: The precursor mRNA containing introns, awaiting cleavage at the poly(A) site.
hnRNA: Heterogeneous nuclear RNAs, a broad category including pre-mRNAs and intermediate products with introns.
snRNA: Small nuclear RNAs, major players in RNA splicing (intron removal).
pre-tRNA: Precursor transfer RNA, with additional bases and potential introns.
pre-rRNA: Precursor ribosomal RNA, processed into mature 18S, 5.8S, and 28S rRNAs.
snoRNA: Small nucleolar RNAs, which guide modifications during rRNA maturation.
siRNA: Short interfering RNAs (approx. 22 bases), major players in RNA cleavage and degradation by perfectly base-pairing with target mRNA.
miRNA: Micro-RNAs (approx. 22 bases), major players that inhibit translation and target mRNAs for degradation by partially base-pairing.
RNA Processing Overview
Broad concepts of RNA processing and post-transcriptional gene control include:
Processing: Direct modifications of primary transcript RNA.
Quality Control: Monitoring RNA processing integrity and determining RNA stability.
Alternative Splicing: A mechanism for generating diverse protein products from a single gene.
mRNA Stability: Regulation of mRNA degradation rates.
Translation Rate: Control over protein synthesis efficiency.
Cellular Localization: Strategic positioning of mRNA within the cell.
Regulated Translation: Control of protein synthesis initiation and extent.
miRNA and RNAi Effects: Post-transcriptional regulation via small RNA molecules, impacting mRNA stability and translation.
Pre-mRNA Processing in Eukaryotes
Processing Steps
5' Capping:
A critical modification added only to pre-mRNAs and certain small nuclear RNAs transcribed by RNA Polymerase II.
Inaugurated after synthesis of 25-30 nucleotides.
The major player is the 5' cap (7-methylguanylate), added via a GTP-dependent mechanism.
Methylation occurs at the N1 and N2 positions of the ribose rings in the cap.
3' End Cleavage and Polyadenylation:
Involves cleavage at the poly(A) site, followed by adding a poly(A) tail.
Major player: Poly(A) polymerase (PAP), which synthesizes the tail with 200-250 A residues.
Specific factors binding to the poly(A) signal are CPSF (cleavage and polyadenylation specificity factor) and CStF (cleavage stimulatory factor).
Splicing:
The process of removing non-coding introns and ligating coding exons through transesterification reactions.
Key sites (major players) include the 5' splice site (GU), 3' splice site (AG), and the branch point A.
Splicing is orchestrated by spliceosomes, macromolecular complexes composed of small nuclear RNAs (snRNAs) and associated proteins (snRNPs).
5' Capping Detailed
The capping process involves enzymes associated with the carboxyl terminal domain (CTD) of RNA Polymerase II.
The linkage is a unique 5'-5' tri-phosphate structure.
Capping profoundly influences mRNA stability and translation efficiency.
Splicing Mechanism Summary
Trans-esterification reactions are the broad concept underlying intron excision (forming a lariat structure) and exon ligation.
Major players like spliceosomes, RNA recognition motifs (RRMs), and various proteins guide this precise process.
RNA Editing
Broad concept: Alteration of mRNA sequences after transcription.
Major pathway (Single-base Editing) involves nucleotide conversions, such as C to U by enzymes like APOBEC.
Nuclear-Cytoplasmic Transport
Broad concept: Facilitating the movement of mature mRNAs from the nucleus to the cytoplasm.
Major players: Nuclear Pore Complexes (NPCs), composed of nucleoporins, selectively transport fully processed, 5'-capped mRNAs.
Shuttling proteins associated with RNA, like NXT1/NXF1 and REF, act as essential transport factors.
Cytoplasmic Mechanisms of Post-transcriptional Control
Broad concepts of mRNA decay pathways include:
Deadenylation-dependent decay: 5' to 3' degradation following poly(A) tail removal.
Deadenylation-independent decay: mRNA cleavage via decapping and exosome pathways.
Endonuclease-mediated decay: Processes involving RNAi and other endonucleolytic activities.
Major players: miRNAs and siRNAs are central to these decay pathways, promoting degradation or inhibiting translation of target mRNAs, thereby contributing to gene silencing and the removal of abnormal mRNAs.
Alternative Splicing and Proteome Expansion
Broad concept: A mechanism leading to the production of many distinct mRNA isoforms and protein variants from a single gene.
Example (major players): Drosophila sex determination, where Sxl and Tra genes exhibit female-specific splice patterns crucial for development.
Conclusion
Post-transcriptional gene regulation is a critical broad concept for cellular function, dynamically influencing RNA processing, stability, and translation.
Understanding these mechanisms and their major players is vital for comprehending gene expression in health and disease.