Post-Transcriptional Gene Control

Post-Transcriptional Gene Control

• Most RNAs are processed in the nucleus, from primary transcripts, before export to the cytoplasm.
• Locations of various mechanisms are important to note, including types of RNA polymerases and RNA.
• Eukaryotic premature mRNA transcript synthesis occurs by RNA polymerase II, and is processed in three steps.

Pre-mRNA Processing

• 5' capping: occurs shortly after RNA polymerase II initiates transcription, involves adding a 7-methylguanylate cap to the 5' end of the transcript.
• It protects the 5' end from enzymatic degradation and assists mRNA export.
• 3' polyadenylation: a large multi-protein complex forms around the poly(A) signals in pre-mRNA, specifically cleaves the pre-mRNA at a poly(A) site.
• The complex adds up to 250 A residues and protects the 3' end from enzymatic degradation.
• Intron removal and exon splicing: introns are removed, and exons are joined, generally at every exon/intron junction.

Pre-mRNA & hnRNP

• pre-mRNA: nascent mRNA transcripts of protein-coding genes that are always associated with proteins.
• hnRNA: heterogeneous nuclear RNA, includes pre-mRNA and other nuclear RNAs which are complexed with RNA-binding proteins.
• hnRNP: Heterogeneous ribonucleoprotein particles, combination of hnRNA and proteins. (hnRNA is associated with an abundant set of nuclear proteins that contain conserved RNA-binding domains)

hnRNP Functions

• Prevents pre-mRNA forming secondary structures to inhibit interactions with other proteins.
• Presents a more uniform substrate for processing steps such as splicing.
• Involved in transport of mRNA from the nucleus to cytoplasm by associating to cytoplasmic proteins. 

5' Capping

• 7-methylguanylate cap is added to the 5' end; first couple ribonucleotides are methylated; the linkage is 5'-5'.
• Protect the 5' end from degradation.
• Aid in export to cytosol.
• Capping enzyme associates with phosphorylated CTD of RNA polymerase II; only RNA polymerase II transcripts are capped.

Polyadenylation

• Large multi-protein cleavage/polyadenylation complex forms around the poly(A) signals in pre-mRNA.
• Cleavage of primary pre-mRNA at poly(A) site produces a free 3' OH.
• Poly(A) polymerase adds up to 250 A residues to the 3' end for protection from degradation.

RNA Splicing

• Introns are removed; exons are joined.
• Intron removal generally occurs at exon/intron junctions.
• Splicing requires conserved sequences at each end of every intron (both the 5' splice site and the 3' splice site).
• Specific nucleotides at the splice sites (G-U @ 5', A @ Branch point) are invariant.

RNA Splicing Mechanism

• snRNPs (5 U-rich small nuclear RNAs): U1, U2, U4, U5, U6 participate in splicing.
• Spliceosome is a large ribonucleoprotein complex of snRNPs assembling on the pre-mRNA to catalyze splicing.
• U1 participates in base pairing with the 5' splice site; U2 interacts with the sequence around the Branch point A.

RNA Splicing Mechanism cont.

• Transesterification reaction: excision of circular lariat intron.
• Exons are ligated together.
• Debranching enzyme converts lariat intron to linear form.
• Nuclear exonucleases cut linear intron.
• Resulting nucleotides are recycled.

Trans-Splicing

• Functional mature mRNAs are derived from processing a single pre-mRNA via cis-splicing, in most eukaryotes.
• Trans-splicing is a special form of RNA processing in eukaryotes, constructing a mature mRNA from multiple different primary RNA transcripts.
• Exons are ligated to form complete molecules.
• Examples: C. elegans, Trypanosomes, and Euglenoids.

Alternative Splicing

• The same pre-mRNA is processed differently in different cells, leading to splicing of different exons from the same gene.
• Different combinations of exons lead to protein isoforms.
• This process is regulated by RNA-binding proteins that bind specific sequences near splice sites.

RNA Editing

• Exon nucleotides are altered prior to mature mRNA production.
• This changes the pre-mRNA sequence in the nucleus and results in differences in the sequence of the corresponding mature mRNA to the genome sequence.
• A particular example is mammalian RNA editing of the apo-B pre-mRNA.

Ribozymes

• Ribozymes are RNA molecules that have catalytic activity.
• 23S and 28S rRNAs of ribosomes have peptidyl transferase activity.
• Group I and II self-splicing introns exist in rRNA and protein-coding genes (most often in rRNA genes in some protozoans and in mitochondrial and chloroplast genes in fungi and plants).

Transport Across the Nuclear Membrane

• The nucleus is surrounded by two membranes.
• Nuclear Pore Complexes (NPCs) allow molecules of all sizes to enter and exit.
• Small molecules and ions diffuse passively through the NPC.
• Larger molecules use energy-dependent transport mediated by RNA molecules.

Nuclear Pore Complex Structure

• NPCs are composed of nucleoporins, attached to nuclear baskets, and cytoplasmic filaments on the cytoplasmic side, and central transporters in the middle.

FG Nucleoporins and Transporters

• FG nucleoporins contain many short hydrophobic FG repeats and long hydrophilic regions.
• Nuclear transporters have hydrophobic regions that bind reversibly to FG domains in FG nucleoporins.
• FG nucleoporins create a molecular sieve that allows small, soluble molecules to pass but not larger molecules.

Import into the Nucleus

• Proteins destined for the nucleus contain a nuclear localization signal (NLS).
• Importins are transport proteins binding to the NLS and carrying cargo into the nucleus.

Mechanism for Nuclear Import

• Free cytosolic importin binds to NLS of cargo protein.
• The complex moves through nuclear pore complexes interacting with nucleoporins.
• Inside the nucleus, conformation change in importin occurs resulting in lower affinity for the NLS of cargo protein causing release.
• Transporters recycle.

Export out of the Nucleus

• Similar mechanism to import: involved exportins, nuclear export signals (NES), and Ran-GTP.
• Proteins, tRNAs, ribosomal subunits move out of the nucleus into the cytoplasm.
• Dissociation of the complex from exportin occurs after Ran-GTP hydrolysis.
• Transporters are recycled. (Ran is a G protein that interacts with Nuclear Pore Complexes during import/export).

Summary: Import & Export of Proteins through NPC

• Cargo proteins contain nuclear localization signals (NLS) or nuclear export signals (NES).
• Some proteins shuttle, and must contain both NLS and NES.
• Import and export both rely on Ran (a G protein) which exists in different conformations when bound to GTP or GDP.

GTP Switch Proteins

• Guanine nucleotide-binding proteins switch "on" when GTP is bound, and "off" when GDP is bound.
• GEFs (guanine nucleotide exchange factors) promote GTP binding and GAPs (GTPase activating proteins) promote GTP hydrolysis.

mRNA Transport out of Nucleus

• mRNA exporter proteins direct most mRNA-protein complexes (mRNPs) through nuclear pores.
• mRNA-exporter diffuses through pores and transiently interacts with FG-nucleoporin proteins. (mRNA exporter proteins have three domains, a domain that binds to mRNPs, a domain that binds to FG nucleoporins, and a C-terminal domain)

Explore the intricate processes of post-transcriptional gene control, focusing on pre-mRNA processing. Learn about key mechanisms such as 5' capping, 3' polyadenylation, and exon splicing. This quiz will test your understanding of how RNAs are processed in the nucleus before their translation in the cytoplasm.