Chapter 12 - Post-Transcriptional Gene Control and Nuclear Transport

12.1: Processing of Eukaryotic Pre-mRNA

Three major events:
- 5’ capping
- Once nascent molecules reach up to 25 to 30 molecules in length, 7-methylguanosine is added to the 5’ cap along with any other components that can be found on eukaryotic mRNA’s.
- 3’ cleavage/polyadenylation
360-kDa (a cleavage and polyadenylation factor; made of four polypeptides) forms an unstable connection with the AAUAAA poly(A) signal.
Then, three additional proteins bind to a CPSF-RNA complex, which later interacts with the Glurich sequence (another cleavage factor), and a poly(A) and polymerase (PAP) bind to the complex before cleavage starts.
RNA splicing
Introns are removed and it results in an A residue that is called a branch point.

Different mRNAs can show the same gene during different development stages or in different types of cells because primary transcripts and the cleavage at different poly(A) sites get alternatively spliced.
RNA- binding proteins can regulate alternative splicing by binding the proteins near splice sites that are regulated.
Splicing factors become enhanced due to the splicing activators interacting with them, so their interaction with the regulated splice site activates.
The pre-mRNA in the nucleus has its nucleotide sequence altered during RNA editing, though this doesn’t happen often invertebrate animals. When it does occur, it causes a change in the amino acids and results in proteins with different functions.

Nuclear envelopes have nuclear pre complexes with many functions:
- They are large structures with 50 to 100 nucleoporins (a type of protein)
- FG- nucleoporins (contain a hydrophobic sequence) help with the transport of macromolecules in nuclear pores.
- These macromolecules can be transported easily if they are under 60 kDa, otherwise, they require the assistance of proteins.
Proteins have a special amino acid sequence if they are imported or exported from the nucleus. These amino acid sequences form nuclear-localization signals (NLS), or nuclear-exporting signals (NES).
NES and NLS come in different forms. They work with a specific receptor protein called karyopherins.
Only fully functional mRNAs can be exported from the nucleus.

Micro RNAs (miRNAs) can repress translations and this helps form hybrids in specific mRNAs.
miRNAs and siRNAs are made from longer precursor molecules and help with either repressing or cleaving target mRNAs.
Because of the degradation of mRNAs, their poly(A) tail shortens, and either a 3’ to 5’ digestion occurs or removal of 5’ cap and digestion of 5’ to 3’ occurs.
Degradation of mRNAs in the cytoplasm happens due to the bindings of proteins in the 3’ or 5’ UTRs.

Precursors of pre-mRNA that are synthesized by polymerase I undergo cleavage, which results in 28S, 18S, and 5.8S rRNAs.
Pre-rRNA is synthesized in the nucleolus. 5S rRNA is synthesized while RNA polymerase III is not processed.
Pre-tRNA can have some of its intron removed near the 5’ sequence.
RNA molecules, in the nucleus and after getting exported from the cytoplasm, are associated with proteins.