RNA post-transcriptional processing

RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules (primary transcripts) undergo various alterations to yield the mature product RNA processing is the collective term used to describe the molecular events allowing the primary transcripts to become the mature RNA.

primary transcript mature RNA. Cytoplasm Nucleus or Nucleolus RNA processing Removal of nucleotides addition of nucleotides to the 5’- or 3’- ends modification of certain nucleotides mature RNA.

Processing Events in Prokaryotes vs Eukaryotes

endonucleases to cut at specific sites within a precursor RNA (1) Removal of nucleotides by both endonucleases and exonucleases endonucleases to cut at specific sites within a precursor RNA exonucleases to trim the ends of a precursor RNA This general process is seen in prokaryotes and eukaryotes for all types of RNA

(2) Addition of nucleotides to 5’-or 3’-ends of the primary transcripts or their cleavage products. Add a cap and a poly(A) tail to pre-mRNA AAAAAA

tRNA 3-D structure

tRNA processing in prokaryotes Mature tRNAs are generated by processing longer pre-tRNA transcripts, which involves specific exo- and endonucleolytic cleavage by RNases D, E, F and P (general) followed by base modifications which are unique to each particular tRNA type.

Primary transcripts RNase D,E,F and P tRNA with mature ends Base modifications mature tRNAs

tRNA processing in eukaryotes The pre-tRNA is synthesized with a 16 nt 5’-leader, a 14 nt intron and two extra 3’-nucleotides.

Primary transcripts forms secondary structures recognized by endonucleases 5’ leader and 3’ extra nucleotide removal tRNA nucleptidyl transferase adds 5’-CCA-3’ to the 3’-end to generate the mature 3’-end Intron removal

Processing of mRNA: prokaryotes There is essentially no processing of prokaryotic mRNA, it can start to be translated before it has finished being transcribed. Prokaryotic mRNA is degraded rapidly from the 5’ end

Processing of mRNA in eukaryotes Pre-mRNA molecules are processed to mature mRNAs by 5’-capping 3’Cleavage and polyadenylation splicing

Eukaryotic mRNA processing: overview

5’ Capping Very soon after RNA Pol II starts making a transcript, and before the RNA chain is more then 20 -30 nt long, the 5’-end is chemically modified. 7-methylguanosine is covalently to the 5´ end of pre-mRNA. Linked 5´  5´ Occurs shortly after initiation

7-methylguanosine (m7G)

Function of 5´cap Protection from degradation Increased translational efficiency Transport to cytoplasm Splicing of first exon

3’ Cleavage and polyadenylation In most pre-mRNAs, the mature 3’-end of the molecule is generated by cleavage followed by the addition of a run, or tail, of A residues which is called the poly(A) tail.

RNA polymerase II does not usually terminate at distinct site Pre-mRNA is cleaved ~20 nucleotides downstream of polyadenylation signal (AAUAAA) ~250 AMPs are then added to the 3´ end Almost all mRNAs have poly(A) tail

Function of poly(A) tail Increased mRNA stability Increased translational efficiency Splicing of last intron AAAAAA

Splicing The process of cutting the pre-mRNA to remove the introns and joining together of the exons is called splicing. It takes place in the nucleus before the mature mRNA can be exported to the cytoplasm.

Introns: non-coding sequences Exons: coding sequences RNA splicing: removal of introns and joining of exons Splicing mechanism must be precise to maintain open reading frame Catalyzed by spliceosome (RNA + protein)