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RNA PROCESSING AND RNPs
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RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Dec 28, 2015

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Alexandrina Bethanie Charles
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Page 1: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

RNA PROCESSING AND RNPs

Page 2: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

RNA ProcessingRNA Processing Very few RNA molecules are transcribed Very few RNA molecules are transcribed

directly into the final directly into the final mature RNA.mature RNA. Most newly transcribed RNA molecules Most newly transcribed RNA molecules

((primary transcriptsprimary transcripts) undergo various ) undergo various alterations to yield the mature productalterations to yield the mature product

RNA processingRNA processing is the collective is the collective term used to describe the molecular term used to describe the molecular events allowing the events allowing the primary primary transcriptstranscripts to become the to become the mature mature RNARNA..

Page 3: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

primary transcriptprimary transcript

mature RNAmature RNA..

Nucleus or Nucleolus

Cytoplasm

RN

A

pro

cessin

g

Romoval of nucleotides

addition of nucleotides to the 5’- or 3’- ends

modification of certain nucleotides

Page 4: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

(1) Removal of nucleotides by both endonucleases and exonucleases

endonucleasesendonucleases to cut at specific to cut at specific sites sites within within a precursor RNAa precursor RNA

exonucleasesexonucleases to trim the to trim the endsends of a of a precursor RNAprecursor RNA

This general process is seen in This general process is seen in prokaryotes and eukaryotes for all prokaryotes and eukaryotes for all types of RNAtypes of RNA

Page 5: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

(2) Addition of nucleotides to 5’-or 3’-ends of the primary transcripts or

their cleavage products.

Add a cap and a Add a cap and a poly(A)poly(A) tail to pre-mRNA tail to pre-mRNA

Page 6: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

(3) Modification of certain nucleotides on either the base or

the sugar moiety.

–Add a methyl group to 2’-OH of ribose in mRNA (A) and rRNA

–Extensive changes of bases in tRNA

Page 7: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

RNPs

Ribonucleoproteins = RNA protein complexs

The RNA molecules in cells usually The RNA molecules in cells usually exist complexed with proteinsexist complexed with proteins

specific proteins attach to specific specific proteins attach to specific RNAsRNAs

RibosomesRibosomes are the largest and most are the largest and most complex RNPscomplex RNPs

Page 8: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

3-D structure

Page 9: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Digital cryo-electron micrographyR

NP

Page 10: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Ribosomes Protein biosynthetic

machinery Made of 2 subunits

(bacterial 30S and 50S, Eukaryotes 40S and 60S)

Intact ribosome referred to as 70S ribosome in Prokaryotes and 80S ribosome in Eukaryotes

In bacteria, 20,000 ribosomes per cell, 25% of cell's mass.

Mass of ribosomes is roughly 2/3 RNA

Page 11: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Prokaryotic Ribosome Structure

Page 12: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Eukaryotic Ribosome Structure larger and more complex than

prokaryotic ribosomes, but with similar structural and functional properties

Page 13: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

tRNA PROCESSING, RNASE P AND RIBOZYMES

tRNA processing in prokaryotes

tRNA processing in eukaryotes

RNase P

Ribozymes

Page 14: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

tRNA 3-D structure

Page 15: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

tRNA processing in prokaryotes

Mature tRNAs are generated by processing longer pre-tRNA transcripts, which involves

1. specific exo- and endonucleolytic cleavage by RNases D, E, F and P (general) followed by

2. base modifications which are unique to each particular tRNA type.

Page 16: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

tRNA processing in prokaryotes

Primary transcripts

RNase D,E,F and P

tRNA with mature ends

Base modifications

mature tRNAs

Page 17: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

tRNA processing in eukaryotes

The pre-tRNA is synthesized with a

1. 16 nt 5’-leader, 2. a 14 nt intron and 3. two extra 3’-nucleotides.

Page 18: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.
Page 19: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

tRNA processing in eukaryotes

1. Primary transcripts forms secondary structures recognized by endonucleases

2. 5’ leader and 3’ extra nucleotide removal

3. tRNA nucleotidyl transferase adds 5’-CCA-3’ to the 3’-end to generate the mature 3’-end

4. Intron removal

Page 20: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

RNase P

Ribonuclease P (RNase P) is an enzyme involved in tRNA processing that removes the 5' leader sequences from tRNA precursors

Page 21: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

RNase P

RNase P enzymes are found in both prokaryotes and eukaryotes, being located in the nucleus of the latter where they are therefore small nuclear RNPs (snRNPs)

Page 22: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

RNase P

RNA component can catalyze pre-tRNA in vitro in the absence of protein. Thus RNase P RNA is a catalytic RNA, or ribozyme.

Page 23: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Ribozyme

Ribozymes are RNAs with catalytic activity that can catalyze particular biochemical reactions depending on their capacity to assume particular structures

RNase P RNA is a ribozyme. Ribozymes function during protein synthesis, in RNA processing reactions, and in the regulation of gene expression

Page 24: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Ribozyme

Self-splicing introns: the intervening RNA that catalyze the splicing of themselves from their precursor RNA, and the joining of the exon sequences

Page 25: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Ribozyme

Self-cleaving RNA encoded by viral genome to resolve the concatameric molecules of the viral genomic RNA produced. These molecules are able to fold up in such a way as to selfcleave themselves into monomeric.

Page 26: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Ribozyme

Ribozymes can be used as therapeutic agents in

1. correcting mutant mRNA in human cells

2. inhibiting unwanted gene expression

Kill cancer cells Prevent virus replication

Page 27: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

The Power of RNA interference

LOSS OF FUNCTION Easy in yeast

Difficult in mammals

RNA Interference (RNAi) isable to block selective mRNA

Page 28: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

RNAi Pathway

RNAi = RNA interference

siRNA = small interfering RNA

siRNP = small interfering Ribonucleoprotein

RISC = RNA Induced Silencing Complex

Dicer

Page 29: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Inhibition the replication of SARS virus by RNA

interference

Page 30: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

mRNA PROCESSING, hnRNPs AND snRNPs

Processing of mRNA hnRNP snRNP particles 5’Capping 3’Cleavage and polyadenylation Splicing Pre-mRNA methylation

Page 31: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Processing of mRNA

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

Page 32: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Processing of mRNA in eukaryotes

In eukaryotes, mRNA is synthesized by RNA Pol II as longer precursors (pre-mRNA), the population of different RNA Pol II transcripts are called heterogeneous nuclear RNA (hnRNA).

Among hnRNA, those processed to give mature mRNAs are called pre-mRNAs

Page 33: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Pre-mRNA molecules are processed to mature mRNAs by 5’-capping, 3’-cleavage and polyadenylation, splicing and methylation.

Processing of mRNA in eukaryotes

Page 34: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Eukaryotic mRNA processing: overview

Page 35: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

hnRNP: hnRNA + proteins

The hnRNA synthesized by RNA Pol II is mainly pre-mRNA and rapidly becomes covered in proteins to form heterogeneous nuclear ribonucleoprotein(hnRNP)

The hnRNP proteins are though to help keep the hnRNA in a single-stranded form and to assist in the various RNA processing reactions

Page 36: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

snRNP particles: snRNA + proteins

1. snRNAs are rich in the base uracil, which complex with specific proteins to form snRNPs.

2. The most abundant snRNP are involved in pre-mRNA splicing, U1,U2,U4,U5 and U6.

3. A large number of snRNP define methylation sites in pre-rRNA.

Page 37: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

snRNP particles

They are synthesized in the nucleus by RNA Pol II and have a normal 5’-cap.

They are exported to the cytoplasm where they associate with the common core proteins and with other specific proteins.

Their 5’-cap gains two methyl groups and they are then imported back into the nucleus where they function in splicing.

Page 38: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.
Page 39: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Splicing

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)

Page 40: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

5’ Capping

Very soon after RNA Pol II starts making a transcript, and before the RNA chain is more than 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

Page 41: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

7-methylguanosine (m7G)

Page 42: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.
Page 43: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Function of 5´ cap

Protection from degradation Increasing translational efficiency Transport to cytoplasm Splicing of first exon

Page 44: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

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.

Page 45: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

3’ Cleavage and polyadenylation

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

Page 46: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Function of poly(A) tail

Increasing mRNA stability Increasing translational efficiency Splicing of last intron

Page 47: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

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.

Page 48: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Splicing

Splicing requires a set of specific sequences to be present. The 5’-end of almost all introns has the sequence 5’-GU-3’ and the 3’-end is usually 5’-AG-3’. The AG at the 3’-end is preceded by a pyrimidine-rich sequence called the polypyrimidine tract

Page 49: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Sequences of (a) a typical polyadenylation site and (b) the splice site consensus.

Page 50: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Spliceosome

Catalyzes pre-mRNA splicing in nucleus

Composed of five small nuclear RNAs (snRNAs) and associated proteins (snRNPs) assembled on the pre-mRNA

Splicing reaction is catalyzed by RNA

Page 51: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.
Page 52: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Splicing cycle

Page 53: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Splicing

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)

Page 54: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Pre-mRNA methylation

The final modification or processing event that many pre-mRNAs undergo is specific methylation of certain bases.

The methylations seem to be largely conserved in the mature mRNA.

Page 55: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

ALTERNATIVE mRNA PROCESSING

Alternative processing

Alternative poly(A) sites

Alternative splicing

RNA editing

Page 56: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Alternative processing

Alternative mRNA processing is the conversion of pre-mRNA species into more than one type of mature mRNA.

Types of alternative RNA processing include alternative (or differential) splicing and alternative (or differential) poly(A) processing.

Page 57: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Alternative poly(A) sites

Some pre-mRNAs contain more than one poly(A) site and these may be used under different circumstances to generate different mature mRNAs.

In one cell the stronger poly(A) site is used by default, but in other cell a factor may prevent stronger site from being used.

Page 58: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Alternative splicing The generation of different mature

mRNAs from a particular type of gene transcript can occur by varying the use of 5’- and 3’- splice sites in four ways:

(i) By using different promoters(ii) By using different poly(A) sites(iii) By retaining certain introns(iv) By retaining or removing certain

exons

Page 59: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Alternative splicing

1. By using different promoters.2. By using different poly(A) sites.3 By retaining certain introns.4. By retaining or removing certain exons

Page 60: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Sex in Drosophila is largely

determined by alternative

splicing

Page 61: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Alternative splicing

• the potential for an increase in phenotypic diversity without increasing the overall number of genes. Is achieved by altering the pattern of exons that are spliced together,

• different proteins can arise from the processed mRNA from a single gene.

Page 62: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Alternative splicing

• Alternative splicing can occur either at specific developmental stages or in different cell types.

• the calcitonin gene yields an mRNA that synthesizes calcitonin (thyroid) or calcitonin gene– related peptide (CGRP, brain): 2 proteins with distinctly different functions.

• the α-tropomyosin mRNA have at least 8 different alternatively spliced α-tropomyosin mRNAs.

Page 63: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.
Page 64: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

Alternative splicing

Many defects in the β-globin genes are known to exist leading to β-thalassemias. Some of these defects are caused by mutations in the sequences of the mRNA required for intron recognition and, therefore, result in abnormal processing of the β-globin primary transcript.

Page 65: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

RNA editing

AN unusual form of RNA processing in which the sequence of the primary transcript is altered is called RNA editing.

Changing RNA sequence (after transcription)

Two types Base modification (A or C deamination) Base (U) insertion and deletion

Page 66: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.
Page 67: RNA PROCESSING AND RNPs. RNA Processing Very few RNA molecules are transcribed directly into the final mature RNA. Most newly transcribed RNA molecules.

End Of The lecture

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