RNA Processing: Definition, Steps, Types and Examples

Transcription is the procedure by which the genetic information stored in DNA is used to produce RNA. The RNA, also known as the primary transcript or pre-mRNA, is processed till it is functional. These transcripts encode proteins which will then go to the ribosomes for protein synthesis. In bacterial cells, the mRNA is translated at the same time it comes off the DNA template. In eukaryotic cells, RNA synthesis occurs in the nucleus, and the translation machinery is in the cytoplasm.

This Story also Contains

1. What is RNA processing?
2. Transcription
3. RNA Splicing
4. RNA Editing
5. RNA Transport
6. MCQs on RNA Processing

Also, the eukaryotic genes have introns, which are non-coding genes. The primary RNA copied from genes that have introns will also have those regions that interrupt the coding sequence of the gene. These regions must be removed before the mRNA is sent to the nucleus for protein synthesis. RNA Processing is an important topic of the chapter Molecular Basis of Inheritance. It is an important chapter in the Biology subject.

What is RNA processing?

RNA processing is an important post-transcriptional modification, which converts a primary transcript of RNA into a mature RNA molecule that is expected to code for proteins. It is a very important process in the expression of material genomics. There are several sets of biochemical alterations important to the stability, exportation, and functionality of nucleic acids that have been introduced.

Viewed from this perspective, RNA processing turns out to be viably important in gene expression modulation. Cellular alteration of RNA transcripts allows representing a suitable mechanism for it to regulate the expression of a given protein in terms of its time and quantity. This is rather essential in supporting cellular activity and responding to new environmental factors.

The key steps in RNA processing include capping, tailing, splicing, and at times, editing. Each of those steps has specific enzymatic actions that are effected to habituate the RNA molecule to proper processing and good functioning in translation into proteins.

Transcription

The first process of gene expression is transcription, where the DNA is copied into a pre-mRNA by the RNA polymerase enzyme. It can be broadly divided into three stages:

Initiation

Binding of RNA polymerase with the promoter region of DNA and initiation to unwind the strands of DNA.

Elongation: As the RNA polymerase moves along the template strand, it synthesises a complementary RNA strand by the addition of ribonucleosides.

Termination: After the transcription of the whole gene, this newly synthesised pre-mRNA would be released along with the release of RNA polymerase from DNA.

This pre-mRNA contains both introns and exons and is thus more or less a bit similar to the final mRNA. More processing is needed for it to be used in the body.

Primary Transcript Processing

This primary transcript is a copy of the gene's DNA sequence and thus contains all information that is contained within a gene. Additionally, it contains exons and introns. The features of this make extensive processing necessary before it is translated into a protein. This is to ensure that the mature mRNA will encode only for the coding regions, the exons, and splice out the non-coding ones known as introns.

Capping

5' capping is the process in which a modified guanine nucleotide, known as 7-methylguanosine, is added to the 5' end of the preRNA. Initiation has just occurred, and this capping event happens very rapidly. The series capping takes the following sequence:-

• Hydrolysis: Getting rid of one phosphate group of the 5′ end of the nascent RNA.

• Guanylation: Attaching a guanosine monophosphate to this 5′ diphosphate end.

• Methylation: Contains a guanine nucleotide. The nucleotide is methylated at the N-7 position to have a cap structure.

The 5' cap has several important functions:

• Methylated nucleotide prevents the mRNA from being broken down by exonucleases that act on the 5' end.

• The cap-binding complex recognises the cap, which is recognised by the eukaryotic initiation factors as a part of the process of translation initiation that aids in the binding of ribosomes to mRNA.

• The 5′ cap functions in exporting mRNA from the nucleus to the cytoplasm by interacting with nuclear export receptors.

Enzymes Involved in Capping: The capping process is catalysed by a capping enzyme complex that contains RNA triphosphatase, guanylyltransferase, and methyl transferase activities.

Tailing

The Addition of Poly-A Tail at the 3' End: In the process, a chain of adenine nucleotides will have to bind with the 3' end of pre-mRNA. This method of binding is referred to as polyadenylation, and it often accounts for about 200 to 250 adenine residues.

Role of Poly (A) tail: This poly(A) tail protects mRNA from exonucleases whose function involves the degradation of RNA through a pathway from the 3'end.

The poly(A) tail can serve as a nuclear export signal, as there are poly(A) binding proteins recognised by nuclear export machinery, which mediate mRNA export from the nucleoplasm into the cytoplasm.

RNA Splicing

RNA Splicing is the process by which the introns that are copied from the DNA into the RNA are removed. This is necessary to remove the non-coding regions from the RNA. RNA splicing can be described below:

Introns and Exons

While exons are the genes corresponding to coding sequences joined in the mature mRNA, introns are discarded sequences in genes. That simply means introns vary to a great extent in their length and sequence, while exons are relatively conserved and shorter.

Mechanism of Splicing

The spliceosome is a single large RNA-protein complex that carries out both of those reactions: intron removal and exon joining. It includes not only the small nuclear RNAs, the snRNAs, but also associated proteins that form small nuclear ribonucleoproteins, or snRNPs.

Splice Site Recognition: The spliceosome recognises the boundaries of the intron. These are the 5′ splice site, also called the donor site, and the 3′ splice site, called the acceptor site.

Formation of the Branch Point: A branch point is identified within the intron that usually consists of an adenine nucleotide.

Formation of Lariat: In the 5' splice site cleavage, the 5' end of the intron may become attached covalently to the adenine of the branch point, forming a lariat structure.

Exon Ligation: At the 3' splice site, cutting occurs and the intron lariat is released, and thereby the exons are ligated in the mature mRNA.

Alternative Splicing

By including or excluding different sets of exons in one gene, one may get different variants of proteins. This will in all probability give a fillip to an increase in the degree of protein diversity from one gene.

Examples of Alternative Splicing

Immunoglobulins: Single pre-mRNA gives rise to several antibodies because the exons encoding different regions of the antibody were differentially included or excluded.

Tropomyosin: This protein participates in the muscle contraction process. Once again, the alternative splicing gives rise to different isoforms of this protein. The isoforms show tissue specificity.

RNA Editing

RNA editing is a post-transcriptional modification in which the nucleotide sequence of an RNA molecule is altered. It changes codons in mRNA and, therefore, may lead to the expression of a distinctly different protein.

RNA Editing Mechanisms

ADAR (Adenosine Deaminase Acting on RNA): It catalyses the hydrolytic deamination of adenosine to inosine, which during translation is recognised as guanine by the translating ribosome.

Cytidine Deaminases: These enzymes mediate the deamination of cytidine to uridine (C-to-U editing).

RNA Transport

The processed mature mRNA is then allowed to pass into the cytoplasm for protein synthesis. The nuclear pore complex allows the export of mRNA by selectively and rapidly transporting millions of mRNA-protein complexes through the nuclear envelope.

This large, multimeric protein complex of NPC regulates and coordinates the transport process for molecules between the nucleus and the cytoplasm and furnishes a filter through which mRNAs can pass only after they are done with processing.

MCQs on RNA Processing

Q1. Which of the following statements are true about poly A tail?

I. It contains the Poly-A-polymerase enzyme

II. It makes RNA unstable

III. It allows mRNA to degradation

IV. Present in prokaryotes

Option 1: I and II

Option 2: II and III

Option 3: I and III

Option 4: II and IV

Correct answer: (3) I and III

Explanation:

The Poly-A- tail is present in the eukaryotic cells and adds "A" at the end of mRNA. The enzyme adds the poly-A tail residue called Poly-A-polymerase. The poly-A-tail Prevents mRNA from degradation and makes RNA stable.

Hence, the correct answer is Option (3) I and III

Q2. Which process eliminates the introns in eukaryotic transcription?

Option 1: Splicing

Option 2: Poly-A- tail

Option 3: Alternative editing

Option 4: Capping

Correct answer: (1) Splicing.

Explanation:

Splicing is important during the process of eukaryotic transcription when introns are removed from the pre-mRNA sequence. Such elimination is required for producing mature mRNA that includes only coding regions referred to as exons. This modification helps in the proper processing of mRNA before translation so that correct proteins can be synthesized. Such a modification is very critical in gene expression and adds diversity to the products made by the eukaryotic cells.

Hence, the correct answer is Option (1) Splicing.

Q3. About mature mRNA in eukaryotes:

Option 1: Exons and introns do not appear in the mature RNA.

Option 2: Exons appear but introns do not appear in the mature RNA.

Option 3: Introns appear but exons do not appear in the mature RNA.

Option 4: Both exons and introns appear in the mature RNA.

Correct answer: 2) Exons appear but introns do not appear in the mature RNA.

Explanation:

• The coding sections of the gene that contain the instructions needed to synthesize proteins are called exons.

• RNA splicing eliminates introns which are non-coding areas that are located in between exons.

• RNA splicing creates the final mature mRNA by joining the exons and removing the introns. The translation process uses this mature mRNA to create proteins.

• Accordingly, only the exons and not the introns are found in the mature mRNA that leaves the nucleus.

Hence, the correct answer is option 2) Exons appear but introns do not appear in the mature RNA.

Also Read-

• Practice MCQs on RNA Processing

• Lac Operon

• Human Genome Project