Ribonucleic acid (RNA) is a fundamental molecule in all living organisms, playing diverse roles beyond carrying genetic information. While DNA stores the cell’s master blueprint, RNA acts as a versatile messenger and worker, translating genetic instructions into functional proteins and performing various regulatory tasks. RNA molecules are not static; they undergo modifications after synthesis, essential for their proper function. These alterations allow RNA to adapt to cellular needs and environmental cues.
Why RNA Undergoes Modification
RNA molecules undergo modification to optimize their function and regulate gene expression. These modifications contribute to RNA stability, protecting them from degradation by cellular enzymes. They also influence proper folding, helping RNA achieve specific three-dimensional structures necessary for its activity.
Modifications facilitate specific interactions between RNA and proteins or other RNA molecules, crucial for many cellular processes. These interactions regulate gene expression by controlling how genetic information is accessed and utilized. Furthermore, modifications direct RNA molecules to their correct locations within the cell, ensuring they are present where their functions are required.
Key Processing Modifications
Several major processing modifications occur during or immediately after RNA synthesis, primarily affecting messenger RNA (mRNA) to prepare it for protein production.
5′ capping
5′ capping adds a specialized 7-methylguanosine (m7G) cap to the beginning of the mRNA molecule. This process occurs co-transcriptionally, while RNA is still being synthesized. Enzymes attach this cap through an unusual 5′-to-5′ triphosphate linkage. The 5′ cap protects mRNA from degradation, assists nuclear export, and helps ribosomes recognize it for protein synthesis.
Splicing
Splicing removes non-coding introns from precursor mRNA (pre-mRNA) and joins the remaining coding exons. This process is carried out by the spliceosome, a molecular machine composed of small nuclear ribonucleoproteins (snRNPs) and other proteins. The spliceosome recognizes specific sequences at intron and exon boundaries, excising introns and ligating exons to form mature mRNA. Splicing allows for alternative splicing, where different exon combinations from a single gene create multiple protein variants.
3′ polyadenylation
3′ polyadenylation adds a poly(A) tail, a stretch of hundreds of adenosine monophosphate units, to the mRNA’s end. This modification begins as transcription terminates; a multi-protein complex cleaves the pre-mRNA, and poly(A) polymerase synthesizes the tail. The poly(A) tail is important for nuclear export of mRNA, protects it from degradation, and enhances its translation. Its length can fluctuate, with shorter tails sometimes marking mRNA for degradation.
Chemical Changes to RNA
Beyond major processing events, RNA molecules undergo diverse chemical modifications directly to their nucleobases, often called the “epitranscriptome.” These modifications alter RNA’s chemical properties, influencing its structure and interactions, without changing the underlying sequence. Over 170 distinct RNA modifications have been identified across various RNA types, including mRNA, tRNA, rRNA, and non-coding RNAs.
Methylation
Methylation is a common chemical modification, adding a methyl group to a nucleotide base. N6-methyladenosine (m6A) is an abundant internal modification in eukaryotic mRNA, added to adenosine. This reversible modification is installed by “writer” enzymes and removed by “eraser” enzymes. Another significant methylation, 5-methylcytosine (m5C), is found in tRNAs, rRNAs, and mRNAs. It affects RNA stability, export, and translation.
Pseudouridylation (Ψ)
Pseudouridylation (Ψ) is another widespread chemical change, converting uridine to pseudouridine. Pseudouridine synthases (PUS enzymes) catalyze this conversion, which alters RNA structure, increases stability, and influences protein interactions. Other modifications include N1-methyladenosine (m1A), N7-methylguanosine (m7G), and 2′-O-methylation. These modifications are often dynamic, adding a layer of regulatory complexity to gene expression.
How Modifications Influence Biology
RNA modifications represent a layer of gene regulation, impacting cellular processes and influencing health and disease. These changes affect RNA stability, influencing how long an RNA molecule survives before degradation. Modifications also modulate translation efficiency, altering how readily ribosomes bind to mRNA and synthesize proteins. RNA modifications play a role in the precise localization of RNA molecules within the cell.
The dynamic nature of these modifications allows cells to rapidly respond to internal and external cues, such as stress or developmental signals. For instance, N6-methyladenosine (m6A) influences mRNA splicing, nuclear export, translation, and degradation, regulating gene expression. Dysregulation of RNA modification patterns has been linked to various conditions, including cancer, neurological disorders, and metabolic imbalances. Understanding these modifications provides insights into fundamental cellular mechanisms and potential avenues for therapeutic development.