RNA is a versatile nucleic acid that functions in information transfer, catalysis, gene regulation, and cellular structure. Its expression and identity are analyzed using RNA sequencing and Northern blot. Unlike DNA, RNA is typically single-stranded, contains ribose instead of deoxyribose, and uses uracil in place of thymine. The 2-prime hydroxyl group of ribose makes RNA chemically more reactive than DNA.
Messenger RNA
Messenger RNA carries genetic information from DNA to the ribosome for protein synthesis. In eukaryotes, pre-mRNA undergoes extensive processing. A 7-methylguanosine cap is added to the 5-prime end, protecting the transcript from degradation and facilitating translation initiation. A poly-A tail of 100 to 250 adenine residues is added to the 3-prime end, enhancing stability and export from the nucleus. Introns are removed by splicing, allowing a single gene to produce multiple protein variants through alternative splicing.
Transfer RNA
Transfer RNA is the adapter molecule that translates the genetic code. Each tRNA has a characteristic cloverleaf secondary structure with three stem-loops and an acceptor stem. The anticodon loop contains three bases that base-pair with the mRNA codon. The 3-prime end always carries the sequence CCA, where the amino acid is attached. tRNAs are heavily modified, with over 100 different base modifications identified. Aminoacyl-tRNA synthetases attach the correct amino acid to each tRNA, a process called charging, which requires ATP and ensures the fidelity of protein synthesis.
Ribosomal RNA
Ribosomal RNA is the catalytic and structural component of ribosomes. In E. coli, the 70S ribosome consists of a 50S large subunit containing 23S and 5S rRNA and a 30S small subunit containing 16S rRNA. In eukaryotes, the 80S ribosome has 60S and 40S subunits with correspondingly larger rRNAs. The 23S rRNA of the large subunit catalyzes peptide bond formation, making the ribosome a ribozyme. rRNA sequences are highly conserved and are used extensively in phylogenetic analysis.
Small Nuclear RNA
Small nuclear RNAs are components of the spliceosome, the complex that removes introns from pre-mRNA. The major snRNPs, U1, U2, U4, U5, and U6, recognize splice sites and catalyze the splicing reaction through RNA-RNA interactions. U1 snRNA base-pairs with the 5-prime splice site, and U2 snRNA recognizes the branch point. The spliceosome assembles stepwise, undergoing multiple conformational rearrangements powered by ATP hydrolysis.
MicroRNA and Small Interfering RNA
MicroRNAs are small non-coding RNAs of about 22 nucleotides that regulate gene expression post-transcriptionally. They are transcribed as primary miRNAs, processed in the nucleus by Drosha, and exported to the cytoplasm where Dicer produces the mature miRNA. The miRNA is loaded into the RNA-induced silencing complex, where it base-pairs with target mRNAs, typically in the 3-prime untranslated region, leading to translational repression or mRNA degradation.
Small interfering RNAs are derived from longer double-stranded RNA molecules of exogenous origin, such as viral RNA. They follow a similar pathway but typically show perfect complementarity to their targets, leading to mRNA cleavage rather than translational repression. The RNA interference pathway is a conserved antiviral defense mechanism and a powerful research tool.
Long Non-Coding RNA
Long non-coding RNAs are transcripts longer than 200 nucleotides that do not encode proteins. They regulate gene expression through diverse mechanisms, including chromatin remodeling, transcriptional regulation, and post-transcriptional processing. XIST mediates X chromosome inactivation in females by coating the inactive X chromosome and recruiting repressive chromatin modifications. Other lncRNAs function as scaffolds for protein complexes, decoys for transcription factors, or guides for chromatin-modifying enzymes.
Other Functional RNAs
Several additional RNA types perform specialized functions. Ribonuclease P is a ribozyme that processes tRNA precursors. The signal recognition particle RNA is part of the complex that targets proteins to the endoplasmic reticulum. Telomerase RNA provides the template for telomere elongation. CRISPR RNAs guide Cas proteins to foreign nucleic acids in bacterial adaptive immunity. Riboswitches are RNA elements in the 5-prime untranslated region of mRNAs that directly bind metabolites and regulate gene expression without protein involvement.
