Non coding RNAs

Lecture on Noncoding RNAs

Introduction to Noncoding RNAs

• Noncoding RNAs: Any RNA that does not code for a protein; includes all types of RNA except messenger RNA (mRNA).

• Types of Noncoding RNAs: Includes transfer RNA (tRNA), ribosomal RNA (rRNA), and microRNAs (miRNAs).

Transfer RNA (tRNA)

• Function: Crucial in protein translation; they act as adapter molecules that translate the nucleotide codons of mRNA into the appropriate amino acids for the growing polypeptide chain.

• Structure:

  • Transcribed from tRNA genes by RNA polymerase as linear RNA that folds into complex secondary and tertiary structures.

  • Typical structure features a cloverleaf shape with four arms:

    • Amino Acid Arm: Contains the attachment site for an amino acid covalently bonded at the 3' end.

    • Anticodon Arm: Contains the anticodon that base pairs with the mRNA codon.

    • T Arm: Important for binding to the ribosome.

    • D Arm: Crucial for amino acid attachment.

• Codon-Anticodon Interaction: e.g., for the mRNA codon 5' GCC 3', the tRNA anticodon would be 3' CGG 5', corresponding to alanine.

• Enzymatic Attachment: Amino acids are attached to tRNAs by enzymes known as tRNA synthetases, with one specific enzyme for each amino acid.

• Three-Dimensional Shape: tRNAs resemble an upside-down L shape in 3D, with the amino acid site at the top and anticodon at the bottom.

Ribosomal RNA (rRNA)

• Prevalence: Most abundant RNA type in living organisms; highly expressed.

• Gene Arrangement: Encoded in the genome in gene arrays, allowing for simultaneous transcription of multiple transcripts.

• Structure of Ribosomes: Ribosomes consist of a large subunit and a small subunit, composed of rRNA and proteins.

  • Prokaryotic Ribosomes: Large subunit consists of 23S and 5S rRNAs, small subunit has 16S rRNA.

  • Eukaryotic Ribosomes: Large subunit contains 28S, 5.8S, and 5S rRNAs, small subunit has 18S rRNA.

• Functionality: Ribosomal RNAs carry out critical functions within the ribosome itself, including binding to tRNAs and forming peptide bonds (peptidyltransferase activity).

RNA Interference (RNAi)

• Discovery and Background: Initially observed in petunias which exhibited white patches instead of deeper purple when trying to enhance purple pigment through chalcone synthase overexpression.

• Mechanism: Found to involve suppression of both transgene and native gene via complementary RNA binding.

• Key Scientists: Craig Mello and Andrew Fire discovered the RNAi process in C. elegans using various RNA forms and conducting genetic screens.

• Double-Stranded RNA: Showed that double-stranded RNA is necessary for inducing RNAi.

• Post-Transcriptional Action: RNAi acts on transcribed mRNA, silencing gene expression without altering DNA.

RNA Interference Pathway

• Short Interfering RNA (siRNA): exogenous double-stranded RNA that can be synthetic or viral. Managed via the Dicer enzyme to become short siRNA.

• RNA Induced Silencing Complex (RISC): Processes the siRNA and targets complementary mRNA for degradation, preventing its translation.

• MicroRNA (miRNA):

  • Endogenous double-stranded RNA part of the organism's genome.

  • Processed and acts similarly to siRNA but typically leads to translational inhibition rather than direct degradation.

• Applications of RNAi: Used in molecular biology as a tool for gene knockdowns, allowing the study of gene function without permanent mutations by delivering double-stranded RNA corresponding to target genes.

• Practical Considerations: Easier in nematodes; in plants, requires genomic incorporation; in animals, viral delivery is often used.

Conclusion

• Noncoding RNAs play critical roles in various cellular processes, notably in protein translation and gene regulation through the RNAi pathway.