Questions: RNA Editing and Post-Transcriptional Modification

Question 1

APOB100 is produced in the liver and APOB48 in the intestine, yet both arise from the same gene. A researcher comparing the genomic DNA of liver and intestinal cells finds no sequence difference. What best explains the distinct proteins?

• A. Alternative splicing generates different mRNAs in liver versus intestine, removing exons that encode the C-terminal domain in intestinal cells
• B. APOBEC1 edits a cytidine to uridine in the intestinal mRNA, creating a premature stop codon that truncates the protein
• C. Post-translational cleavage removes the C-terminal portion of APOB100 specifically in intestinal cells
• D. The intestinal gene promoter drives translation from a different start codon, producing a shorter reading frame

Answer: (B)

This is the canonical example of C-to-U RNA editing. APOBEC1 converts a specific cytidine to uridine in the APOB mRNA in intestinal cells, changing a glutamine codon (CAA) into a stop codon (UAA). The genomic DNA is identical in both tissues — the difference is a single post-transcriptional nucleotide substitution. This is distinct from alternative splicing (which rearranges exons) and from post-translational modification (which modifies the protein, not the message).

Question 2

ADAR enzymes convert adenosine to inosine in RNA. Why does this effectively change an A to G in the resulting protein sequence?

• A. Inosine is chemically identical to guanosine and has the same base-pairing geometry
• B. The translation machinery reads inosine as if it were guanosine, so a codon containing inosine specifies a different amino acid than the original adenosine-containing codon
• C. The ribosome skips inosine-containing codons, producing a frameshift that generates a new amino acid sequence downstream
• D. Inosine pairs with cytosine in the edited strand, which then serves as template for producing a guanosine-containing mRNA in subsequent transcription

Answer: (B)

Inosine is not identical to guanosine, but it is read as guanosine by the ribosome because their base-pairing geometries are similar enough that tRNAs recognizing G also recognize I. This functional equivalence is what makes A-to-I editing consequential: changing one nucleotide can alter the amino acid at that position. In GluA2, a single A-to-I edit changes a glutamine codon to an arginine codon — a substitution that fundamentally alters calcium permeability of the receptor channel.

Question 3

RNA editing is a rare mechanism affecting primarily a handful of specialized transcripts, making it a minor contributor to protein diversity in mammals.

• T. True
• F. False

Answer: False

Estimates based on transcriptome sequencing suggest that more than 50% of human genes show evidence of A-to-I editing. Most editing occurs in non-coding regions — Alu elements in introns and UTRs — where it influences RNA folding, stability, and interactions with RNA-binding proteins. Editing in coding sequences is rarer but functionally critical. RNA editing is a widespread, physiologically important regulatory layer, not a curiosity confined to a few genes.

Question 4

RNA editing is conceptually distinct from alternative splicing because it chemically modifies individual nucleotides in the existing sequence, rather than selecting which exon segments to include.

• T. True
• F. False

Answer: True

Alternative splicing rearranges which pre-mRNA exon segments are joined — the nucleotide sequences within exons remain unchanged. RNA editing changes the actual nucleotide identity within the transcript. Both mechanisms expand proteomic diversity beyond what genomic sequence alone predicts, but they operate at entirely different levels. Editing can create changes that are invisible when comparing only DNA sequences from different tissues, because the DNA is identical.

Question 5

Why does the existence of widespread RNA editing challenge the concept of the genome as a fixed blueprint for cellular identity?

Model answer: If the genome were a fixed blueprint, every cell with the same DNA would produce the same proteins. RNA editing shows that the same genomic sequence is chemically rewritten post-transcriptionally in a tissue-specific, developmentally regulated way — producing functionally distinct proteins in different cell types without any change to the DNA. The genome is better described as a draft that cells revise according to their regulatory context.

This has implications for understanding how cell-type identity is established and maintained. Two cells with identical DNA can have different functional states because their editing machinery (ADAR and APOBEC expression levels) differs. It also complicates sequencing-based disease diagnosis: a disease-causing amino acid change could exist at the RNA level in certain tissues without being detectable in genomic DNA.