Coding RNA

Question 1

Define coding RNA and explain why alterations to coding RNAs are important in cancer.

Answer 1

Answer:
Coding RNAs are messenger RNAs (mRNAs) that carry genetic information from DNA to ribosomes for protein synthesis. Alterations to coding RNAs are important in cancer because they affect the expression and processing of oncogenes and tumor suppressors. Increased levels of oncogenic mRNAs promote proliferation, while decreased levels of tumor suppressor mRNAs enable evasion of apoptosis and unchecked growth. These alterations therefore contribute to multiple cancer hallmarks such as proliferation, invasion, and resistance to cell death
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Question 2

List and briefly describe three main types of coding RNA alterations in cancer.

Answer 2

Answer:

Changes in mRNA abundance – oncogene mRNAs may increase due to higher transcription factor/coactivator activity; tumour suppressor mRNAs may decrease due to transcriptional repression or epigenetic silencing.

Alternative splicing – errors in exon/intron processing produce isoforms that disrupt apoptosis or differentiation (e.g., BCL-XL, MCL1L, GCSFR isoforms).

RNA modifications (epitranscriptomics) – chemical changes such as m6A methylation alter mRNA stability, splicing, translation, and degradation, often promoting oncogenesis

Question 3

Explain the role of intron retention (IR) in both normal physiology and cancer.

Answer 3

Answer:

Normal physiology: IR is coupled to nonsense-mediated decay (NMD) to regulate gene expression. For example, in granulocyte differentiation, IR of Lmnb1 suppresses lamin B1 expression, ensuring proper nuclear morphology.

Cancer: IR can inactivate tumor suppressor genes such as TP53 by introducing premature stop codons, preventing their proper expression. Mutations at splice junctions (e.g., last base exonic mutations) disrupt splicing, causing pathological IR

Question 4

Describe how alternative splicing errors can contribute to leukemia, giving specific gene examples.

Answer 4

Answer:

BCL-X: Normal blood cells express BCL-XS (pro-apoptotic). Splicing errors generate BCL-XL (anti-apoptotic), helping cancer cells evade apoptosis.

MCL1: Isoform switching produces MCL1L, which is anti-apoptotic, instead of the pro-apoptotic isoform.

GCSFR: Aberrant splicing removes exonic regions, blocking granulocyte differentiation, leading to leukemia.

TERT: Complex splicing changes alter telomerase activity, enhancing cancer cell immortality

Question 5

What is m6A RNA modification, and how does it influence cancer biology?

Answer 5

Answer:
m6A (N6-methyladenosine) is the most common internal, reversible modification of mRNAs. It is added co-transcriptionally in the nucleus by writers (e.g., METTL3, VIRMA), removed by erasers (e.g., ALKBH5), and recognized by readers (e.g., YTHDF proteins).
In cancer, abnormal m6A deposition promotes translation of oncogenes and inhibits tumor suppressor expression, driving proliferation, survival, and invasiveness

Question 6

Q6.

Discuss how mRNA abundance, alternative splicing, and epitranscriptomic modifications can each contribute to cancer. Provide mechanistic examples for each.

Answer 6

Answer:

mRNA abundance: Oncogene mRNAs (e.g., MYC, BCL2) increase through enhanced transcription factor or enhancer activity. Tumor suppressor mRNAs decrease via loss of transcriptional activators or silencing by non-coding RNAs. This imbalance promotes proliferation and survival.

Alternative splicing: Errors in exon choice create pathogenic isoforms. For instance, BCL-XL and MCL1L prevent apoptosis, while GCSFR mis-splicing blocks granulocyte differentiation, causing leukemia.

Epitranscriptomics (m6A): METTL3 overexpression in AML increases m6A marks on MYC and BCL2, enhancing their translation and supporting leukemogenesis. Similarly, full-length VIRMA in breast cancer promotes m6A deposition and tumor growth.
Together, these mechanisms interfere with tumor suppressors, apoptosis, differentiation, and cell cycle regulation, enabling cancer progression

Question 7

Explain the functional differences between full-length VIRMA and its N-terminal isoform in breast cancer, and discuss what this reveals about isoform-specific oncogenic functions.

Answer 7

Answer:

Full-length VIRMA (nuclear localized):

Functions as a scaffold in the m6A writer complex, enabling METTL3 activity.

Increases m6A deposition on oncogenic transcripts.

Promotes cancer cell proliferation, colony formation, and tumor growth in xenografts.

N-terminal VIRMA (cytoplasmic localized):

Lacks the C-terminal region necessary for nuclear localization.

Does not increase m6A deposition.

Does not enhance proliferation or tumorigenicity.
This demonstrates that isoform-specific localization and function determine whether an RNA-binding protein like VIRMA contributes to cancer. It underscores the importance of alternative splicing and isoform expression in oncogenesis