Genome Architecture, Gene Regulation, and Editability
Genome Organization Beyond Coding Sequence
Structural view
Eukaryotic genomes contain coding exons, introns, promoters, enhancers, silencers, insulators, noncoding RNAs, and repetitive elements that all influence engineering outcomes.
Design implication
A mutation that leaves protein sequence unchanged can still profoundly alter expression if it disrupts regulatory DNA or splicing.
Chromatin and Accessibility
Why context matters
Genome editing efficiency depends on chromatin state, nucleosome occupancy, replication timing, and nuclear localization of the target locus.
Editability at different genomic contexts
Open chromatin
- Higher nuclease accessibility
- Often stronger editing efficiency
- Can vary across cell state
Heterochromatin
- Reduced accessibility
- May require enhanced delivery or prolonged exposure
- Can limit repair outcomes
Why can noncoding mutations be difficult to interpret in engineering experiments?
Noncoding changes can alter transcription, splicing, chromatin interactions, or RNA stability in context-dependent ways.
Correct answer: Their effects often depend on regulation, timing, and cell type
Name one chromatin feature that may influence CRISPR editing efficiency.
Accessible chromatin often improves Cas access to the target DNA.
Correct answer: Chromatin accessibility
Genome features relevant to engineering
| Feature | Engineering relevance |
|---|---|
| Promoter | Controls transcription initiation |
| Enhancer | Modulates tissue- or context-specific expression |
| Splice site | Affects mRNA processing |
| Repeat element | Can complicate mapping and repair |
| Epigenetic state | Influences accessibility and expression |
What is the most likely consequence of disrupting a splice donor site?
Splice donor disruption can cause exon skipping, intron retention, or cryptic splice site usage.
Correct answer: Altered pre-mRNA splicing
Why is promoter choice critical in transgene design?
Different promoters enable tissue specificity, inducibility, or constitutive expression.
Correct answer: It determines where, when, and how strongly the transgene is expressed