Epigenetics, Chromatin Modifiers, and Heritable Gene State
Molecular Memory Without Sequence Change
Epigenetic regulation
Epigenetic mechanisms include DNA methylation, histone modifications, histone variants, chromatin remodeling, and RNA-mediated pathways. These marks influence transcriptional potential and can be mitotically stable.
Key mechanisms
Classes of epigenetic effect
Local chromatin effects
- Promoter accessibility changes
- Nucleosome repositioning
Long-range effects
- Domain-level repression or activation
- Nuclear compartment association
Interpretation caution
A correlation between a chromatin mark and gene expression does not by itself prove causality; perturbation is needed.
Which statement about histone methylation is most accurate?
Specific methyl marks can correlate with activation or repression depending on histone site and context.
Correct answer: Its effect depends on the residue and degree of methylation
Why is causality difficult to infer from a single ChIP-seq experiment?
Perturbation and time-resolved assays are needed to establish directionality.
Correct answer: Because occupancy or enrichment alone does not show whether a chromatin mark drives expression or merely correlates with it
Common chromatin assays
| Assay | Primary use |
|---|---|
| Bisulfite sequencing | DNA methylation mapping |
| ChIP-seq | Protein or histone mark occupancy |
| ATAC-seq | Accessible chromatin |
| CUT&Tag | Targeted chromatin profiling |
| HiChIP | Protein-linked chromatin contacts |
What is the strongest conceptual distinction between genetic and epigenetic information?
Epigenetic mechanisms alter expression potential without changing the underlying DNA sequence.
Correct answer: Epigenetic information modifies regulatory state without altering nucleotide sequence
Give one example of a process that depends on stable epigenetic regulation.
These processes require long-lived gene-state differences across cell divisions.
Correct answer: X-chromosome inactivation or genomic imprinting