Module 4 Epigenetics: Chromatin Modifications & RNA Effects

Gene regulation via epigenetic changes on DNA: DNA methylation; chromatin changes via histone modifications; RNA-mediated epigenetic effects.
Key components: DNA methylation; ncRNAs; histone modifications; RNA-mediated epigenetic effects.
Tools: CRISPR genome editing mentioned in course materials.

Chromatin = DNA + proteins; main proteins are histones.
Nucleosome = core histones + linker histone H1.
Core histones: $H2A, H2B, H3, H4$ (2 copies each) with positively charged tails.
Histone tails: length of about $11-37$ amino acids, rich in arginine/lysine.
Positive charges on histones help DNA interaction.

Modifications include acetylation, methylation, ubiquitination, phosphorylation.
Modifications alter DNA-histone interactions and can activate or repress gene expression.

Acetyl groups ( $CH_3CO$ ) added to tails by histone acetyltransferases (HATs).
Result: open chromatin configuration and stimulated transcription.
Deacetylation by histone deacetylases (HDACs) condenses chromatin and represses transcription.
Example (flowering time): under unfavorable conditions chromatin is acetylated → FLC expressed → flowering inhibited; under favorable conditions FLD (a deacetylase) is transcribed → acetyl groups removed → chromatin condensed → FLC not expressed → flowering not inhibited.

Methyl groups added by histone methyltransferases; can activate or repress transcription depending on the residue.
Demethylation by histone demethylases.
Common marks: H3K4me3 (activation) and H3K9me3 (repression).
H3K4me3 associated with transcription activation; H3K9me3 associated with heterochromatin and repression (HP1 involvement).
Visualization/analysis often uses chromatin immunoprecipitation (ChIP) to detect these marks.

Chromatin immunoprecipitation (ChIP) can detect histone modifications on histones or other DNA-binding proteins (e.g., transcription factors).

Noncoding RNAs (ncRNAs) can mediate epigenetic effects: siRNA, miRNA, lncRNA.
Roles include paramutations, X chromosome inactivation, genomic imprinting, and broader gene regulation.
RNA-induced effects include recruitment of DNA/histone modifying enzymes to target loci.

siRNA molecules associate with proteins to form RNA-induced transcriptional silencing complexes (RITS).
RITS attaches to complementary RNA sequences and recruits methylating enzymes.
Methylation of histone H3 on lysine 9 (H3K9me3) represses transcription.

Paramutation: transgenerational epigenetic interaction where two alleles interact to produce a heritable change in expression without DNA sequence changes.
Epialleles: alleles that are genetically identical but differ in expression due to epigenetic state (e.g., B-I vs B' in corn).

Occurs early in placental mammal development; in each female cell, one X chromosome is randomly inactivated to equalize X-linked gene expression between sexes.
X-inactivation center (XIC) region contains Xist, a key lncRNA of $17\text{kb}$ that coats the inactive X.
Xist RNA recruits Polycomb repressive complexes (PRC2 and PRC1) to deposit repressive histone marks and silence transcription on the inactive X.
Active X uses regulatory interactions to prevent Xist expression (e.g., Tsix antisense to Xist; Jpx stimulates Xist on the inactive X; Xite sustains Tsix on the active X).

Xist: coats inactive X and silences transcription; lncRNA.
Tsix: antisense to Xist; inhibits Xist on the active X.
Jpx: lncRNA that stimulates Xist transcription on the inactive X.
Xite: lncRNA that sustains Tsix expression on the active X.
Summary table (conceptual): Xist, Tsix, Jpx, Xite act as a regulatory network controlling XCI status.

Imprinting: gene expression determined by the parent of origin (maternal vs paternal).
Most imprinted genes are clustered in regions containing multiple genes (often 3–12 genes per cluster) and frequently include lncRNA genes.
Imprinted clusters show parent-of-origin-specific expression without changes to DNA sequence.

Paramutation: transgenerational epigenetic change in allele expression without DNA sequence change.
Epialleles: genetically identical alleles with different phenotypes due to epigenetic state.
Genomic imprinting: parent-origin specific expression of genes.
X inactivation: dosage compensation in female mammals via Xist-mediated silencing of one X chromosome.
ChIP: method to map histone modifications and DNA-binding proteins across the genome.
ncRNAs: include siRNA, miRNA, and lncRNA; mediators of epigenetic regulation.

Topics align with modules on DNA methylation, histone modifications (acetylation and methylation), RNA-mediated epigenetics, and genome editing (CRISPR) as part of broader gene regulation studies.