Genomic Architecture & Regulatory Logic
A structural and functional roadmap of the DNA strand.
Course Overview • Advanced Molecular Genetics
Core Promoter Architecture
The Gateway to Transcription and polymerase docking.
TATA Box
Primary docking site (-30 bp).
Initiator (Inr) & DPE
Start site precision (+1) and downstream elements.
BRE
B-Recognition Element for TFIIB.
Regulatory Modules
Proximal and Distal sequence volume knobs.
Enhancers
Distal sequences that loop to increase transcription.
Silencers
Inhibitory counterparts to enhancers.
Locus Control Regions
Master enhancers for gene clusters.
The Recruitment Layer
Protein assembly points and bridging.
Coactivators
e.g., p300/CBP. Bridge TFs to open chromatin.
Corepressors
e.g., NCoR. Recruit machinery to silence regions.
Enhanceosomes
Massive protein complexes formed at enhancers.
Boundary Elements
Preserving regulatory identity & preventing crosstalk.
Insulators
Genetic fences blocking improper enhancer action.
Barrier Elements
Stop the spread of silent heterochromatin.
CTCF Binding Sites
Specific sequences dictating 3D loop domains.
Epigenetic Landmarks
Chemical modifications directly on the code.
CpG Islands
Regions dense in Cytosine-Guanine pairs.
DNA Methylation Sites
CH3 tags added to Cytosine to mute genes.
Untranslated Info (UTRs)
Sensors and instructions outside the coding region.
5' UTR & Kozak Sequence
Directs ribosome assembly and translation start.
3' UTR & Poly-A Signal
Transcript termination and lifespan control.
Riboswitches & Sensors
Metabolite or temperature responsive structures.
Post-Transcriptional Motifs
The splicing code and editing punctuation.
Donor/Acceptor Sites
5' and 3' splice site boundaries (GT/AG).
Branch Point Sequence
Internal Adenine for lariat formation.
Exonic Splicing Enhancers
Internal exon tags guiding the spliceosome.
Trans-Acting Binding Sites
The interpretive machinery docking locations.
Transcription Factor Sites
Short DNA motifs scattered in enhancers/promoters.
Hormone Response Elements
Specific targets (e.g., GRE, HRE) for cellular signals.