The Regulatory Code

The genome is not merely a list of genes, but a sophisticated information-processing machine. Through a complex cis-regulatory grammar of Promoters, Enhancers, and Response Elements, DNA orchestrates life with precise spatial and temporal control.

Linear Genome Navigator

Explore the anatomy of a gene locus. This interactive model visualizes the spatial relationships essential for gene regulation. Scroll horizontally along the 5' to 3' strand and click any element to inspect its molecular function.

Select an Element

Interactive Model

Click on the colored blocks in the strand above to reveal their specific biological functions, location relative to the Transcription Start Site (TSS), and their role in the regulatory grammar.

Transcriptional Logic Lab

Gene expression is a combinatorial decision process. Act as the cellular nucleus: combine transcription factors to see if the gene turns ON or OFF.

1. General Machinery (Basal)

General TFs (TFIID/B)

RNA Polymerase II

2. Specific Regulators

Specific Activator

Co-Activator (Mediator)

3. Inhibitors

Repressor Protein

Heterochromatin (Closed)

Expression Output

SILENT

Select factors to initiate transcription.

Element Encyclopedia

Comprehensive inventory of functional sequence elements.

Structural Analytics

Quantitative breakdown of the regulatory landscape, contrasting functional roles and spatial distribution as defined in the report.

Functional Distribution

Relative frequency of Initiation vs. Modulation elements.

Spatial Architecture (Distance from TSS)

Comparison of proximal (Promoter) vs. distal (Enhancer/Silencer) locations.

The Molecular Readers: Transcription Factor Architecture

Regulatory elements are biologically inert until recognized by trans-acting factors (Transcription Factors or TFs). TFs possess specialized DNA-Binding Domains (DBDs) that read the edges of base pairs in the major groove of DNA. The data below illustrates the dominance of specific structural motifs in the human proteome.

Dominant TF Families (Human Genome)

The C2H2 Zinc Finger is the most common structural motif, allowing modular recognition of diverse sequences.

Structural Motif Mechanics

How proteins physically grip the DNA helix.

Zinc Finger (C2H2)

Uses a zinc ion to stabilize a small finger-like loop. Inserted directly into the major groove. Modular design allows stringing multiple fingers to read long sequences.

Leucine Zipper (bZIP)

Functions as a dimer (like chopsticks). The "zipper" region holds two proteins together, while basic regions grip the DNA. Common in stress response factors (e.g., AP-1).

Hth

Homeodomain (HTH)

Ancient motif essential for developmental body patterning (Hox genes). One helix stabilizes, the other ("recognition helix") reads the sequence.

The Epigenetic Landscape: Chromatin Context

DNA is not free-floating; it is wrapped around histone octamers to form nucleosomes. The accessibility of regulatory elements is controlled by the density of this packaging. Use the slider below to simulate the transition from active Euchromatin to silenced Heterochromatin.

Chromatin Compaction Level

Open (Active) Closed (Silent)

State Euchromatin

Histone Mark H3K4me3 / H3K27ac

Transcription POSSIBLE