Coordinated regulation without operons: In eukaryotes, how can dispersed genes be turned on together if they are not physically linked in an operon?

Introduction / Context:
Unlike bacteria, eukaryotes rarely use operons. Instead, they coordinate gene expression through shared regulatory logic encoded in promoters and enhancers recognized by common transcription factors.

Given Data / Assumptions:

• Multiple genes can carry the same response elements (for example, estrogen response elements, heat-shock elements).
• Transcription factors bind these elements to co-activate or co-repress sets of genes.
• Baseline core promoter motifs (TATA/CAAT/GC) are not sufficient by themselves to confer signal-specific coordination.

Concept / Approach:
Coordination arises because one signal activates a TF, and that TF binds its motif across the genome wherever it appears, turning on (or off) many genes simultaneously.

Step-by-Step Solution:
Identify required mechanism → shared TF binding sites in cis-regulatory DNA. Eliminate options that overemphasize isolated core motifs without TF context. Select the explanation that matches genome-wide regulation in eukaryotes.

Verification / Alternative check:
ChIP-seq data show TFs binding common motifs upstream of co-regulated gene sets (for example, HSF1 at heat-shock genes).

Why Other Options Are Wrong:
TATA/CAAT/GC boxes are general promoter features and insufficient alone; random chance cannot reliably coordinate complex programs.

Common Pitfalls:
Assuming only operons can coordinate expression; overlooking enhancer logic and combinatorial control.

Final Answer:
By sharing common transcription factor binding sites in their regulatory regions.