Transcription and gene regulation

Transcription is the synthesis of RNA from a DNA template by RNA polymerase. In eukaryotes, transcription occurs in the nucleus and is tightly regulated by promoters, transcription factors, and enhancers/silencers. Dysregulation of transcription underlies many inherited and acquired diseases, from imprinting disorders to cancer.

• RNA polymerase II transcribes all protein-coding (mRNA) genes. Pol I makes rRNA; Pol III makes tRNA and 5S rRNA.
• Promoter: a sequence upstream of the gene where RNA Pol II and transcription factors assemble. The TATA box (about 25 bp upstream) is a classic promoter element.
• General transcription factors (TFIID, TFIIA-H) form the preinitiation complex at the promoter.
• Mediator complex links the preinitiation complex to distal regulators.

1. Initiation: transcription factors assemble at the promoter; RNA Pol II binds and begins synthesizing RNA.
2. Elongation: Pol II moves 5'→3' along the template strand, synthesizing mRNA 5'→3'. Co-transcriptional modifications begin.
3. Termination: Pol II releases; the nascent RNA is capped, polyadenylated (poly-A tail), and spliced.

• Enhancers: distal DNA elements (kilobases or megabases away) that loop back to contact the promoter, amplifying transcription. Disrupted by 3D-genome alterations (e.g., TAD boundary loss in limb malformations).
• Silencers: DNA elements that repress transcription when bound by repressive TFs.
• Insulators: block enhancer-promoter interactions across topologically associated domain (TAD) boundaries. CTCF is the key insulator protein.
• Transcription factors (TFs) bind specific DNA sequences to activate or repress transcription. Loss-of-function TF mutations cause many developmental syndromes (PAX3 in Waardenburg, SOX9 in campomelic dysplasia, TBX5 in Holt-Oram).
• Chromatin state: DNA must be accessible. Histone acetylation (HATs) opens chromatin; deacetylation (HDACs) closes it. DNA methylation at CpG islands typically silences transcription.

• 5' cap (7-methylguanosine): protects from exonucleases; required for translation initiation.
• Polyadenylation (3' poly-A tail): 100–250 adenines added at the 3' end; extends mRNA half-life.
• Splicing: introns removed, exons joined by the spliceosome. Splice-site mutations (canonical GT...AG) are a common disease mechanism.
• Alternative splicing: one gene produces multiple protein isoforms (e.g., DSCAM has tens of thousands of isoforms).

• Splice-site mutations: about 10–15% of disease-causing variants (e.g., NF1, BRCA1, DMD).
• Promoter/5'UTR mutations: can ablate gene expression (alpha-thalassemia deletions, hereditary persistence of fetal hemoglobin).
• TF mutations: cause syndromic and nonsyndromic developmental disorders.
• Enhancer hijacking: cancer driver in T-ALL (TAL1), Burkitt lymphoma (MYC-IGH translocation).